Wed Oct 16 00:15:34 UTC 2024 I: starting to build kmer/unstable/armhf on jenkins on '2024-10-16 00:15' Wed Oct 16 00:15:34 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_34/11286/console.log Wed Oct 16 00:15:34 UTC 2024 I: Downloading source for unstable/kmer=0~20150903+r2013-9 --2024-10-16 00:15:34-- http://deb.debian.org/debian/pool/main/k/kmer/kmer_0%7e20150903%2br2013-9.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2371 (2.3K) [text/prs.lines.tag] Saving to: ‘kmer_0~20150903+r2013-9.dsc’ 0K .. 100% 49.3M=0s 2024-10-16 00:15:35 (49.3 MB/s) - ‘kmer_0~20150903+r2013-9.dsc’ saved [2371/2371] Wed Oct 16 00:15:35 UTC 2024 I: kmer_0~20150903+r2013-9.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kmer Binary: kmer, libkmer-dev, meryl, libmeryl-dev, leaff, sim4db, atac, kmer-examples Architecture: any all Version: 0~20150903+r2013-9 Maintainer: Debian Med Packaging Team Uploaders: Afif Elghraoui Homepage: http://kmer.sourceforge.net Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/kmer Vcs-Git: https://salsa.debian.org/med-team/kmer.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-exec, dh-sequence-python3, python3-dev Package-List: atac deb science optional arch=any kmer deb science optional arch=all kmer-examples deb science optional arch=all leaff deb science optional arch=any libkmer-dev deb libdevel optional arch=any libmeryl-dev deb libdevel optional arch=any meryl deb science optional arch=any sim4db deb science optional arch=any Checksums-Sha1: 6da7324491e761437f27207f0b9135d767452e7a 1251653 kmer_0~20150903+r2013.orig.tar.gz bff8b0b6f815807795d55bf9adb33c18dee8cf94 2380056 kmer_0~20150903+r2013-9.debian.tar.xz Checksums-Sha256: 8fd9c289244e69e38bb7709f3523d39edf1c2ced2cbcc687fcf00ecfca78ea47 1251653 kmer_0~20150903+r2013.orig.tar.gz 27e69d0ec3c9f716d2a81a0aedd9c0d48c9807abf17815db0327f0f8901a0758 2380056 kmer_0~20150903+r2013-9.debian.tar.xz Files: 30b66a10ddc64022509dd8b85425880f 1251653 kmer_0~20150903+r2013.orig.tar.gz 5fb535fd2ba7759f38b418f0008eb2d5 2380056 kmer_0~20150903+r2013-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmbgD4MACgkQPCZ2P2xn 5uKZKA/+ItZCQH6KTrqdKHP/e+NVJ89S9hoixlgaKwxFxp+4xlJNQAxK22CN7mWe QFzs2miUWNDtrs1LwEjvCCcubEvwdsqy8w524udkZ8cXcOIPpbiamvFVT9CBH9mv GhYquR3pLIsNvJP4V2Wg0YpI4VO+AnLObpxhfAPw3YXFFV3yEsxV10XuoEwRJlSb DENV12lmnUlT2SmErXD+rwv/xBAIEsTBc5Jh6S0AJetqScE5d0uoBtpy0/bfShkj ebBCJYH2ufELcXm5ujgoHTBx1O+vjwtitHvYTdR7KIOFjNFTJeTBIBrTXNW4gxYg uXo+iS14JrHDDDLW01a8utkiVJaJfNRmNKUhSKAgBCHY2uQKVVZZhqfr93gzcNM+ GesWALfRz2kMmBP88GRV9Q2QyP7xmunAC/sLCS3r1eBOp5eM5W7ntkiM7hgdyvaI tMsXOC7rvN73pCd2PHu++mF1VbGM3vMR0lhQ8k+uDkFFCtqmbOBEurnW/HJvtHLa nm3yhWD3VjEjqHwr6QOKumfBPKdSdeMAnPX6FTrJnEyhEWLajKmDoGCXcZ9yDY5z tuQGDtx5+iYEvxl1Nyj9VpOVEfZtFq4CWBOak5GnCmzlL97IE66OaXGrDtLvb70p McpVXmtFKDvfVq/bhXYs3WNP3Y3snHh1p2DO8ee/71n4hE3rX0Y= =hXe+ -----END PGP SIGNATURE----- Wed Oct 16 00:15:35 UTC 2024 I: Checking whether the package is not for us Wed Oct 16 00:15:35 UTC 2024 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Wed Oct 16 00:15:35 UTC 2024 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Wed Oct 16 00:22:11 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 15 12:15:40 -12 2024 I: pbuilder-time-stamp: 1729037740 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [kmer_0~20150903+r2013-9.dsc] I: copying [./kmer_0~20150903+r2013.orig.tar.gz] I: copying [./kmer_0~20150903+r2013-9.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Sep 10 09:21:07 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kmer_0~20150903+r2013-9.dsc: no acceptable signature found dpkg-source: info: extracting kmer in kmer-0~20150903+r2013 dpkg-source: info: unpacking kmer_0~20150903+r2013.orig.tar.gz dpkg-source: info: unpacking kmer_0~20150903+r2013-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying allow-freebsd-build.patch dpkg-source: info: applying atac-helper-script-paths.patch dpkg-source: info: applying atac-readme.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying linux-cflags.patch dpkg-source: info: applying fix_wrong_evaluation_order.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying drop_distutils I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/23629/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='2327be63651d44be90a9f1c01a065d12' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='23629' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.zKLWRx5E/pbuilderrc_Ko9Q --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zKLWRx5E/b1 --logfile b1/build.log kmer_0~20150903+r2013-9.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32z 6.1.0-26-armmp-lpae #1 SMP Debian 6.1.112-1 (2024-09-30) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/23629/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-exec, dh-sequence-python3, python3-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 21597 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 34.7 MB of archives. After unpacking 129 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libpython3.12-minimal armhf 3.12.7-1 [800 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.3-1 [83.2 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf python3.12-minimal armhf 3.12.7-1 [1809 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.1-1 [22.1 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 12 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3 [71.1 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libnsl2 armhf 1.3.0-3+b2 [34.9 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-5 [146 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libpython3.12-stdlib armhf 3.12.7-1 [1820 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf python3.12 armhf 3.12.7-1 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-9 [88.8 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-7 [517 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.191-2 [183 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5 [9075 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.1 [604 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf dh-exec armhf 0.30 [24.3 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf python3-typeguard all 4.3.0-1 [36.5 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian unstable/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf python3-pkg-resources all 74.1.2-2 [213 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf python3-zipp all 3.20.2-1 [10.3 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf python3-setuptools all 74.1.2-2 [736 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf dh-python all 6.20240824 [109 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libexpat1-dev armhf 2.6.3-1 [139 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libpython3.12t64 armhf 3.12.7-1 [1848 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libpython3.12-dev armhf 3.12.7-1 [3808 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libpython3-dev armhf 3.12.6-1 [9952 B] Get: 72 http://deb.debian.org/debian unstable/main armhf python3.12-dev armhf 3.12.7-1 [505 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf python3-dev armhf 3.12.6-1 [26.1 kB] Fetched 34.7 MB in 0s (73.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:armhf. 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Preparing to unpack .../python3.12-minimal_3.12.7-1_armhf.deb ... Unpacking python3.12-minimal (3.12.7-1) ... Setting up libpython3.12-minimal:armhf (3.12.7-1) ... Setting up libexpat1:armhf (2.6.3-1) ... Setting up python3.12-minimal (3.12.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21917 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_armhf.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../04-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../05-libcom-err2_1.47.1-1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../06-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../14-libreadline8t64_8.2-5_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:armhf. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-1_armhf.deb ... Unpacking libpython3.12-stdlib:armhf (3.12.7-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-1_armhf.deb ... Unpacking python3.12 (3.12.7-1) ... 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Setting up libcom-err2:armhf (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:armhf (0.191-2) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Oct 16 00:16:22 UTC 2024. Universal Time is now: Wed Oct 16 00:16:22 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:armhf (2.6.3-1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:armhf (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:armhf (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:armhf (3.12.7-1) ... Setting up python3.12 (3.12.7-1) ... Setting up debhelper (13.20) ... Setting up dh-exec (0.30) ... Setting up libpython3.12t64:armhf (3.12.7-1) ... Setting up libpython3-stdlib:armhf (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:armhf (3.12.7-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3.12-dev (3.12.7-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:armhf (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up dh-python (6.20240824) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/kmer-0~20150903+r2013/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kmer_0~20150903+r2013-9_source.changes dpkg-buildpackage: info: source package kmer dpkg-buildpackage: info: source version 0~20150903+r2013-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/kmer-0~20150903+r2013' /usr/bin/make real-clean make[2]: Entering directory '/build/reproducible-path/kmer-0~20150903+r2013' rm -f ESTmapper/*.o ESTmapper/mergeCounts ESTmapper/terminate ESTmapper/Make.depends ESTmapper/mergeCounts.C.d ESTmapper/terminate.C.d ESTmapper/mergeCounts ESTmapper/terminate rm -f atac-driver/libatac/*.o atac-driver/libatac/*~ atac-driver/libatac/libatac.a atac-driver/libatac/Make.depends atac-driver/libatac/atacFeature.C.d atac-driver/libatac/atacFeatureList.C.d atac-driver/libatac/atacFile.C.d atac-driver/libatac/atacFileStreamMerge.C.d atac-driver/libatac/atacMatch.C.d atac-driver/libatac/atacMatchList.C.d atac-driver/libatac/atacMatchOrder.C.d rm -f atac-driver/alignOverlap/*.o atac-driver/alignOverlap/*~ atac-driver/alignOverlap/core atac-driver/alignOverlap/overlap-process1.C atac-driver/alignOverlap/overlap-process2.C atac-driver/alignOverlap/overlap atac-driver/alignOverlap/Make.depends atac-driver/alignOverlap/overlap.C.d atac-driver/alignOverlap/overlap-sort.C.d atac-driver/alignOverlap/overlap-printAnno.C.d atac-driver/alignOverlap/overlap-find.C.d rm -f atac-driver/gapShifter/*.o atac-driver/gapShifter/*~ atac-driver/gapShifter/core atac-driver/gapShifter/gapShifter atac-driver/gapShifter/extractSequence atac-driver/gapShifter/extractUnmapped atac-driver/gapShifter/coalesceMatches atac-driver/gapShifter/correctGaps atac-driver/gapShifter/testAtac atac-driver/gapShifter/cleanAtac atac-driver/gapShifter/projectFeatures atac-driver/gapShifter/Make.depends atac-driver/gapShifter/gapShifter.C.d atac-driver/gapShifter/extractSequence.C.d atac-driver/gapShifter/extractUnmapped.C.d atac-driver/gapShifter/coalesceMatches.C.d atac-driver/gapShifter/correctGaps.C.d atac-driver/gapShifter/testAtac.C.d atac-driver/gapShifter/cleanAtac.C.d atac-driver/gapShifter/projectFeatures.C.d rm -f atac-driver/lengthFilter/*.o atac-driver/lengthFilter/*~ atac-driver/lengthFilter/core atac-driver/lengthFilter/lengthFilter atac-driver/lengthFilter/Make.depends atac-driver/lengthFilter/lengthFilter.C.d rm -f atac-driver/matchExtender/*.o atac-driver/matchExtender/*~ atac-driver/matchExtender/core atac-driver/matchExtender/matchExtender atac-driver/matchExtender/Make.depends atac-driver/matchExtender/matchExtender.C.d atac-driver/matchExtender/matchExtender-dump.C.d atac-driver/matchExtender/matchExtender-func.C.d rm -f atac-driver/mismatchCounter/*.o atac-driver/mismatchCounter/*~ atac-driver/mismatchCounter/core atac-driver/mismatchCounter/mismatchCounter atac-driver/mismatchCounter/Make.depends atac-driver/mismatchCounter/mismatchCounter.C.d rm -f atac-driver/statsGenerator/*.o atac-driver/statsGenerator/*~ atac-driver/statsGenerator/core atac-driver/statsGenerator/statsGenerator atac-driver/statsGenerator/Make.depends atac-driver/statsGenerator/statsGenerator.C.d rm -f atac-driver/uniqueFilter/*.o atac-driver/uniqueFilter/*~ atac-driver/uniqueFilter/core atac-driver/uniqueFilter/uniqueFilter atac-driver/uniqueFilter/Make.depends atac-driver/uniqueFilter/uniqueFilter.C.d rm -f atac-driver/clumpMaker/*.o atac-driver/clumpMaker/*~ atac-driver/clumpMaker/core atac-driver/clumpMaker/clumpMaker atac-driver/clumpMaker/Make.depends atac-driver/clumpMaker/clumpMaker.C.d rm -f atac-driver/chainer/*.o atac-driver/chainer/*/*.o atac-driver/chainer/*.so atac-driver/chainer/python/*.pyc atac-driver/chainer/localAlignerInterfacemodule.so atac-driver/chainer/halignmodule.so atac-driver/chainer/Make.depends atac-driver/chainer/localalign/GF_ALN_dpaligner.C.d atac-driver/chainer/localalign/GF_ALN_local.C.d atac-driver/chainer/localalign/GF_ALN_overlap.C.d atac-driver/chainer/localalign/GF_ALN_loverlapper.C.d atac-driver/chainer/localalign/GF_ALN_pieceOlap.C.d atac-driver/chainer/localalign/localAlignerInterfacemodule.C.d atac-driver/chainer/halign/halign.C.d atac-driver/chainer/halign/halignmodule.C.d rm -f atac-driver/chimera/*.o atac-driver/chimera/*~ atac-driver/chimera/core atac-driver/chimera/happy-clones-span-clumps atac-driver/chimera/Make.depends atac-driver/chimera/happy-clones-span-clumps.C.d rm -f atac-driver/Make.depends rm -f seatac/*.o seatac/seatac seatac/heavychains seatac/filter-nop.so seatac/filter-heavychains.so seatac/Make.depends seatac/seatac.C.d seatac/configuration.C.d seatac/encodedQuery.C.d seatac/hitMatrix.C.d seatac/thr-search.C.d seatac/thr-loader.C.d seatac/thr-deadlock.C.d seatac/hitMatrix-sort.C.d rm -f leaff/*.o leaff/leaff leaff/Make.depends leaff/leaff.C.d leaff/blocks.C.d leaff/dups.C.d leaff/gc.C.d leaff/partition.C.d leaff/simseq.C.d leaff/stats.C.d rm -f meryl/*.o meryl/meryl meryl/simple meryl/mapMers meryl/mapMers-depth meryl/kmer-mask meryl/libmerylguts.a meryl/Make.depends meryl/args.C.d meryl/binaryOp.C.d meryl/build.C.d meryl/build-threads.C.d meryl/dump.C.d meryl/estimate.C.d meryl/merge.C.d meryl/unaryOp.C.d meryl/meryl.C.d meryl/simple.C.d meryl/mapMers.C.d meryl/mapMers-depth.C.d meryl/kmer-mask.C.d rm -f seagen/*.o seagen/seagen seagen/hitConverter seagen/filterEST seagen/filterMRNA seagen/filterNULL seagen/filtertest seagen/sortHits seagen/filterESTsimple seagen/Make.depends seagen/searchGENOME.C.d seagen/configuration.C.d seagen/encodedQuery.C.d seagen/thr-deadlock.C.d seagen/thr-loader.C.d seagen/thr-search.C.d seagen/thr-output.C.d seagen/hitMatrix-sort.C.d seagen/aHit.C.d seagen/hitConverter.C.d seagen/filterEST.C.d seagen/filterEST-complicated.C.d seagen/filterMRNA.C.d seagen/filterNULL.C.d seagen/sortHits.C.d seagen/filtertest.C.d seagen/hitReader.C.d seagen/hitMatrix.C.d rm -f sim4dbutils/*.o sim4dbutils/cleanPolishes sim4dbutils/fixPolishesIID sim4dbutils/comparePolishes sim4dbutils/convertToAtac sim4dbutils/convertToExtent sim4dbutils/convertPolishes sim4dbutils/detectChimera sim4dbutils/depthOfPolishes sim4dbutils/filterPolishes sim4dbutils/headPolishes sim4dbutils/mappedCoverage sim4dbutils/mergePolishes sim4dbutils/parseSNP sim4dbutils/pickBestPolish sim4dbutils/pickBestPair sim4dbutils/pickUniquePolish sim4dbutils/plotCoverageVsIdentity sim4dbutils/removeDuplicate sim4dbutils/sortPolishes sim4dbutils/summarizePolishes sim4dbutils/uniqPolishes sim4dbutils/vennPolishes sim4dbutils/realignPolishes sim4dbutils/removeRedundant sim4dbutils/reportAlignmentDifferences sim4dbutils/Make.depends sim4dbutils/cleanPolishes.C.d sim4dbutils/fixPolishesIID.C.d sim4dbutils/comparePolishes.C.d sim4dbutils/convertToAtac.C.d sim4dbutils/convertToExtent.C.d sim4dbutils/convertPolishes.C.d sim4dbutils/detectChimera.C.d sim4dbutils/depthOfPolishes.C.d sim4dbutils/filterPolishes.C.d sim4dbutils/headPolishes.C.d sim4dbutils/mappedCoverage.C.d sim4dbutils/mergePolishes.C.d sim4dbutils/parseSNP.C.d sim4dbutils/pickBestPolish.C.d sim4dbutils/pickBestPair.C.d sim4dbutils/pickUniquePolish.C.d sim4dbutils/plotCoverageVsIdentity.C.d sim4dbutils/removeDuplicate.C.d sim4dbutils/sortPolishes.C.d sim4dbutils/summarizePolishes.C.d sim4dbutils/uniqPolishes.C.d sim4dbutils/vennPolishes.C.d sim4dbutils/realignPolishes.C.d sim4dbutils/removeRedundant.C.d sim4dbutils/reportAlignmentDifferences.C.d sim4dbutils/s4p_overlap.C.d rm -f sim4db/*.o sim4db/sim4db sim4db/Make.depends sim4db/sim4th.C.d rm -f snapper/*.o snapper/snapper2 snapper/Make.depends snapper/snapper2.C.d snapper/configuration.C.d snapper/thr-search.C.d snapper/thr-filter.C.d snapper/thr-polish.C.d snapper/thr-polish-dp.C.d snapper/hitMatrix.C.d snapper/hitMatrix-sort.C.d rm -f tapper/*.o tapper/tagger tapper/tapper tapper/tapperconvert tapper/tappermerge tapper/tappersort tapper/tappererrorcorrect tapper/Make.depends tapper/tagger.C.d tapper/tapper.C.d tapper/tapperconvert.C.d tapper/tappermerge.C.d tapper/tappersort.C.d tapper/tappererrorcorrect.C.d rm -f /build/reproducible-path/kmer-0~20150903+r2013/libsim4/*.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/*.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/*.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libsim4/Make.depends /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/extend.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/poly.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/splice.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/util.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C.d /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C.d rm -f /build/reproducible-path/kmer-0~20150903+r2013/libkmer/*.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libkmer/Make.depends /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C.d /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C.d rm -f /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/*.o /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/Make.depends /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C.d rm -f /build/reproducible-path/kmer-0~20150903+r2013/libbio/*.o /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/Make.depends /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet.c.d /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.c.d /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-colorspace.c.d /build/reproducible-path/kmer-0~20150903+r2013/libbio/halign.c.d /build/reproducible-path/kmer-0~20150903+r2013/libbio/reversecomplement.c.d /build/reproducible-path/kmer-0~20150903+r2013/libbio/kmer.C.d rm -f /build/reproducible-path/kmer-0~20150903+r2013/libseq/*.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/Make.depends /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/sffFile.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/merStream.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C.d /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C.d rm -f /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/*.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/test.c /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/diffs /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/Make.depends /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/test.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/*.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/test.c /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/diffs /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test rm -f /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/*.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/Make.depends /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/dict.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/except.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/hash.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/list.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/sfx.c.d rm -f /build/reproducible-path/kmer-0~20150903+r2013/libutil/*.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/Make.depends /build/reproducible-path/kmer-0~20150903+r2013/libutil/file.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/md5.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/palloc.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.c.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.C.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.C.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.C.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/speedCounter.C.d /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C.d rm -f Make.depends Make.compilers make[2]: Leaving directory '/build/reproducible-path/kmer-0~20150903+r2013' rm -rf installdir make[1]: Leaving directory '/build/reproducible-path/kmer-0~20150903+r2013' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/kmer-0~20150903+r2013' # The Makefile apparently doesn't use regular LDFLAGS. # It defines CLDFLAGS and CXXLDFLAGS as empty strings, so let's # use them here. /usr/bin/make install \ CLDFLAGS="-Wl,-z,relro -Wl,-z,now" \ CXXLDFLAGS="-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/kmer-0~20150903+r2013' making /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/sfx.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/list.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/hash.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/except.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/dict.c.d gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c: In function 'mtRandomGaussian': /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c:166:34: warning: variable 'y2' set but not used [-Wunused-but-set-variable] 166 | double x1=0, x2=0, w=0, y1=0, y2=0; | ^~ gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test.c gcc -Wl,-z,relro -Wl,-z,now -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test.o -pthread -ldl -lm /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test | diff - /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.out > /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/diffs 2>&1 if test -s /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/diffs ; then echo 'MT19937: TEST FAILED'; else echo 'MT19937: Test Passed'; fi MT19937: Test Passed touch /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/test.c /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test | diff - /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.out making /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/test.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/speedCounter.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/palloc.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/md5.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libutil/file.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/merStream.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/sffFile.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libbio/kmer.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libbio/reversecomplement.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libbio/halign.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-colorspace.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet.c.d making /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/util.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/splice.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/poly.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/extend.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C.d making /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C.d making tapper/tappererrorcorrect.C.d making tapper/tappersort.C.d making tapper/tappermerge.C.d making tapper/tapperconvert.C.d making tapper/tapper.C.d making tapper/tagger.C.d making snapper/hitMatrix-sort.C.d making snapper/hitMatrix.C.d making snapper/thr-polish-dp.C.d making snapper/thr-polish.C.d making snapper/thr-filter.C.d making snapper/thr-search.C.d making snapper/configuration.C.d making snapper/snapper2.C.d making sim4db/sim4th.C.d making sim4dbutils/s4p_overlap.C.d making sim4dbutils/reportAlignmentDifferences.C.d making sim4dbutils/removeRedundant.C.d making sim4dbutils/realignPolishes.C.d making sim4dbutils/vennPolishes.C.d making sim4dbutils/uniqPolishes.C.d making sim4dbutils/summarizePolishes.C.d making sim4dbutils/sortPolishes.C.d making sim4dbutils/removeDuplicate.C.d making sim4dbutils/plotCoverageVsIdentity.C.d making sim4dbutils/pickUniquePolish.C.d making sim4dbutils/pickBestPair.C.d making sim4dbutils/pickBestPolish.C.d making sim4dbutils/parseSNP.C.d making sim4dbutils/mergePolishes.C.d making sim4dbutils/mappedCoverage.C.d making sim4dbutils/headPolishes.C.d making sim4dbutils/filterPolishes.C.d making sim4dbutils/depthOfPolishes.C.d making sim4dbutils/detectChimera.C.d making sim4dbutils/convertPolishes.C.d making sim4dbutils/convertToExtent.C.d making sim4dbutils/convertToAtac.C.d making sim4dbutils/comparePolishes.C.d making sim4dbutils/fixPolishesIID.C.d making sim4dbutils/cleanPolishes.C.d making seagen/hitMatrix.C.d making seagen/hitReader.C.d making seagen/filtertest.C.d making seagen/sortHits.C.d making seagen/filterNULL.C.d making seagen/filterMRNA.C.d making seagen/filterEST-complicated.C.d making seagen/filterEST.C.d making seagen/hitConverter.C.d making seagen/aHit.C.d making seagen/hitMatrix-sort.C.d making seagen/thr-output.C.d making seagen/thr-search.C.d making seagen/thr-loader.C.d making seagen/thr-deadlock.C.d making seagen/encodedQuery.C.d making seagen/configuration.C.d making seagen/searchGENOME.C.d making meryl/kmer-mask.C.d making meryl/mapMers-depth.C.d making meryl/mapMers.C.d making meryl/simple.C.d making meryl/meryl.C.d making meryl/unaryOp.C.d making meryl/merge.C.d making meryl/estimate.C.d making meryl/dump.C.d making meryl/build-threads.C.d making meryl/build.C.d making meryl/binaryOp.C.d making meryl/args.C.d making leaff/stats.C.d making leaff/simseq.C.d making leaff/partition.C.d making leaff/gc.C.d making leaff/dups.C.d making leaff/blocks.C.d making leaff/leaff.C.d making seatac/hitMatrix-sort.C.d making seatac/thr-deadlock.C.d making seatac/thr-loader.C.d making seatac/thr-search.C.d making seatac/hitMatrix.C.d making seatac/encodedQuery.C.d making seatac/configuration.C.d making seatac/seatac.C.d making atac-driver/chimera/happy-clones-span-clumps.C.d making atac-driver/chainer/halign/halignmodule.C.d making atac-driver/chainer/halign/halign.C.d making atac-driver/chainer/localalign/localAlignerInterfacemodule.C.d making atac-driver/chainer/localalign/GF_ALN_pieceOlap.C.d making atac-driver/chainer/localalign/GF_ALN_loverlapper.C.d making atac-driver/chainer/localalign/GF_ALN_overlap.C.d making atac-driver/chainer/localalign/GF_ALN_local.C.d making atac-driver/chainer/localalign/GF_ALN_dpaligner.C.d making atac-driver/clumpMaker/clumpMaker.C.d making atac-driver/uniqueFilter/uniqueFilter.C.d making atac-driver/statsGenerator/statsGenerator.C.d making atac-driver/mismatchCounter/mismatchCounter.C.d making atac-driver/matchExtender/matchExtender-func.C.d making atac-driver/matchExtender/matchExtender-dump.C.d making atac-driver/matchExtender/matchExtender.C.d making atac-driver/lengthFilter/lengthFilter.C.d making atac-driver/gapShifter/projectFeatures.C.d making atac-driver/gapShifter/cleanAtac.C.d making atac-driver/gapShifter/testAtac.C.d making atac-driver/gapShifter/correctGaps.C.d making atac-driver/gapShifter/coalesceMatches.C.d making atac-driver/gapShifter/extractUnmapped.C.d making atac-driver/gapShifter/extractSequence.C.d making atac-driver/gapShifter/gapShifter.C.d making atac-driver/alignOverlap/overlap-find.C.d making atac-driver/alignOverlap/overlap-printAnno.C.d making atac-driver/alignOverlap/overlap-sort.C.d making atac-driver/alignOverlap/overlap.C.d making atac-driver/libatac/atacMatchOrder.C.d making atac-driver/libatac/atacMatchList.C.d making atac-driver/libatac/atacMatch.C.d making atac-driver/libatac/atacFileStreamMerge.C.d making atac-driver/libatac/atacFile.C.d making atac-driver/libatac/atacFeatureList.C.d making atac-driver/libatac/atacFeature.C.d making ESTmapper/terminate.C.d making ESTmapper/mergeCounts.C.d g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ESTmapper/mergeCounts.o -c ESTmapper/mergeCounts.C ESTmapper/mergeCounts.C: In function 'int main(int, char**)': ESTmapper/mergeCounts.C:33:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | fgets(buf, 256, Fs[i]); | ~~~~~^~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o ESTmapper/mergeCounts ESTmapper/mergeCounts.o -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ESTmapper/terminate.o -c ESTmapper/terminate.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from ESTmapper/terminate.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from ESTmapper/terminate.C:3: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ ESTmapper/terminate.C: In member function 'void iidReaderWriter::load(uint32)': ESTmapper/terminate.C:82:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fscanf(inFile, uint32FMT, &iid); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ESTmapper/terminate.C:85:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 85 | fscanf(inFile, uint32FMT, &iid); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C: In member function 'void sim4command::finalize()': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:147:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 147 | if (_genLo > _genHi) | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C: In member function 'char* sim4command::getESTheader()': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:184:22: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 184 | static char *xxx = "anonymous cDNA sequence"; | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C: In member function 'char* sim4command::getGENheader()': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:222:15: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 222 | char *xxx = "anonymous genomic sequence"; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.H:8, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C:2: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C: In member function 'void Sim4::IDISPLAY(sim4polishBuilder&, char*, char*, char*, char*, int, int, int*, int, int, int, Exon*)': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:681:30: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 681 | builder.addExonAlignment("Empty exon list; no alignment possible!", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:682:30: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 682 | "Empty exon list; no alignment possible!"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:694:30: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 694 | builder.addExonAlignment("Alignment fragment not found; no alignment possible!", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:695:30: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 695 | "Alignment fragment not found; no alignment possible!"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.C: In member function 'void Sim4::path(int, int, char, int, int, char, int, edit_script**, edit_script**)': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.C:777:13: warning: 'head2' may be used uninitialized [-Wmaybe-uninitialized] 777 | if (head2) *tail = tail2; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.C:557:38: note: 'head2' declared here 557 | edit_script *head1, *tail1, *head2, *tail2; | ^~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/extend.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/extend.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/extend.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C: In function 'void readModel(Fixed_Length_ICM_t*, const char*)': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C:53:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 53 | fread (line, sizeof (char), ID_STRING_LEN, fp); // skip the text header line | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C:84:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 84 | fread ((*fixed).permutation, sizeof (int), (*fixed).length, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/greedy.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C:2: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/poly.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/poly.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/poly.C:2: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.C:4: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.C: In function 'int readtree(Sim4*, char*, tree*, int)': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.C:452:6: warning: variable 'len' set but not used [-Wunused-but-set-variable] 452 | int len; | ^~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.C: In function 'int Is_Cod_NonCod(const int*, double*, int)': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.C:751:12: warning: 'scores' may be used uninitialized [-Wmaybe-uninitialized] 751 | double *scores; | ^~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/splice.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/splice.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/splice.C:2: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.C: In member function 'void Sim4::bld_table(char*, int, mss_t, int)': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.C:112:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 112 | if (emer < 0) | ^~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.C:115:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 115 | ecode <<= 2; | ^~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/util.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/util.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/util.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:17: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/../sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:249:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 249 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:249:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 249 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:365:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:365:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:58:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | sprintf(gpp, "%c"uint32FMT" ", gaptyp, gapcnt); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:68:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | sprintf(gpp, "%c"uint32FMT" ", gaptyp, gapcnt); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:80:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 80 | sprintf(gpp, "%c"uint32FMT" ", gaptyp, gapcnt); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:91:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | sprintf(gpp, "%c"uint32FMT"", gaptyp, gapcnt); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:163:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 163 | fprintf(stderr, "sim4reader: Unknown matchOrientation '"uint32FMT"' in printPolish()\n", _matchOrientation); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:176:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stderr, "sim4reader: Unknown strandOrientation '"uint32FMT"' in printPolish()\n", _matchOrientation); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:88: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:100: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:323:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 323 | fprintf(stderr, "sim4reader: Unknown strandOrientation '"uint32FMT"' in printPolishGFF3()\n", _matchOrientation); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:346:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | sprintf(outc, uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:346:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | sprintf(outc, uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:346:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | sprintf(outc, uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:91: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:363:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 363 | sprintf(outc, uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:363:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 363 | sprintf(outc, uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:363:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 363 | sprintf(outc, uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:91: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:91: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:46:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(stderr, "sim4reader: Got '%s', expecting 'sim4begin' at byte "uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:65:2: warning: #warning LAZY PROGRAMMER did not extend an array [-Wcpp] 65 | #warning LAZY PROGRAMMER did not extend an array | ^~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:126:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 126 | fprintf(stderr, "sim4reader: Got '%s', expecting GFF3 mRNA line at byte "uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:150:2: warning: #warning LAZY PROGRAMMER did not extend an array [-Wcpp] 150 | #warning LAZY PROGRAMMER did not extend an array | ^~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:55:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:72:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 72 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:169:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:246:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 246 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:275:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 275 | r = sscanf(crttok, "ID=sim4db"uint32FMT"", &matchID); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:280:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 280 | r = sscanf(crttok, "Name="uint32FMT":%s", &_estID, _estDefLine); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:285:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | r = sscanf(crttok, "Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c", &_estID, _estDefLine, &dummy1, &dummy2, &mOri); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:285:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | r = sscanf(crttok, "Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c", &_estID, _estDefLine, &dummy1, &dummy2, &mOri); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:285:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | r = sscanf(crttok, "Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c", &_estID, _estDefLine, &dummy1, &dummy2, &mOri); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:293:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 293 | r = sscanf(crttok, "targetLen="uint32FMT"", &_estLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:296:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | r = sscanf(crttok, "pA="uint32FMT"", &_estPolyA); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:299:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 299 | r = sscanf(crttok, "pT="uint32FMT"", &_estPolyT); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:302:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 302 | r = sscanf(crttok, "genRegion="uint32FMT"-"uint32FMT"", &_genRegionOffset, &dummy1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:302:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 302 | r = sscanf(crttok, "genRegion="uint32FMT"-"uint32FMT"", &_genRegionOffset, &dummy1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:313:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 313 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:342:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 342 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:366:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 366 | r = sscanf(crttok, "Parent=sim4db"uint32FMT"", &dummy1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:370:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | r = sscanf(crttok, "Target=%s "uint32FMT" "uint32FMT" %c", &dummybuf, &exon._estFrom, &exon._estTo, &mOri); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:370:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | r = sscanf(crttok, "Target=%s "uint32FMT" "uint32FMT" %c", &dummybuf, &exon._estFrom, &exon._estTo, &mOri); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:377:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 377 | r = sscanf(crttok, "nMatches="uint32FMT"", &exon._numMatches); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:403:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 403 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:437:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 437 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C: In member function 'void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:140:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class sim4polishExon'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 140 | memcpy(nnn, _exons, sizeof(sim4polishExon) * _numExons); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: 'class sim4polishExon' declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C: In member function 'void sim4polish::s4p_linesToPolishGFF3(uint32, uint32, char**, uint32*)': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:261:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 261 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:261:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 261 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:262:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 262 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:262:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 262 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:263:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 263 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:263:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 263 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:264:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 264 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:264:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 264 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:265:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 265 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:265:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 265 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:266:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 266 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:266:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 266 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:267:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 267 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:267:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 267 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:268:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 268 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:268:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 268 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:346:17: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 346 | if ((dummy1 != _genID) || strcmp(dummybuf, _genDefLine) || | ~~~~~~~^~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:347:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 347 | (sOri != '+') && (sOri != '-') && (sOri != '.')) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:352:7: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 352 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:352:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 352 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:353:7: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 353 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:353:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 353 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:354:7: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 354 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:354:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 354 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:355:7: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 355 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:355:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 355 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:356:7: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 356 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:356:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 356 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:357:7: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 357 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:357:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 357 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:358:7: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 358 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:358:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 358 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:359:7: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 359 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:359:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 359 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:370:30: warning: format '%s' expects argument of type 'char*', but argument 3 has type 'char (*)[1000]' [-Wformat=] 370 | r = sscanf(crttok, "Target=%s "uint32FMT" "uint32FMT" %c", &dummybuf, &exon._estFrom, &exon._estTo, &mOri); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ | | | char (*)[1000] /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:383:39: warning: format '%s' expects argument of type 'char*', but argument 3 has type 'char (*)[1000]' [-Wformat=] 383 | r = sscanf(crttok, "intron=%s", &dummybuf); | ~^ ~~~~~~~~~ | | | | | char (*)[1000] | char* /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:414:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class sim4polishExon'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 414 | memcpy(nnn, _exons, sizeof(sim4polishExon) * _numExons); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: 'class sim4polishExon' declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C:2: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C:8: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C: In member function 'sim4polish* sim4polishBuilder::release()': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C:246:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class sim4polishExon'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 246 | memcpy(it->_exons + i, ex[i], sizeof(sim4polishExon)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: 'class sim4polishExon' declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Failed to reposition %s to record "uint32FMT", only "uint32FMT" records\n", _path, ordinal, _polishRecordLen), exit(1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:120:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Failed to reposition %s to record "uint32FMT", only "uint32FMT" records\n", _path, ordinal, _polishRecordLen), exit(1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:248:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stderr, "polishes: "uint32FMT"\r", _polishRecordLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C: In member function 'void sim4polishFile::loadIndex()': /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:141:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 141 | fread(&magic, sizeof(char), 8, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:145:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 145 | fread(&_polishRecordLen, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:151:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 151 | fread( _polishRecord, sizeof(polishRecord), _polishRecordLen, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:152:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | fread( _polishRecordEST, sizeof(uint32), _polishRecordLen, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:153:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 153 | fread( _polishRecordGEN, sizeof(uint32), _polishRecordLen, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:155:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | fread(&_maxEST, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:156:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 156 | fread(&_maxGEN, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:161:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 161 | fread( _ESTiidLocation, sizeof(uint32), _maxEST, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:162:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 162 | fread( _GENiidLocation, sizeof(uint32), _maxGEN, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.o -c /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ rm -f /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a && ar ruvs /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/extend.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/greedy.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/poly.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/splice.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/util.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/align.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/extend.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/greedy.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/poly.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/splice.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/table.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4core/util.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.o a - /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:151:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stderr, "fastaFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:151:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stderr, "fastaFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:224:9: warning: this decimal constant is unsigned only in ISO C90 224 | if (sMax == 4294967295) // 4G - 1 | ^~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:226:9: warning: this decimal constant is unsigned only in ISO C90 226 | if (sMax >= 2147483648) // 2G | ^~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:227:11: warning: this decimal constant is unsigned only in ISO C90 227 | sMax = 4294967295; | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:252:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 252 | fprintf(stderr, "fastaFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:252:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 252 | fprintf(stderr, "fastaFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C: In member function 'void fastaFile::loadIndex(char*)': /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:357:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 357 | fread(&_header, sizeof(fastaFileHeader), 1, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:379:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 379 | fread(_index, sizeof(fastaFileIndex), _header._numberOfSequences, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.C:380:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(_names, sizeof(char), _header._namesLength, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.C: In member function 'virtual bool fastaStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)': /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.C:110:9: warning: unused variable 'ret' [-Wunused-variable] 110 | bool ret = true; | ^~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:141:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 141 | fprintf(stderr, "fastqFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:141:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 141 | fprintf(stderr, "fastqFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:214:9: warning: this decimal constant is unsigned only in ISO C90 214 | if (sMax == 4294967295) // 4G - 1 | ^~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:216:9: warning: this decimal constant is unsigned only in ISO C90 216 | if (sMax >= 2147483648) // 2G | ^~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:217:11: warning: this decimal constant is unsigned only in ISO C90 217 | sMax = 4294967295; | ^~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:253:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 253 | fprintf(stderr, "fastqFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:253:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 253 | fprintf(stderr, "fastqFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:533:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 533 | fprintf(stderr, "REALLOC len="uint32FMT" from "uint32FMT" to "uint32FMT"\n", indexLen, indexMax, indexMax * 2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:533:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 533 | fprintf(stderr, "REALLOC len="uint32FMT" from "uint32FMT" to "uint32FMT"\n", indexLen, indexMax, indexMax * 2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:533:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 533 | fprintf(stderr, "REALLOC len="uint32FMT" from "uint32FMT" to "uint32FMT"\n", indexLen, indexMax, indexMax * 2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C: In member function 'void fastqFile::loadIndex(char*)': /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:354:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 354 | fread(&_header, sizeof(fastqFileHeader), 1, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:374:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 374 | fread(_index, sizeof(fastqFileIndex), _header._numberOfSequences, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.C:375:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 375 | fread(_names, sizeof(char), _header._namesLength, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.C: In member function 'virtual bool fastqStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)': /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.C:110:9: warning: unused variable 'ret' [-Wunused-variable] 110 | bool ret = true; | ^~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:2: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:129:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "seqStore::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:129:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "seqStore::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:197:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stderr, "seqStore::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:197:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stderr, "seqStore::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:203:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:203:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:203:96: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:203:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:463:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 463 | fprintf(stderr, "constructSeqStore()-- sequence %s too long, must be shorter than "uint64FMT" Gbp.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:467:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 467 | fprintf(stderr, "constructSeqStore()-- too many sequences, must be fewer than "uint64FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:620:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:620:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:620:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:620:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C: In function 'void constructSeqStore(char*, seqCache*)': /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:410:9: warning: 'memset' used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args] 410 | memset(&HEAD, sizeof(seqStoreHeader), 0); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C: In constructor 'seqStore::seqStore(const char*)': /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:21:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 21 | fread(&_header, sizeof(seqStoreHeader), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C: In member function 'virtual seqFile* seqStore::openFile(const char*)': /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:73:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | fread(&magic1, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:74:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | fread(&magic2, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C: In member function 'void seqStore::loadIndex()': /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:318:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 318 | fread(&_header, sizeof(seqStoreHeader), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:329:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 329 | fread( _index, sizeof(seqStoreIndex), _header._numberOfSequences, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:343:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 343 | fread( _block, sizeof(seqStoreBlock), _header._numberOfBlocks, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.C:347:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 347 | fread( _names, sizeof(char), _header._namesLength, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/sffFile.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/sffFile.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/sffFile.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/sffFile.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.C:3: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.C:171:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stderr, "seqCache::loadAllSequences()-- Failed to load iid "uint32FMT".\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:2: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:236:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "seqStream::setRange()-- ERROR: range ("uint64FMT","uint64FMT") too big; only "uint64FMT" positions.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:236:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "seqStream::setRange()-- ERROR: range ("uint64FMT","uint64FMT") too big; only "uint64FMT" positions.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:236:82: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "seqStream::setRange()-- ERROR: range ("uint64FMT","uint64FMT") too big; only "uint64FMT" positions.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:268:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 268 | fprintf(stderr, "seqStream::sequenceNumberOfPosition()-- WARNING: position p="uint64FMT" too big; only "uint64FMT" positions.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:268:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 268 | fprintf(stderr, "seqStream::sequenceNumberOfPosition()-- WARNING: position p="uint64FMT" too big; only "uint64FMT" positions.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:340:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:340:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:340:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:386:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 386 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:386:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 386 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.C:386:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 386 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/merStream.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/merStream.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/merStream.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/merStream.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:3: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:33:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stderr, "generateCorrectSequence()-- Using seed "uint32FMT"\n", seed); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:15:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 15 | fprintf(stderr, "testID:"uint32FMT" - empty sequence\n", testID); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:22:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 22 | fprintf(stderr, "testID:"uint32FMT" - header differs '%s' vs '%s'\n", testID, S->header(), correctSequence[sid].header); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:26:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "testID:"uint32FMT" - header length differs "uint32FMT" vs "uint32FMT"\n", testID, S->headerLength(), correctSequence[sid].headerLength); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:26:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "testID:"uint32FMT" - header length differs "uint32FMT" vs "uint32FMT"\n", testID, S->headerLength(), correctSequence[sid].headerLength); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:26:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "testID:"uint32FMT" - header length differs "uint32FMT" vs "uint32FMT"\n", testID, S->headerLength(), correctSequence[sid].headerLength); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:30:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 30 | fprintf(stderr, "testID:"uint32FMT" - sequence differs\n", testID); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:34:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs strlen "uint32FMT" vs "uint32FMT"\n", testID, (uint32)strlen(S->sequence()), correctSequence[sid].sequenceLength); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:34:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs strlen "uint32FMT" vs "uint32FMT"\n", testID, (uint32)strlen(S->sequence()), correctSequence[sid].sequenceLength); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:34:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs strlen "uint32FMT" vs "uint32FMT"\n", testID, (uint32)strlen(S->sequence()), correctSequence[sid].sequenceLength); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:38:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs "uint32FMT" vs "uint32FMT"\n", testID, S->sequenceLength(), correctSequence[sid].sequenceLength); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:38:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs "uint32FMT" vs "uint32FMT"\n", testID, S->sequenceLength(), correctSequence[sid].sequenceLength); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.C:38:77: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs "uint32FMT" vs "uint32FMT"\n", testID, S->sequenceLength(), correctSequence[sid].sequenceLength); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:3: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:33:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stderr, "generateCorrectSequence()-- Using seed "uint32FMT"\n", seed); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:17:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | fprintf(stderr, "testIndexing()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:17:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | fprintf(stderr, "testIndexing()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:55:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "lengthOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:55:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "lengthOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:55:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "lengthOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:60:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stderr, "startOf "uint32FMT" returned "uint64FMT", not correct "uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:60:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stderr, "startOf "uint32FMT" returned "uint64FMT", not correct "uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:60:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stderr, "startOf "uint32FMT" returned "uint64FMT", not correct "uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:65:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "IIDOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:65:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "IIDOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:65:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "IIDOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:74:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stderr, "sequenceNumberOfPosition "uint64FMT" returned "uint32FMT", not correct "uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:74:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stderr, "sequenceNumberOfPosition "uint64FMT" returned "uint32FMT", not correct "uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:74:82: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stderr, "sequenceNumberOfPosition "uint64FMT" returned "uint32FMT", not correct "uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:95:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 95 | fprintf(stderr, "wrong separator at sep "uint32FMT" got %d expected %d\n", x, s, sep); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:124:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- letter wrong got'%c'\n", sp, si, st, ch, chainSeq[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:124:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- letter wrong got'%c'\n", sp, si, st, ch, chainSeq[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:124:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- letter wrong got'%c'\n", sp, si, st, ch, chainSeq[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:145:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 145 | fprintf(stderr, "iterated length wrong; sib="uint32FMT" sie="uint32FMT"\n", sib, sie); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:145:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 145 | fprintf(stderr, "iterated length wrong; sib="uint32FMT" sie="uint32FMT"\n", sib, sie); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:159:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 159 | fprintf(stderr, "testChaining()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.C:159:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 159 | fprintf(stderr, "testChaining()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.o -c /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:3: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:33:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stderr, "generateCorrectSequence()-- Using seed "uint32FMT"\n", seed); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:11:2: warning: #warning HOW DO WE TEST IF WE GET ALL THE MERS? [-Wcpp] 11 | #warning HOW DO WE TEST IF WE GET ALL THE MERS? | ^~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:33:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:33:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:33:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:33:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:39:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(stdout, "MS pos="uint32FMT" failed '%s' != '%s'.\n", pos, testmer, seq + pos); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:124:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "mer stream position out of range; at "uint32FMT", range "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:124:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "mer stream position out of range; at "uint32FMT", range "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:124:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "mer stream position out of range; at "uint32FMT", range "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C: In function 'int main(int, char**)': /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:223:33: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 223 | testMerStreamSimple(MS, 20, "GGGTCAACTCCGCCCGCACTCTAGC", SP); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:225:33: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 225 | testMerStreamSimple(MS, 20, "GGGTCAACTCCGCCCGCACTCTAGC", SP); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:228:33: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 228 | testMerStreamSimple(MS, 20, "GGGTCAACTCCGCCCGCACTCTAGC", SP); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:243:33: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 243 | testMerStreamSimple(MS, 20, "GATCACTCGCGCACTCTAGCA", SP); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:245:33: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 245 | testMerStreamSimple(MS, 20, "GATCACTCGCGCACTCTAGCA", SP); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.C:248:33: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 248 | testMerStreamSimple(MS, 20, "GATCACTCGCGCACTCTAGCA", SP); | ^~~~~~~~~~~~~~~~~~~~~~~ rm -f /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a && ar ruvs /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/sffFile.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/merStream.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaFile.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastaStdin.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqFile.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/fastqStdin.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStore.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/sffFile.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqFactory.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqCache.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/seqStream.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/merStream.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.o a - /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet.o -c /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.o -c /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-colorspace.o -c /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-colorspace.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libbio/halign.o -c /build/reproducible-path/kmer-0~20150903+r2013/libbio/halign.c /build/reproducible-path/kmer-0~20150903+r2013/libbio/halign.c: In function 'align_path': /build/reproducible-path/kmer-0~20150903+r2013/libbio/halign.c:385:7: warning: 'head2' may be used uninitialized [-Wmaybe-uninitialized] 385 | if (head2) *tail = tail2; | ^~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libbio/halign.c:163:32: note: 'head2' declared here 163 | edit_script *head1, *tail1, *head2, *tail2; | ^~~~~ gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libbio/reversecomplement.o -c /build/reproducible-path/kmer-0~20150903+r2013/libbio/reversecomplement.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libbio/kmer.o -c /build/reproducible-path/kmer-0~20150903+r2013/libbio/kmer.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/kmer.H:28, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/kmer.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/kmer.H:29: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ rm -f /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a && ar ruvs /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet.o /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.o /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-colorspace.o /build/reproducible-path/kmer-0~20150903+r2013/libbio/halign.o /build/reproducible-path/kmer-0~20150903+r2013/libbio/reversecomplement.o /build/reproducible-path/kmer-0~20150903+r2013/libbio/kmer.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a a - /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet.o a - /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.o a - /build/reproducible-path/kmer-0~20150903+r2013/libbio/alphabet-colorspace.o a - /build/reproducible-path/kmer-0~20150903+r2013/libbio/halign.o a - /build/reproducible-path/kmer-0~20150903+r2013/libbio/reversecomplement.o a - /build/reproducible-path/kmer-0~20150903+r2013/libbio/kmer.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/file.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/file.c /build/reproducible-path/kmer-0~20150903+r2013/libutil/file.c: In function 'openFile': /build/reproducible-path/kmer-0~20150903+r2013/libutil/file.c:382:9: warning: variable 'isRW' set but not used [-Wunused-but-set-variable] 382 | int isRW = 1; | ^~~~ gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/md5.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/md5.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/palloc.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/palloc.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.c /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.c: In function 'qsort_algo': /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.c:264:13: warning: variable 'id' set but not used [-Wunused-but-set-variable] 264 | pthread_t id; | ^~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.c: In function 'qsort_thread': /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.c:370:13: warning: variable 'id' set but not used [-Wunused-but-set-variable] 370 | pthread_t id; | ^~ gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.C: In member function 'void bigQueue::mergeTemporaryFiles()': /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.C:204:16: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 204 | fread(thing, _objectSize, 1, _temporaryFiles[i]); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.C:255:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 255 | fread(thing, _objectSize, 1, _temporaryFiles[fileid]); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.C: In member function 'bool bigQueue::next()': /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.C:302:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 302 | fread(_thingBuffer, _objectSize, 1, _temporaryFiles[0]); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.C:8: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.C:35:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(stderr, "bitPackedArray::get()-- element index "uint64FMT" is out of range, only "uint64FMT" elements.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.C:35:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(stderr, "bitPackedArray::get()-- element index "uint64FMT" is out of range, only "uint64FMT" elements.\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C:168:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 168 | fprintf(stderr, " at position "uint64HEX"\n", file_offset); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C:367:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 367 | fprintf(stderr, "bitPackedFile::seekNormal() '%s' seek to pos="uint64FMT" failed: %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C:376:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 376 | fprintf(stderr, "bitPackedFile::seekNormal() '%s' read of "uint64FMT" bytes failed': %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C: In constructor 'bitPackedFile::bitPackedFile(const char*, uint64, bool)': /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C:109:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 109 | write(_file, t, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C:110:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 110 | write(_file, &at, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C:111:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | write(_file, &bt, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C: In member function 'void bitPackedFile::flushDirty()': /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.C:232:8: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 232 | write(_file, _bfr, sizeof(uint64) * _bfrmax); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/fibonacciNumbers.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.C:132:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "readBuffer::fillBuffer()-- only read "uint64FMT" bytes, couldn't read "uint64FMT" bytes from '%s': %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.C:132:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "readBuffer::fillBuffer()-- only read "uint64FMT" bytes, couldn't read "uint64FMT" bytes from '%s': %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.C:165:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stderr, "readBuffer()-- '%s' couldn't seek to position "int64FMT": %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.C:228:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(stderr, "readBuffer()-- couldn't read "uint64FMT" bytes from '%s': n%s\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:227:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 227 | fprintf(stderr, "recordFile::seek() '%s' seek to record="uint64FMT" at fileposition="uint64FMT" failed: %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:227:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 227 | fprintf(stderr, "recordFile::seek() '%s' seek to record="uint64FMT" at fileposition="uint64FMT" failed: %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:233:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 233 | fprintf(stderr, "recordFile::seek() '%s' read of "uint64FMT" bytes failed at record "uint64FMT", fileposition "uint64FMT"': %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:233:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 233 | fprintf(stderr, "recordFile::seek() '%s' read of "uint64FMT" bytes failed at record "uint64FMT", fileposition "uint64FMT"': %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:233:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 233 | fprintf(stderr, "recordFile::seek() '%s' read of "uint64FMT" bytes failed at record "uint64FMT", fileposition "uint64FMT"': %s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C: In constructor 'recordFile::recordFile(const char*, uint32, uint32, char)': /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:68:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 68 | write(_file, &recordFileMagic1, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:69:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | write(_file, &recordFileMagic2, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:70:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | write(_file, &_numRecords, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:71:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 71 | write(_file, &_recordSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:72:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | write(_file, &_headerSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:73:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | write(_file, _header, sizeof(char) * _headerSize); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:112:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 112 | read(_file, &m1, sizeof(uint64)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:113:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 113 | read(_file, &m2, sizeof(uint64)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:114:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 114 | read(_file, &_numRecords, sizeof(uint64)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:115:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | read(_file, &_recordSize, sizeof(uint32)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:116:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 116 | read(_file, &_headerSize, sizeof(uint32)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:117:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 117 | read(_file, _header, sizeof(char) * _headerSize); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C: In destructor 'recordFile::~recordFile()': /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:151:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 151 | write(_file, &recordFileMagic1, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:152:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | write(_file, &recordFileMagic2, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:153:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 153 | write(_file, &_numRecords, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:154:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 154 | write(_file, &_recordSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:155:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | write(_file, &_headerSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:156:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 156 | write(_file, _header, sizeof(char) * _headerSize); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C: In member function 'void recordFile::flushDirty()': /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:197:8: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 197 | write(_file, _bfr, _recordSize * _rec); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C: In member function 'void recordFile::seek(uint64, bool)': /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.C:231:7: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 231 | read(_file, _bfr, _recordSize * _bfrmax); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/speedCounter.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/speedCounter.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/speedCounter.C:4: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.H:7, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:127:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "sweatShop::setThreadData()-- worker ID "uint32FMT" more than number of workers="uint32FMT"\n", t, _numberOfWorkers), exit(1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:127:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "sweatShop::setThreadData()-- worker ID "uint32FMT" more than number of workers="uint32FMT"\n", t, _numberOfWorkers), exit(1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:390:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:390:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:390:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:390:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:390:135: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:425:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 425 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" queued for output)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:425:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 425 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" queued for output)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:425:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 425 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" queued for output)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:560:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 560 | fprintf(stderr, "sweatShop::run()-- Failed to launch worker thread "uint32FMT": %s.\n", i, strerror(err)), exit(1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.C:580:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 580 | fprintf(stderr, "sweatShop::run()-- Failed to join worker thread "uint32FMT": %s.\n", i, strerror(err)), exit(1); | ^ gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/dict.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/dict.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/except.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/except.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/hash.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/hash.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/list.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/list.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/sfx.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/sfx.c rm -f /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a && ar ruvs /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/file.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/md5.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/palloc.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/fibonacciNumbers.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/speedCounter.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/dict.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/except.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/hash.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/list.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/sfx.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/file.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/md5.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/palloc.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/qsort_mt.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/bigQueue.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/fibonacciNumbers.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/readBuffer.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/speedCounter.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/sweatShop.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/dict.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/except.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/hash.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/list.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/sfx.o g++ -Wl,-z,relro -Wl,-z,now -o ESTmapper/terminate ESTmapper/terminate.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFeature.o -c atac-driver/libatac/atacFeature.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFeature.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFeature.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.C:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "Feature longer than sequence (by "uint32FMT"bp): seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacFeature.C:109:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "Feature longer than sequence (by "uint32FMT"bp): seqLen="uint32FMTW(8)" %s\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFeatureList.o -c atac-driver/libatac/atacFeatureList.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFeatureList.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFeatureList.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFeatureList.C: In member function 'void atacFeatureList::add(atacFeature&)': atac-driver/libatac/atacFeatureList.C:50:52: warning: operation on '((atacFeatureList*)this)->atacFeatureList::_featuresLen' may be undefined [-Wsequence-point] 50 | _features[_featuresLen].featureiid = _featuresLen++; | ~~~~~~~~~~~~^~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFile.o -c atac-driver/libatac/atacFile.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFile.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFile.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFile.C: In member function 'void atacFileBase::readHeader(char*, FILE*)': atac-driver/libatac/atacFile.C:255:7: warning: the address of 'atacFileBase::_fileA' will never be NULL [-Waddress] 255 | if (_fileA && _fileA[0]) { | ^~~~~~ atac-driver/libatac/atac.H:59:22: note: 'atacFileBase::_fileA' declared here 59 | char _fileA[1024]; // The name of our genome files | ^~~~~~ atac-driver/libatac/atacFile.C:262:7: warning: the address of 'atacFileBase::_fileB' will never be NULL [-Waddress] 262 | if (_fileB && _fileB[0]) { | ^~~~~~ atac-driver/libatac/atac.H:60:22: note: 'atacFileBase::_fileB' declared here 60 | char _fileB[1024]; | ^~~~~~ atac-driver/libatac/atacFile.C: In member function 'atacMatch* atacFileStream::nextMatch(char)': atac-driver/libatac/atacFile.C:76:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fgets(_inLine, 1024, _inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C: In member function 'atacFeature* atacFileStream::nextFeature(char*)': atac-driver/libatac/atacFile.C:105:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 105 | fgets(_inLine, 1024, _inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C: In constructor 'atacFile::atacFile(const char*)': atac-driver/libatac/atacFile.C:171:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 171 | fgets(inLine, 1024, inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C: In member function 'void atacFileBase::readHeader(char*, FILE*)': atac-driver/libatac/atacFile.C:206:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 206 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C:245:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 245 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFileStreamMerge.o -c atac-driver/libatac/atacFileStreamMerge.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFileStreamMerge.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFileStreamMerge.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFileStreamMerge.C: In member function 'void atacFileStreamMerge::addFile(const char*)': atac-driver/libatac/atacFileStreamMerge.C:86:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class afsm'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 86 | memcpy(F, _files, sizeof(afsm) * _filesLen); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFileStreamMerge.C:27:7: note: 'class afsm' declared here 27 | class afsm { | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacMatch.o -c atac-driver/libatac/atacMatch.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atac.H:26, from atac-driver/libatac/atacMatch.C:19: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacMatch.C:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 1: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C:131:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 1: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C:139:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 2: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C:139:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 2: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C: In constructor 'atacMatch::atacMatch(char*, char*, uint32, char*, uint32, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': atac-driver/libatac/atacMatch.C:50:10: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 16 equals destination size [-Wstringop-truncation] 50 | strncpy(matchuid, muid, 16); | ^ atac-driver/libatac/atacMatch.C: In member function 'void atacMatch::decode(char*)': atac-driver/libatac/atacMatch.C:100:10: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 16 equals destination size [-Wstringop-truncation] 100 | strncpy(matchuid, S[2], 16); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacMatchList.o -c atac-driver/libatac/atacMatchList.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacMatchList.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacMatchList.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacMatchOrder.o -c atac-driver/libatac/atacMatchOrder.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacMatchOrder.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacMatchOrder.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacMatchOrder.C:38:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | sprintf(n.matchuid, "merge"uint32FMT, mergeuid); | ^ rm -f atac-driver/libatac/libatac.a && ar ruvs atac-driver/libatac/libatac.a atac-driver/libatac/atacFeature.o atac-driver/libatac/atacFeatureList.o atac-driver/libatac/atacFile.o atac-driver/libatac/atacFileStreamMerge.o atac-driver/libatac/atacMatch.o atac-driver/libatac/atacMatchList.o atac-driver/libatac/atacMatchOrder.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating atac-driver/libatac/libatac.a a - atac-driver/libatac/atacFeature.o a - atac-driver/libatac/atacFeatureList.o a - atac-driver/libatac/atacFile.o a - atac-driver/libatac/atacFileStreamMerge.o a - atac-driver/libatac/atacMatch.o a - atac-driver/libatac/atacMatchList.o a - atac-driver/libatac/atacMatchOrder.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap.o -c atac-driver/alignOverlap/overlap.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap.C:19: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ atac-driver/alignOverlap/overlap.C:123:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 123 | fprintf(stderr, "unmapped: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.unmapped.getSum(), statsB.unmapped.getSum()); | ^ atac-driver/alignOverlap/overlap.C:123:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 123 | fprintf(stderr, "unmapped: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.unmapped.getSum(), statsB.unmapped.getSum()); | ^ atac-driver/alignOverlap/overlap.C:124:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "unique mapping 1: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map1unique.getSum(), statsB.map1unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:124:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "unique mapping 1: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map1unique.getSum(), statsB.map1unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:125:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 125 | fprintf(stderr, "unique mapping 2: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map2unique.getSum(), statsB.map2unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:125:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 125 | fprintf(stderr, "unique mapping 2: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map2unique.getSum(), statsB.map2unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:126:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 126 | fprintf(stderr, "different: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.different.getSum(), statsB.different.getSum()); | ^ atac-driver/alignOverlap/overlap.C:126:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 126 | fprintf(stderr, "different: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.different.getSum(), statsB.different.getSum()); | ^ atac-driver/alignOverlap/overlap.C:127:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "wild diff: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.wilddiff.getSum(), statsB.wilddiff.getSum()); | ^ atac-driver/alignOverlap/overlap.C:127:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "wild diff: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.wilddiff.getSum(), statsB.wilddiff.getSum()); | ^ atac-driver/alignOverlap/overlap.C:128:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "same: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.same.getSum(), statsB.same.getSum()); | ^ atac-driver/alignOverlap/overlap.C:128:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "same: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.same.getSum(), statsB.same.getSum()); | ^ atac-driver/alignOverlap/overlap.C:129:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "inconsistent: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.inconsistent.getSum(), statsB.inconsistent.getSum()); | ^ atac-driver/alignOverlap/overlap.C:129:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "inconsistent: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.inconsistent.getSum(), statsB.inconsistent.getSum()); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-find.o -c atac-driver/alignOverlap/overlap-find.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-find.C:19: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ atac-driver/alignOverlap/overlap-find.C:45:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 45 | fprintf(stderr, "isolated Unique: map1: "uint32FMT" map2: "uint32FMT"\n", sumA, sumB); | ^ atac-driver/alignOverlap/overlap-find.C:45:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 45 | fprintf(stderr, "isolated Unique: map1: "uint32FMT" map2: "uint32FMT"\n", sumA, sumB); | ^ atac-driver/alignOverlap/overlap-find.C:59:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(stderr, "got invalid type; "uint32FMT" -- %c\n", type, (char)type), exit(1); | ^ atac-driver/alignOverlap/overlap-find.C:91:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "%s: "uint32FMT" len:"uint32FMT"\n", msg, count, len); | ^ atac-driver/alignOverlap/overlap-find.C:91:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "%s: "uint32FMT" len:"uint32FMT"\n", msg, count, len); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-matchTree.o -c atac-driver/alignOverlap/overlap-matchTree.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-matchTree.C:19: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-printAnno.o -c atac-driver/alignOverlap/overlap-printAnno.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-printAnno.C:19: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:14: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:63:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 63 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:63:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 63 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:63:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 63 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:65:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid1, m1->pos1 + off1, m1->pos1 + off1 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:65:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid1, m1->pos1 + off1, m1->pos1 + off1 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:65:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid1, m1->pos1 + off1, m1->pos1 + off1 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:69:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:69:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:69:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:85:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 85 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:85:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 85 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:85:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 85 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:87:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid1, m2->pos1 + off2, m2->pos1 + off2 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:87:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid1, m2->pos1 + off2, m2->pos1 + off2 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:87:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid1, m2->pos1 + off2, m2->pos1 + off2 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:91:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:91:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:91:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C: In function 'void printAnno(FILE*, annoList*, uint32&, char, uint32, span_t*, uint32, atacMatch*, uint32, atacMatch*)': /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:64:26: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 60 | #define uint32ZERO uint32NUMBER(0x00000000) | ~ | | | long unsigned int ...... 64 | #define uint32FMTW(X) "%" #X PRIu32 atac-driver/alignOverlap/overlap-printAnno.C:68:16: note: in expansion of macro 'uint32FMTW' 68 | fprintf(F, uint32FMTW(07)" ", uint32ZERO); | ^~~~~~~~~~ atac-driver/alignOverlap/overlap-printAnno.C:69:16: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/alignOverlap/overlap-printAnno.C:69:16: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/alignOverlap/overlap-printAnno.C:69:16: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:64:26: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 60 | #define uint32ZERO uint32NUMBER(0x00000000) | ~ | | | long unsigned int ...... 64 | #define uint32FMTW(X) "%" #X PRIu32 atac-driver/alignOverlap/overlap-printAnno.C:90:16: note: in expansion of macro 'uint32FMTW' 90 | fprintf(F, uint32FMTW(07)" ", uint32ZERO); | ^~~~~~~~~~ atac-driver/alignOverlap/overlap-printAnno.C:91:16: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/alignOverlap/overlap-printAnno.C:91:16: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/alignOverlap/overlap-printAnno.C:91:16: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-sort.o -c atac-driver/alignOverlap/overlap-sort.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-sort.C:19: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ ln -f /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process.C /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process1.C g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -DINDEX=1 -DNAME=process1 -DPOS1=pos1 -DPOS2=pos2 -DLEN2=len2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-process1.o -c atac-driver/alignOverlap/overlap-process1.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-process1.C:19: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ ln -f /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process.C /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process2.C g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -DINDEX=2 -DNAME=process2 -DPOS1=pos2 -DPOS2=pos1 -DLEN2=len1 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-process2.o -c atac-driver/alignOverlap/overlap-process2.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-process2.C:19: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/alignOverlap/overlap atac-driver/alignOverlap/overlap.o atac-driver/alignOverlap/overlap-find.o atac-driver/alignOverlap/overlap-matchTree.o atac-driver/alignOverlap/overlap-printAnno.o atac-driver/alignOverlap/overlap-sort.o atac-driver/alignOverlap/overlap-process1.o atac-driver/alignOverlap/overlap-process2.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/gapShifter.o -c atac-driver/gapShifter/gapShifter.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/gapShifter/gapShifter.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:203:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:203:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:223:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 223 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:223:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 223 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:510:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:515:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:523:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:528:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:738:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 738 | fprintf(stderr, "Shifting gaps of length at most "uint32FMT" bases, to the %s.\n", gapLimit, (shiftRight) ? "right" : "left"); | ^ atac-driver/gapShifter/gapShifter.C:750:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 750 | fprintf(stderr, "numShifted = "uint32FMT"\n", numShifted); | ^ atac-driver/gapShifter/gapShifter.C:751:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 751 | fprintf(stderr, "numNotShifted = "uint32FMT"\n", numNotShifted); | ^ atac-driver/gapShifter/gapShifter.C:752:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 752 | fprintf(stderr, "numDiffSeq = "uint32FMT"\n", numDiffSeq); | ^ atac-driver/gapShifter/gapShifter.C:753:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 753 | fprintf(stderr, "numDiffOri = "uint32FMT"\n", numDiffOri); | ^ atac-driver/gapShifter/gapShifter.C:754:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 754 | fprintf(stderr, "numZeroLen = "uint32FMT"\n", numZeroLen); | ^ atac-driver/gapShifter/gapShifter.C:755:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 755 | fprintf(stderr, "numOutOfOrder = "uint32FMT"\n", numOutOfOrder); | ^ atac-driver/gapShifter/gapShifter.C:756:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 756 | fprintf(stderr, "numNotAdjacent = "uint32FMT"\n", numNotAdjacent); | ^ atac-driver/gapShifter/gapShifter.C:757:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 757 | fprintf(stderr, "numNoGap = "uint32FMT"\n", numNoGap); | ^ atac-driver/gapShifter/gapShifter.C:758:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 758 | fprintf(stderr, "numGapTooBig = "uint32FMT"\n", numGapTooBig); | ^ atac-driver/gapShifter/gapShifter.C:759:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 759 | fprintf(stderr, "numOverlapping = "uint32FMT"\n", numOverlapping); | ^ atac-driver/gapShifter/gapShifter.C:762:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "amountShifted["uint32FMT"] = "uint32FMT" (number of gaps shifted by [number of bases])\n", x, amountShifted[x]); | ^ atac-driver/gapShifter/gapShifter.C:762:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "amountShifted["uint32FMT"] = "uint32FMT" (number of gaps shifted by [number of bases])\n", x, amountShifted[x]); | ^ atac-driver/gapShifter/gapShifter.C:764:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 764 | fprintf(stderr, "shifted "uint32FMT" out of "uint32FMT" (%6.2f%%)\n", gapsShifted, ML.numMatches(), (double)gapsShifted / (double)ML.numMatches() * 100.0); | ^ atac-driver/gapShifter/gapShifter.C:764:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 764 | fprintf(stderr, "shifted "uint32FMT" out of "uint32FMT" (%6.2f%%)\n", gapsShifted, ML.numMatches(), (double)gapsShifted / (double)ML.numMatches() * 100.0); | ^ atac-driver/gapShifter/gapShifter.C:780:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/gapShifter atac-driver/gapShifter/gapShifter.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/extractSequence.o -c atac-driver/gapShifter/extractSequence.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/gapShifter/extractSequence.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/extractSequence.C:110:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(Aoutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:110:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(Aoutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:110:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(Aoutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:121:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(Boutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:121:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(Boutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:121:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(Boutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/extractSequence atac-driver/gapShifter/extractSequence.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/extractUnmapped.o -c atac-driver/gapShifter/extractUnmapped.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/extractUnmapped.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/extractUnmapped.C:24: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/extractUnmapped.C:105:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 105 | fprintf(output, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" between match %s(%s) and %s(%s)\n", | ^ atac-driver/gapShifter/extractUnmapped.C:105:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 105 | fprintf(output, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" between match %s(%s) and %s(%s)\n", | ^ atac-driver/gapShifter/extractUnmapped.C:105:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 105 | fprintf(output, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" between match %s(%s) and %s(%s)\n", | ^ atac-driver/gapShifter/extractUnmapped.C:583:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 583 | fprintf(stderr, "Done masking. "uint32FMT" in A, "uint32FMT" in B.\n", stats[0], stats[1]); | ^ atac-driver/gapShifter/extractUnmapped.C:583:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 583 | fprintf(stderr, "Done masking. "uint32FMT" in A, "uint32FMT" in B.\n", stats[0], stats[1]); | ^ atac-driver/gapShifter/extractUnmapped.C: In function 'int main(int, char**)': atac-driver/gapShifter/extractUnmapped.C:541:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fgets(L, 1024, F); | ~~~~~^~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/extractUnmapped atac-driver/gapShifter/extractUnmapped.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/coalesceMatches.o -c atac-driver/gapShifter/coalesceMatches.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/coalesceMatches.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/coalesceMatches.C:24: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/coalesceMatches atac-driver/gapShifter/coalesceMatches.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/correctGaps.o -c atac-driver/gapShifter/correctGaps.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/correctGaps.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/correctGaps.C:24: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/correctGaps.C:138:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 138 | fprintf(logFile, "HEY! F gap of size "uint32FMT" not in a run?\n", gap1); | ^ atac-driver/gapShifter/correctGaps.C:200:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(logFile, "HEY! R gap of size "uint32FMT" not in a run?\n", gap1); | ^ atac-driver/gapShifter/correctGaps.C:222:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(logFile, "CLOSE "uint32FMT"----------------------------------------\n", gap1); | ^ atac-driver/gapShifter/correctGaps.C:235:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 235 | fprintf(logFile, "At gapSize="uint32FMT" closed "uint32FMT" f-gaps and "uint32FMT" r-gaps.\n", gapsize, fgaps, rgaps); | ^ atac-driver/gapShifter/correctGaps.C:235:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 235 | fprintf(logFile, "At gapSize="uint32FMT" closed "uint32FMT" f-gaps and "uint32FMT" r-gaps.\n", gapsize, fgaps, rgaps); | ^ atac-driver/gapShifter/correctGaps.C:235:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 235 | fprintf(logFile, "At gapSize="uint32FMT" closed "uint32FMT" f-gaps and "uint32FMT" r-gaps.\n", gapsize, fgaps, rgaps); | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/correctGaps atac-driver/gapShifter/correctGaps.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/testAtac.o -c atac-driver/gapShifter/testAtac.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/testAtac.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/testAtac.C:24: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/testAtac.C:89:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "match "uint32FMT" is only %6.2f%% identity: ", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/testAtac atac-driver/gapShifter/testAtac.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/cleanAtac.o -c atac-driver/gapShifter/cleanAtac.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/cleanAtac.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/cleanAtac.C:24: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/cleanAtac.C:149:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 149 | fprintf(stderr, "match "uint32FMT" is only %6.2f%% identity and "uint32FMT" long: ", | ^ atac-driver/gapShifter/cleanAtac.C:149:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 149 | fprintf(stderr, "match "uint32FMT" is only %6.2f%% identity and "uint32FMT" long: ", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/cleanAtac atac-driver/gapShifter/cleanAtac.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/projectFeatures.o -c atac-driver/gapShifter/projectFeatures.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/projectFeatures.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/projectFeatures.C:24: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/projectFeatures.C:72:2: warning: #warning BROKEN [-Wcpp] 72 | #warning BROKEN | ^~~~~~~ atac-driver/gapShifter/projectFeatures.C:132:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/projectFeatures atac-driver/gapShifter/projectFeatures.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/lengthFilter/lengthFilter.o -c atac-driver/lengthFilter/lengthFilter.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from atac-driver/lengthFilter/lengthFilter.C:24: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ atac-driver/lengthFilter/lengthFilter.C:46:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | sprintf(inLine, "/globalMatchMinSize="uint32FMT"\n", minLength); | ^ atac-driver/lengthFilter/lengthFilter.C:57:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 57 | fprintf(stdout, "/globalMatchMinSize="uint32FMT"\n", minLength); | ^ atac-driver/lengthFilter/lengthFilter.C:114:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stderr, "lengthFilter: Discarded "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C:114:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stderr, "lengthFilter: Discarded "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C:116:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "lengthFilter: Saved "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C:116:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "lengthFilter: Saved "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C: In function 'void readHeader(char*, FILE*, uint32&, FILE*)': atac-driver/lengthFilter/lengthFilter.C:34:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ atac-driver/lengthFilter/lengthFilter.C:53:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 53 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ atac-driver/lengthFilter/lengthFilter.C: In function 'int main(int, char**)': atac-driver/lengthFilter/lengthFilter.C:111:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | fgets(inLine, 1024, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/lengthFilter/lengthFilter atac-driver/lengthFilter/lengthFilter.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/matchExtender/matchExtender.o -c atac-driver/matchExtender/matchExtender.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/matchExtender/matchExtender.C:27: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/matchExtender/matchExtender.C:192:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/matchExtender/matchExtender-dump.o -c atac-driver/matchExtender/matchExtender-dump.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/matchExtender/matchExtender-dump.C:25: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/matchExtender/match.H:8, from atac-driver/matchExtender/matchExtender-dump.C:26: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/matchExtender/matchExtender-func.o -c atac-driver/matchExtender/matchExtender-func.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/matchExtender/matchExtender-func.C:26: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/matchExtender/matchExtender-func.C:27: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/matchExtender/matchExtender atac-driver/matchExtender/matchExtender.o atac-driver/matchExtender/matchExtender-dump.o atac-driver/matchExtender/matchExtender-func.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/mismatchCounter/mismatchCounter.o -c atac-driver/mismatchCounter/mismatchCounter.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/mismatchCounter/mismatchCounter.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/mismatchCounter/mismatchCounter.C:25: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/mismatchCounter/mismatchCounter.C:197:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stderr, "globalSequence = "uint32FMT"\n", globalSequence); | ^ atac-driver/mismatchCounter/mismatchCounter.C:198:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 198 | fprintf(stderr, "globalMismatches = "uint32FMT"\n", globalMismatches); | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/mismatchCounter/mismatchCounter atac-driver/mismatchCounter/mismatchCounter.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/statsGenerator/statsGenerator.o -c atac-driver/statsGenerator/statsGenerator.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/statsGenerator/statsGenerator.C:26: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/statsGenerator/statsGenerator.C:91:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stdout, "histogram %s "uint32FMT" items %8.3f average %8.3f std.dev.\n", | ^ atac-driver/statsGenerator/statsGenerator.C:102:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 102 | fprintf(out, uint64FMT" "uint32FMT"\n", i * _b, _h[i]); | ^ atac-driver/statsGenerator/statsGenerator.C:103:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 103 | fprintf(out, ">"uint64FMT" "uint32FMT"\n", _m, _l); | ^ atac-driver/statsGenerator/statsGenerator.C:103:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 103 | fprintf(out, ">"uint64FMT" "uint32FMT"\n", _m, _l); | ^ atac-driver/statsGenerator/statsGenerator.C:133:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 133 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:133:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 133 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:136:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:136:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:172:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # all letters, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:172:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # all letters, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:193:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C:193:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C:282:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 282 | fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)ifa.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:283:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 283 | fprintf(stdout, "totalLength "uint64FMT" # sum of lengths of all features\n", ifa.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:285:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions\n", (uint64)ifa.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:286:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, including N\n", ifa.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:287:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 287 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, ACGT only\n", tandemRepeatACGTLength(ifa, offset1, A)); | ^ atac-driver/statsGenerator/statsGenerator.C:289:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 289 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions, only in matches\n", (uint64)mma.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:290:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 290 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, including N\n", mma.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:291:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 291 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, ACGT only\n", tandemRepeatACGTLength(mma, offset1, A)); | ^ atac-driver/statsGenerator/statsGenerator.C:295:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)ifb.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:296:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | fprintf(stdout, "totalLength "uint64FMT" # sum of lengths of all features\n", ifb.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:298:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 298 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions\n", (uint64)ifb.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:299:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 299 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, including N\n", ifb.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:300:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 300 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, ACGT only\n", tandemRepeatACGTLength(ifb, offset2, B)); | ^ atac-driver/statsGenerator/statsGenerator.C:302:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 302 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions, only in matches\n", (uint64)mmb.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:303:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 303 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, including N\n", mmb.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:304:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 304 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, ACGT only\n", tandemRepeatACGTLength(mmb, offset2, B)); | ^ atac-driver/statsGenerator/statsGenerator.C:335:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 335 | fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)matches.numberOfMatches()); | ^ atac-driver/statsGenerator/statsGenerator.C:337:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 337 | fprintf(stdout, "matchLength %s "uint64FMT" %s "uint64FMT" # Sum of lengths of sequence in matches\n", | ^ atac-driver/statsGenerator/statsGenerator.C:337:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 337 | fprintf(stdout, "matchLength %s "uint64FMT" %s "uint64FMT" # Sum of lengths of sequence in matches\n", | ^ atac-driver/statsGenerator/statsGenerator.C:349:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 349 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:349:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 349 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:353:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 353 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, ACGT only (new)\n", | ^ atac-driver/statsGenerator/statsGenerator.C:353:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 353 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, ACGT only (new)\n", | ^ atac-driver/statsGenerator/statsGenerator.C:409:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 409 | fprintf(out, uint64FMT" "uint32FMT"\n", n, n50[iter-1]); | ^ atac-driver/statsGenerator/statsGenerator.C:507:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:82: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:516:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 516 | sprintf(label, "chr"uint32FMTW(02)"full", c); | ^ atac-driver/statsGenerator/statsGenerator.C:520:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | sprintf(label, "chr"uint32FMTW(02)"acgt", c); | ^ atac-driver/statsGenerator/statsGenerator.C:628:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 628 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:628:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 628 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:631:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 631 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C:631:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 631 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C: In function 'void tandemRepeatStats(atacFileStream&, atacFileStream&, atacFile&, seqCache*, seqCache*)': atac-driver/statsGenerator/statsGenerator.C:267:37: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 267 | while ((f = featuresA.nextFeature("tr")) != 0L) | ^~~~ atac-driver/statsGenerator/statsGenerator.C:269:37: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 269 | while ((f = featuresB.nextFeature("tr")) != 0L) | ^~~~ atac-driver/statsGenerator/statsGenerator.C: In function 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)': atac-driver/statsGenerator/statsGenerator.C:99:29: warning: '.histogramdat' directive writing 13 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 99 | sprintf(filename, "%s.%s.histogramdat", prefix, label); | ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from atac-driver/statsGenerator/statsGenerator.C:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'void histogram::dump(const char*, const char*)' at atac-driver/statsGenerator/statsGenerator.C:99:12, inlined from 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)' at atac-driver/statsGenerator/statsGenerator.C:517:23: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 15 or more bytes (assuming 1038) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)': atac-driver/statsGenerator/statsGenerator.C:127:29: warning: '.histogram.gnuplot' directive writing 18 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 127 | sprintf(filename, "%s.%s.histogram.gnuplot", prefix, label); | ^~~~~~~~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void histogram::plot(const char*, const char*)' at atac-driver/statsGenerator/statsGenerator.C:127:12, inlined from 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)' at atac-driver/statsGenerator/statsGenerator.C:518:23: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 20 or more bytes (assuming 1043) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)': atac-driver/statsGenerator/statsGenerator.C:140:37: warning: '%s' directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] 140 | sprintf(filename, "gnuplot < %s.%s.histogram.gnuplot", prefix, label); | ^~ ...... 518 | hist1full[c]->plot(prefix, label); | ~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void histogram::plot(const char*, const char*)' at atac-driver/statsGenerator/statsGenerator.C:140:12, inlined from 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)' at atac-driver/statsGenerator/statsGenerator.C:518:23: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 1053) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)': atac-driver/statsGenerator/statsGenerator.C:99:29: warning: '.histogramdat' directive writing 13 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 99 | sprintf(filename, "%s.%s.histogramdat", prefix, label); | ^~~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void histogram::dump(const char*, const char*)' at atac-driver/statsGenerator/statsGenerator.C:99:12, inlined from 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)' at atac-driver/statsGenerator/statsGenerator.C:521:23: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 15 or more bytes (assuming 1038) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)': atac-driver/statsGenerator/statsGenerator.C:127:29: warning: '.histogram.gnuplot' directive writing 18 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 127 | sprintf(filename, "%s.%s.histogram.gnuplot", prefix, label); | ^~~~~~~~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void histogram::plot(const char*, const char*)' at atac-driver/statsGenerator/statsGenerator.C:127:12, inlined from 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)' at atac-driver/statsGenerator/statsGenerator.C:522:23: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 20 or more bytes (assuming 1043) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)': atac-driver/statsGenerator/statsGenerator.C:140:37: warning: '%s' directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] 140 | sprintf(filename, "gnuplot < %s.%s.histogram.gnuplot", prefix, label); | ^~ ...... 522 | hist1acgt[c]->plot(prefix, label); | ~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void histogram::plot(const char*, const char*)' at atac-driver/statsGenerator/statsGenerator.C:140:12, inlined from 'void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)' at atac-driver/statsGenerator/statsGenerator.C:522:23: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 1053) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/statsGenerator/statsGenerator atac-driver/statsGenerator/statsGenerator.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/uniqueFilter/uniqueFilter.o -c atac-driver/uniqueFilter/uniqueFilter.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from atac-driver/uniqueFilter/uniqueFilter.C:23: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/uniqueFilter/uniqueFilter.C:24: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:226:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 226 | fprintf(stderr, "Sorting error -- have negative coverage (axis="uint32FMT" position="uint32FMT")!\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:226:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 226 | fprintf(stderr, "Sorting error -- have negative coverage (axis="uint32FMT" position="uint32FMT")!\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:236:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "offsetsToCoverage()-- Found "uint64FMT" bases at coverage "uint32FMT" or greater.\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:236:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "offsetsToCoverage()-- Found "uint64FMT" bases at coverage "uint32FMT" or greater.\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:370:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | fprintf(stderr, "Got fwd intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:370:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | fprintf(stderr, "Got fwd intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:374:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 374 | fprintf(stdout, "--key1 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:374:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 374 | fprintf(stdout, "--key1 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:379:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 379 | fprintf(stderr, "Got rev intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:379:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 379 | fprintf(stderr, "Got rev intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:383:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 383 | fprintf(stdout, "--key2 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:383:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 383 | fprintf(stdout, "--key2 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:418:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 418 | #define D08D2 uint32FMTW(8)" "uint32FMTW(8) | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:818:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 818 | fprintf(stderr, "match "uint32FMT" is outside the extent!\n", i); | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/uniqueFilter/uniqueFilter atac-driver/uniqueFilter/uniqueFilter.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/clumpMaker/clumpMaker.o -c atac-driver/clumpMaker/clumpMaker.C In file included from atac-driver/clumpMaker/clumpMaker.C:4: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15, from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/clumpMaker/clumpMaker.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/clumpMaker/clumpMaker.C:341:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 341 | sprintf(C.matchuid, "clump"int32FMTW(06), cc); | ^ atac-driver/clumpMaker/clumpMaker.C:377:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 377 | sprintf(hits[mm].match.parentuid, "clump"int32FMTW(06), cc); | ^ atac-driver/clumpMaker/clumpMaker.C: In function 'int main(int, char**)': atac-driver/clumpMaker/clumpMaker.C:220:12: warning: variable 'isSorted' set but not used [-Wunused-but-set-variable] 220 | bool isSorted = false; | ^~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/clumpMaker/clumpMaker atac-driver/clumpMaker/clumpMaker.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_dpaligner.o -c atac-driver/chainer/localalign/GF_ALN_dpaligner.C g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_local.o -c atac-driver/chainer/localalign/GF_ALN_local.C atac-driver/chainer/localalign/GF_ALN_local.C: In function 'void Align_Recursion(const char*, int, const char*, int, const Trapezoid*, int, int, int, double, int)': atac-driver/chainer/localalign/GF_ALN_local.C:872:15: warning: variable 'indel' set but not used [-Wunused-but-set-variable] 872 | int j, mid, indel; | ^~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_overlap.o -c atac-driver/chainer/localalign/GF_ALN_overlap.C atac-driver/chainer/localalign/GF_ALN_overlap.C: In function 'void AVLinit()': atac-driver/chainer/localalign/GF_ALN_overlap.C:93:17: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 93 | OutOfMemory("Candidate list"); | ^~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C: In function 'AVLnode* NEW(AVLnode*, Candidate*, AVLnode*)': atac-driver/chainer/localalign/GF_ALN_overlap.C:125:21: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 125 | OutOfMemory("Candidate list"); | ^~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C: In function 'Local_Overlap* Find_Local_Overlap(int, int, int, int, Local_Segment*, int, int, double)': atac-driver/chainer/localalign/GF_ALN_overlap.C:396:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 396 | OutOfMemory("Overlap Trace Array"); | ^~~~~~~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C:662:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 662 | OutOfMemory("Overlap descriptor"); | ^~~~~~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C:614:20: warning: variable 'beg' set but not used [-Wunused-but-set-variable] 614 | int best, end, beg; | ^~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_loverlapper.o -c atac-driver/chainer/localalign/GF_ALN_loverlapper.C g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_pieceOlap.o -c atac-driver/chainer/localalign/GF_ALN_pieceOlap.C g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -I/usr/include/python3.12 -o atac-driver/chainer/localalign/localAlignerInterfacemodule.o -c atac-driver/chainer/localalign/localAlignerInterfacemodule.C atac-driver/chainer/localalign/localAlignerInterfacemodule.C: In function 'PyObject* spam_syntenicSegments(PyObject*, PyObject*)': atac-driver/chainer/localalign/localAlignerInterfacemodule.C:176:18: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 176 | char *Aseq = "undefined"; | ^~~~~~~~~~~ atac-driver/chainer/localalign/localAlignerInterfacemodule.C:179:18: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 179 | char *Bseq = "undefined"; | ^~~~~~~~~~~ rm -f atac-driver/chainer/localAlignerInterfacemodule.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o atac-driver/chainer/localAlignerInterfacemodule.so atac-driver/chainer/localalign/GF_ALN_dpaligner.o atac-driver/chainer/localalign/GF_ALN_local.o atac-driver/chainer/localalign/GF_ALN_overlap.o atac-driver/chainer/localalign/GF_ALN_loverlapper.o atac-driver/chainer/localalign/GF_ALN_pieceOlap.o atac-driver/chainer/localalign/localAlignerInterfacemodule.o -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/halign/halign.o -c atac-driver/chainer/halign/halign.C atac-driver/chainer/halign/halign.C: In function 'int diff(const char*, const char*, int, int, int*, int*, int*, int*, int, int, int, int, int, int, int, int, int, EditScript**, EditScript**)': atac-driver/chainer/halign/halign.C:295:9: warning: variable 'cost1' set but not used [-Wunused-but-set-variable] 295 | int cost1, cost2; | ^~~~~ atac-driver/chainer/halign/halign.C:295:16: warning: variable 'cost2' set but not used [-Wunused-but-set-variable] 295 | int cost1, cost2; | ^~~~~ atac-driver/chainer/halign/halign.C:345:9: warning: variable 'cost1' set but not used [-Wunused-but-set-variable] 345 | int cost1, cost2; | ^~~~~ atac-driver/chainer/halign/halign.C:345:16: warning: variable 'cost2' set but not used [-Wunused-but-set-variable] 345 | int cost1, cost2; | ^~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -I/usr/include/python3.12 -o atac-driver/chainer/halign/halignmodule.o -c atac-driver/chainer/halign/halignmodule.C rm -f atac-driver/chainer/halignmodule.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o atac-driver/chainer/halignmodule.so atac-driver/chainer/halign/halign.o atac-driver/chainer/halign/halignmodule.o -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chimera/happy-clones-span-clumps.o -c atac-driver/chimera/happy-clones-span-clumps.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from atac-driver/chimera/happy-clones-span-clumps.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ atac-driver/chimera/happy-clones-span-clumps.C:202:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "ERROR: increase scaffoldsMax "uint32FMT"\n", scaffoldid); | ^ atac-driver/chimera/happy-clones-span-clumps.C:229:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(stderr, "Deleted "uint32FMT" scaffolds with less than 2 clumps.\n", deleted); | ^ atac-driver/chimera/happy-clones-span-clumps.C:230:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 230 | fprintf(stderr, "Remain "uint32FMT" scaffolds with more than 2 clumps.\n", remain); | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:255:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and clump "uint32FMT" OVERLAP\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:255:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and clump "uint32FMT" OVERLAP\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:255:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and clump "uint32FMT" OVERLAP\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:85: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:449:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 449 | fprintf(stdout, "%s spans clump in scaffold %s,"uint32FMT"\n", ina, A[7], scfa); | ^ atac-driver/chimera/happy-clones-span-clumps.C:453:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 453 | fprintf(stdout, "%s spans clump in scaffold %s,"uint32FMT" \n", inb, B[7], scfb); | ^ atac-driver/chimera/happy-clones-span-clumps.C:464:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 464 | fprintf(stdout, "scaffold %s,"uint32FMT" clump "uint32FMT" "uint32FMT" confirmed by %s\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:464:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 464 | fprintf(stdout, "scaffold %s,"uint32FMT" clump "uint32FMT" "uint32FMT" confirmed by %s\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:464:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 464 | fprintf(stdout, "scaffold %s,"uint32FMT" clump "uint32FMT" "uint32FMT" confirmed by %s\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C: In function 'int main(int, char**)': atac-driver/chimera/happy-clones-span-clumps.C:393:24: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 393 | char *uidmapName = "/project/huref6/assembly/fasta/HUREF6A.info"; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C: In function 'atacClumpCoordTree* buildCoordTree(char*)': atac-driver/chimera/happy-clones-span-clumps.C:313:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 313 | fgets(inl, 1024, inf); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:340:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 340 | fgets(inl, 1024, inf); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C: In function 'int main(int, char**)': atac-driver/chimera/happy-clones-span-clumps.C:402:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 402 | fgets(L, 1024, F); | ~~~~~^~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:409:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 409 | fgets(L, 1024, F); | ~~~~~^~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:426:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 426 | fgets(ina, 1024, inf); chomp(ina); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:427:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 427 | fgets(inb, 1024, inf); chomp(inb); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:473:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 473 | fgets(ina, 1024, inf); chomp(ina); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:474:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 474 | fgets(inb, 1024, inf); chomp(inb); | ~~~~~^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:62, from atac-driver/chimera/happy-clones-span-clumps.C:5: /usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Alloc_node; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/14/bits/stl_tree.h:2267:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2267 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, const value_type&) [with _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(iterator, const value_type&) [with _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_map.h:913:38, inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_map.h:517:16, inlined from 'int main(int, char**)' at atac-driver/chimera/happy-clones-span-clumps.C:407:42: /usr/include/c++/14/bits/stl_tree.h:1143:33: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 1143 | return _M_insert_unique_(__pos, __x, __an); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, const value_type&) [with _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(iterator, const value_type&) [with _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_map.h:913:38, inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_map.h:517:16, inlined from 'int main(int, char**)' at atac-driver/chimera/happy-clones-span-clumps.C:438:50: /usr/include/c++/14/bits/stl_tree.h:1143:33: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 1143 | return _M_insert_unique_(__pos, __x, __an); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, const value_type&) [with _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(iterator, const value_type&) [with _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_map.h:913:38, inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_map.h:517:16, inlined from 'int main(int, char**)' at atac-driver/chimera/happy-clones-span-clumps.C:439:50: /usr/include/c++/14/bits/stl_tree.h:1143:33: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 1143 | return _M_insert_unique_(__pos, __x, __an); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/chimera/happy-clones-span-clumps atac-driver/chimera/happy-clones-span-clumps.o /build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/seatac.o -c seatac/seatac.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/seatac.C:4: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/seatac.C:201:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:201:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:201:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:201:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:239:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "\n"uint32FMTW(7)" sequences (%5.1f%%; %8.3f/sec) %5.2f seconds.\n", | ^ seatac/filterObj.H: In member function 'void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': seatac/filterObj.H:146:21: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seatac/hitMatrix.H:82:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/configuration.o -c seatac/configuration.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/configuration.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/configuration.C:259:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 259 | fprintf(out, "/seatacNumSearchThreads="uint32FMT"\n", _numSearchThreads); | ^ seatac/configuration.C:260:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 260 | fprintf(out, "/seatacLoaderHighWaterMark="uint32FMT"\n", _loaderHighWaterMark); | ^ seatac/configuration.C:264:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 264 | fprintf(out, "/seatacWriterHighWaterMark="uint32FMT"\n", _writerHighWaterMark); | ^ seatac/configuration.C:267:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 267 | fprintf(out, "/seatacMaxDiagonal="uint32FMT"\n", _maxDiagonal); | ^ seatac/configuration.C:268:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 268 | fprintf(out, "/seatacMaxGap="uint32FMT"\n", _maxGap); | ^ seatac/configuration.C:269:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(out, "/seatacQsOverlap="uint32FMT"\n", _qsOverlap); | ^ seatac/configuration.C:270:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 270 | fprintf(out, "/seatacDsOverlap="uint32FMT"\n", _dsOverlap); | ^ seatac/configuration.C:271:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 271 | fprintf(out, "/seatacMinLength="uint32FMT"\n", _minLength + _merSize); | ^ seatac/configuration.C:272:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 272 | fprintf(out, "/seatacMerSize="uint32FMT"\n", _merSize); | ^ seatac/configuration.C:273:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 273 | fprintf(out, "/seatacMerSkip="uint32FMT"\n", _merSkip); | ^ seatac/filterObj.H: In member function 'void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': seatac/filterObj.H:146:21: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seatac/hitMatrix.H:82:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/encodedQuery.o -c seatac/encodedQuery.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/encodedQuery.C:3: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function 'void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': seatac/filterObj.H:146:21: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seatac/hitMatrix.H:82:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/hitMatrix.o -c seatac/hitMatrix.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/hitMatrix.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function 'void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': seatac/filterObj.H:146:21: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seatac/hitMatrix.H:82:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/thr-search.o -c seatac/thr-search.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/thr-search.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/thr-search.C:3:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 3 | char const *srchGbye = "[%ld] computed: "uint64FMTW(8)" blocked: "uint64FMTW(4)"/"uint64FMTW(4)" encodeTime: %7.2f searchTime: %7.2f processTime: %7.2f\n"; | ^ seatac/thr-search.C:3:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 3 | char const *srchGbye = "[%ld] computed: "uint64FMTW(8)" blocked: "uint64FMTW(4)"/"uint64FMTW(4)" encodeTime: %7.2f searchTime: %7.2f processTime: %7.2f\n"; | ^ seatac/thr-search.C:3:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 3 | char const *srchGbye = "[%ld] computed: "uint64FMTW(8)" blocked: "uint64FMTW(4)"/"uint64FMTW(4)" encodeTime: %7.2f searchTime: %7.2f processTime: %7.2f\n"; | ^ seatac/thr-search.C:130:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, uint64FMT" Blocked by output (idx = "uint32FMT", outputPos = "uint32FMT").\n", (long)U, idx, outputPos); | ^ seatac/thr-search.C:130:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, uint64FMT" Blocked by output (idx = "uint32FMT", outputPos = "uint32FMT").\n", (long)U, idx, outputPos); | ^ seatac/filterObj.H: In member function 'void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': seatac/filterObj.H:146:21: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seatac/hitMatrix.H:82:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/thr-search.C: In function 'void* searchThread(void*)': /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long int' [-Wformat=] 55 | #define uint64FMT "%"PRIu64 seatac/thr-search.C:130:29: note: in expansion of macro 'uint64FMT' 130 | fprintf(stderr, uint64FMT" Blocked by output (idx = "uint32FMT", outputPos = "uint32FMT").\n", (long)U, idx, outputPos); | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/thr-loader.o -c seatac/thr-loader.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/thr-loader.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function 'void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': seatac/filterObj.H:146:21: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seatac/hitMatrix.H:82:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/thr-loader.C: In function 'void* loaderThread(void*)': seatac/thr-loader.C:68:21: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 68 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/thr-deadlock.o -c seatac/thr-deadlock.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/thr-deadlock.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function 'void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': seatac/filterObj.H:146:21: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seatac/hitMatrix.H:82:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/hitMatrix-sort.o -c seatac/hitMatrix-sort.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/hitMatrix.H:8, from seatac/hitMatrix-sort.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/hitMatrix.H:9: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function 'void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': seatac/filterObj.H:146:21: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seatac/hitMatrix.H:82:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:136:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "existDB::createFromFastA()-- hashTable is "uint64FMT"MB\n", _hashTableWords >> 17); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:137:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | fprintf(stderr, "existDB::createFromFastA()-- buckets is "uint64FMT"MB\n", _bucketsWords >> 17); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:139:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "existDB::createFromFastA()-- counts is "uint64FMT"MB\n", _countsWords >> 17); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:239:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:239:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:239:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:27:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 27 | fprintf(stderr, "createFromMeryl()-- ERROR: requested merSize ("uint32FMT") is different than merSize in meryl database ("uint32FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:27:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 27 | fprintf(stderr, "createFromMeryl()-- ERROR: requested merSize ("uint32FMT") is different than merSize in meryl database ("uint32FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:54:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stderr, "createFromMeryl()-- tableSizeInEntries "uint64FMT"\n", tableSizeInEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:55:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "createFromMeryl()-- count range "uint32FMT"-"uint32FMT"\n", lo, hi); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:55:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "createFromMeryl()-- count range "uint32FMT"-"uint32FMT"\n", lo, hi); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:104:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 104 | fprintf(stderr, "createFromMeryl()-- numberOfMers "uint64FMT"\n", numberOfMers); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:116:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "existDB::createFromMeryl()-- Found "uint64FMT" mers between count of "uint32FMT" and "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:116:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "existDB::createFromMeryl()-- Found "uint64FMT" mers between count of "uint32FMT" and "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:116:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "existDB::createFromMeryl()-- Found "uint64FMT" mers between count of "uint32FMT" and "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:135:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 135 | fprintf(stderr, "existDB::createFromMeryl()-- hashTable is "uint64FMT"MB\n", _hashTableWords >> 17); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:136:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "existDB::createFromMeryl()-- buckets is "uint64FMT"MB\n", _bucketsWords >> 17); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:138:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 138 | fprintf(stderr, "existDB::createFromMeryl()-- counts is "uint64FMT"MB\n", _countsWords >> 17); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:136:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "existDB::createFromSequence()-- hashTable is "uint64FMT"MB\n", _hashTableWords >> 17); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:137:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | fprintf(stderr, "existDB::createFromSequence()-- buckets is "uint64FMT"MB\n", _bucketsWords >> 17); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:139:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "existDB::createFromSequence()-- counts is "uint64FMT"MB\n", _countsWords >> 17); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:239:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:239:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:239:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:169:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(stream, "merSizeInBases: "uint32FMT"\n", _merSizeInBases); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:170:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 170 | fprintf(stream, "tableBits "uint32FMT"\n", 2 * _merSizeInBases - _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:172:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stream, "_hashTableWords "uint64FMT" ("uint64FMT" KB)\n", _hashTableWords, _hashTableWords >> 7); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:172:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stream, "_hashTableWords "uint64FMT" ("uint64FMT" KB)\n", _hashTableWords, _hashTableWords >> 7); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:173:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 173 | fprintf(stream, "_bucketsWords "uint64FMT" ("uint64FMT" KB)\n", _bucketsWords, _bucketsWords >> 7); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:173:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 173 | fprintf(stream, "_bucketsWords "uint64FMT" ("uint64FMT" KB)\n", _bucketsWords, _bucketsWords >> 7); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:174:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(stream, "_countsWords "uint64FMT" ("uint64FMT" KB)\n", _countsWords, _countsWords >> 7); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:174:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(stream, "_countsWords "uint64FMT" ("uint64FMT" KB)\n", _countsWords, _countsWords >> 7); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:176:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stream, "_shift1: "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:177:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 177 | fprintf(stream, "_shift2 "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:178:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stream, "_mask1 "uint64HEX"\n", _mask1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:179:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 179 | fprintf(stream, "_mask2 "uint64HEX"\n", _mask2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:183:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 183 | fprintf(stream, "_hshWidth "uint32FMT"\n", _hshWidth); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:191:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stream, "_chkWidth "uint32FMT"\n", _chkWidth); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:199:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 199 | fprintf(stream, "_cntWidth "uint32FMT"\n", _cntWidth); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C: In member function 'bool existDB::loadState(const char*, bool, bool)': /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:80:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | fread(cigam, sizeof(char), 16, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:124:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 124 | fread(&_merSizeInBases, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:125:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fread(&_shift1, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:126:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 126 | fread(&_shift2, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:127:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | fread(&_mask1, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:128:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 128 | fread(&_mask2, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:129:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | fread(&_hshWidth, sizeof(uint32), 1, F); // only valid if _compressedHash | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:130:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | fread(&_chkWidth, sizeof(uint32), 1, F); // only valid if _compressedBucket | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:131:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | fread(&_cntWidth, sizeof(uint32), 1, F); // only valid if _compressedCounts | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:133:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 133 | fread(&_hashTableWords, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:134:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 134 | fread(&_bucketsWords, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:135:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 135 | fread(&_countsWords, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:148:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 148 | fread(_hashTable, sizeof(uint64), _hashTableWords, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:149:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 149 | fread(_buckets, sizeof(uint64), _bucketsWords, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:152:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | fread(_counts, sizeof(uint64), _countsWords, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C: In member function 'void existDB::saveState(const char*)': /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.C:24:10: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] 24 | strncpy(cigam, magic, 16); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.C:44:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 44 | fprintf(stderr, "existDB::existDB()-- Got "uint32FMT", expected "uint32FMT"\n", _merSizeInBases, merSize); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.C:44:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 44 | fprintf(stderr, "existDB::existDB()-- Got "uint32FMT", expected "uint32FMT"\n", _merSizeInBases, merSize); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:2: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:22:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 22 | fprintf(stderr, "positionDB::get()-- Can't allocate space for more positions, requested "uint64FMT" uint64's.\n", posnMax); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:215:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 215 | fprintf(stderr, "positionDB::filter()-- Filtering out kmers less than "uint64FMT" and more than "uint64FMT"\n", lo, hi); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:215:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 215 | fprintf(stderr, "positionDB::filter()-- Filtering out kmers less than "uint64FMT" and more than "uint64FMT"\n", lo, hi); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:339:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers less than "uint64FMT"\n", loCount, lo); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:339:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers less than "uint64FMT"\n", loCount, lo); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:340:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers more than "uint64FMT"\n", hiCount, hi); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:340:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers more than "uint64FMT"\n", hiCount, hi); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:341:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 341 | fprintf(stderr, "positionDB::filter()-- Saved "uint64FMT" kmers with acceptable count\n", okCount); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C: In member function 'void positionDB::filter(uint64, uint64)': /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.C:204:11: warning: unused variable 'vv' [-Wunused-variable] 204 | uint64 vv; | ^~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:4: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:25:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(F, "B "uint64FMT" "uint64FMT"-"uint64FMT"\n", h, st, ed); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:25:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(F, "B "uint64FMT" "uint64FMT"-"uint64FMT"\n", h, st, ed); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:25:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(F, "B "uint64FMT" "uint64FMT"-"uint64FMT"\n", h, st, ed); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:32:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(F, "%c chk="uint64HEX" pos="uint64FMT" siz="uint64FMT, | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:32:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(F, "%c chk="uint64HEX" pos="uint64FMT" siz="uint64FMT, | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:32:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(F, "%c chk="uint64HEX" pos="uint64FMT" siz="uint64FMT, | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:40:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(F, " "uint64FMT, getDecodedValue(_positions, pos, _posnWidth)); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:197:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stream, "merSizeInBases: "uint32FMT"\n", _merSizeInBases); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:198:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 198 | fprintf(stream, "merSkipInBases: "uint32FMT"\n", _merSkipInBases); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:199:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 199 | fprintf(stream, "tableSizeInBits: "uint32FMT"\n", _tableSizeInBits); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:200:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stream, "tableSizeInEntries: "uint64FMT"\n", _tableSizeInEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:201:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stream, "hashWidth: "uint32FMT"\n", _hashWidth); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:202:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stream, "chckWidth: "uint32FMT"\n", _chckWidth); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:203:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stream, "posnWidth: "uint32FMT"\n", _posnWidth); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:204:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stream, "numberOfMers: "uint64FMT"\n", _numberOfMers); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:205:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 205 | fprintf(stream, "numberOfPositions: "uint64FMT"\n", _numberOfPositions); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:206:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 206 | fprintf(stream, "numberOfDistinct: "uint64FMT"\n", _numberOfDistinct); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:207:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 207 | fprintf(stream, "numberOfUnique: "uint64FMT"\n", _numberOfUnique); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:208:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 208 | fprintf(stream, "numberOfEntries: "uint64FMT"\n", _numberOfEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:209:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 209 | fprintf(stream, "maximumEntries: "uint64FMT"\n", _maximumEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C: In member function 'void positionDB::saveState(const char*)': /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:37:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | write(F, magic, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:39:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | write(F, faild, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.C:95:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | write(F, magic, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C:324:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 324 | fprintf(stderr, "positionDB::getUpToNMismatches()-- Can't allocate space for initial positions, requested "uint64FMT" uint64's.\n", posnMax); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:37:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, "ERROR: Bucket "uint64FMT" starts at "uint64FMT" ends at "uint64FMT"?\n", b, st, ed); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:37:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, "ERROR: Bucket "uint64FMT" starts at "uint64FMT" ends at "uint64FMT"?\n", b, st, ed); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:37:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, "ERROR: Bucket "uint64FMT" starts at "uint64FMT" ends at "uint64FMT"?\n", b, st, ed); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:78:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 78 | fprintf(stdout, "ERROR: unset posn bucket="uint64FMT" t="int64FMT" le="uint32FMT"\n", b, t, le); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:78:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 78 | fprintf(stdout, "ERROR: unset posn bucket="uint64FMT" t="int64FMT" le="uint32FMT"\n", b, t, le); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:78:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 78 | fprintf(stdout, "ERROR: unset posn bucket="uint64FMT" t="int64FMT" le="uint32FMT"\n", b, t, le); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:86:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 86 | fprintf(stdout, uint32FMTW(4)"] chck="uint64HEX" posn="uint64FMT"\n", t, _sortedChck[t], _sortedPosn[t]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:86:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 86 | fprintf(stdout, uint32FMTW(4)"] chck="uint64HEX" posn="uint64FMT"\n", t, _sortedChck[t], _sortedPosn[t]); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:77: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:46:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer size is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:46:107: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer size is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:52:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 52 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer skip is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:52:107: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 52 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer skip is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:58:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but max number of mismatches is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:58:123: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but max number of mismatches is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:127:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, " sm = "uint64FMT"\n", sm); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:128:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, " lg = "uint64FMT"\n", lg); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:129:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, " merSize = "uint32FMT" bits\n", 2 * merSize); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:130:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, " approxMers = "uint64FMT" mers\n", approxMers); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:131:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, " posnWidth = "uint64FMT" bits\n", posnWidth); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:142:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "potential configurations for approximately "uint64FMT" "uint32FMT"-mers (posnW="uint64FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:142:77: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "potential configurations for approximately "uint64FMT" "uint32FMT"-mers (posnW="uint64FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:142:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "potential configurations for approximately "uint64FMT" "uint32FMT"-mers (posnW="uint64FMT").\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:200:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stderr, "tblBits="uint64FMTW(2)" shifts="uint32FMTW(02)","uint32FMTW(02)" -- size %8.3fGB -- work %8.3f%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:200:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stderr, "tblBits="uint64FMTW(2)" shifts="uint32FMTW(02)","uint32FMTW(02)" -- size %8.3fGB -- work %8.3f%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:200:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stderr, "tblBits="uint64FMTW(2)" shifts="uint32FMTW(02)","uint32FMTW(02)" -- size %8.3fGB -- work %8.3f%s\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:217:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:217:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:217:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:217:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:217:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:217:122: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:326:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 326 | fprintf(stderr, "positionDB()-- bktAlloc = new uint64 ["uint64FMT"]\n", _tableSizeInEntries / 2 + 4); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:348:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 348 | fprintf(stderr, " Allocated bucket size counting space with total size "uint64FMT" KB\n", _tableSizeInEntries >> 8); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:392:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 392 | fprintf(stderr, " Found "uint64FMT" mers (max position = "uint64FMT")\n", _numberOfMers, _numberOfPositions); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:392:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 392 | fprintf(stderr, " Found "uint64FMT" mers (max position = "uint64FMT")\n", _numberOfMers, _numberOfPositions); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:430:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 430 | fprintf(stderr, " Allocated "uint64FMT"KB for buckets ("uint64FMT" 64-bit words)\n", bucketsSpace >> 7, bucketsSpace); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:430:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 430 | fprintf(stderr, " Allocated "uint64FMT"KB for buckets ("uint64FMT" 64-bit words)\n", bucketsSpace >> 7, bucketsSpace); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:435:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 435 | fprintf(stderr, "positionDB()-- _countingBuckets = new uint64 ["uint64FMT"]\n", bucketsSpace); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:553:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 553 | fprintf(stderr, " Sorting and repacking buckets ("uint64FMT" buckets).\n", _tableSizeInEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:565:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 565 | " Found "uint64FMTW(12)" total mers\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:566:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 566 | " Found "uint64FMTW(12)" distinct mers\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:567:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 567 | " Found "uint64FMTW(12)" unique mers\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:568:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 568 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:568:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 568 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:637:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 637 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for hash table ("uint64FMT" 64-bit words)\n", hs >> 7, hs); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:637:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 637 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for hash table ("uint64FMT" 64-bit words)\n", hs >> 7, hs); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:643:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 643 | fprintf(stderr, "positionDB()-- _hashTable_BP = new uint64 ["uint64FMT"]\n", hs); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:662:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 662 | fprintf(stderr, " Reusing bucket space; Have: "uint64FMT" Need: "uint64FMT" (64-bit words)\n", bucketsSpace, bs); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:662:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 662 | fprintf(stderr, " Reusing bucket space; Have: "uint64FMT" Need: "uint64FMT" (64-bit words)\n", bucketsSpace, bs); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:669:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 669 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for buckets ("uint64FMT" 64-bit words)\n", bs >> 7, bs); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:669:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 669 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for buckets ("uint64FMT" 64-bit words)\n", bs >> 7, bs); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:674:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 674 | fprintf(stderr, "positionDB()-- _buckets = new uint64 ["uint64FMT"]\n", bs); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:680:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 680 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for positions ("uint64FMT" 64-bit words)\n", ps >> 7, ps); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:680:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 680 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for positions ("uint64FMT" 64-bit words)\n", ps >> 7, ps); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:685:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 685 | fprintf(stderr, "positionDB()-- _positions = new uint64 ["uint64FMT"\n", ps); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:695:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 695 | fprintf(stderr, " Transferring to final structure ("uint64FMT" buckets).\n", _tableSizeInEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:878:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 878 | fprintf(stderr, "positionDB()-- ERROR: Got position "uint64FMT", but only "uint64FMT" available!\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:878:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 878 | fprintf(stderr, "positionDB()-- ERROR: Got position "uint64FMT", but only "uint64FMT" available!\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:916:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 916 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", bs, ps); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:916:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 916 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", bs, ps); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:917:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 917 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:917:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 917 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:918:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 918 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", currentBbit / 64, currentPbit / 64); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:918:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 918 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", currentBbit / 64, currentPbit / 64); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:928:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 928 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:928:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 928 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:930:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 930 | " Found "uint64FMTW(12)" total mers\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:931:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 931 | " Found "uint64FMTW(12)" distinct mers\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:932:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 932 | " Found "uint64FMTW(12)" unique mers\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:933:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 933 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:933:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 933 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:955:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 955 | fprintf(stderr, " Rebuilding the hash table, from "uint32FMT" bits wide to "uint32FMT" bits wide.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:955:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 955 | fprintf(stderr, " Rebuilding the hash table, from "uint32FMT" bits wide to "uint32FMT" bits wide.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:990:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 990 | fprintf(stderr, " Loading "uint64FMT" mercounts.\n", counts->numberOfDistinctMers()); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:1013:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1013 | fprintf(stderr, " Loaded "uint64FMT" mercounts; largest is "uint64FMT".\n", countsLoaded, largestMerylCount); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:1013:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1013 | fprintf(stderr, " Loaded "uint64FMT" mercounts; largest is "uint64FMT".\n", countsLoaded, largestMerylCount); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:1017:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1017 | fprintf(stderr, " Compress sizes from "uint32FMT" bits to "uint32FMT" bits.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:1017:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1017 | fprintf(stderr, " Compress sizes from "uint32FMT" bits to "uint32FMT" bits.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C: In member function 'void positionDB::build(merStream*, existDB*, existDB*, merylStreamReader*, uint32, uint32, bool)': /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:324:17: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 324 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:433:17: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 433 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:641:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 641 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:672:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 672 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.C:683:17: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 683 | } catch (std::bad_alloc) { | ^~~~~~~~~ rm -f /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a && ar ruvs /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB-state.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-access.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-dump.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-file.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB-sort.o a - /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.o -c /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:72:2: warning: #warning not checking pmagic [-Wcpp] 72 | #warning not checking pmagic | ^~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:134:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 134 | fprintf(stderr, "merylStreamReader()-- ERROR: User requested mersize "uint32FMT" but '%s' is mersize "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:134:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 134 | fprintf(stderr, "merylStreamReader()-- ERROR: User requested mersize "uint32FMT" but '%s' is mersize "uint32FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:6:24: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 6 | static char *ImagicV = "merylStreamIv03\n"; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:7:24: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 7 | static char *ImagicX = "merylStreamIvXX\n"; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:8:24: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 8 | static char *DmagicV = "merylStreamDv03\n"; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:9:24: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 9 | static char *DmagicX = "merylStreamDvXX\n"; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:10:24: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 10 | static char *PmagicV = "merylStreamPv03\n"; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:11:24: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 11 | static char *PmagicX = "merylStreamPvXX\n"; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C: In constructor 'merylStreamReader::merylStreamReader(const char*, uint32)': /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:42:11: warning: variable 'Pmagic' set but not used [-Wunused-but-set-variable] 42 | char Pmagic[16] = {0}; | ^~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C: In member function 'void merylStreamWriter::addMer(uint64, uint32, uint64, uint32, uint32, uint32*)': /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.C:469:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 469 | (prefix <= _thisMerPre) && (mer < _thisMerMer)) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ rm -f /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a && ar ruvs /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a a - /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.o g++ -Wl,-z,relro -Wl,-z,now -o seatac/seatac seatac/seatac.o seatac/configuration.o seatac/encodedQuery.o seatac/hitMatrix.o seatac/thr-search.o seatac/thr-loader.o seatac/thr-deadlock.o seatac/hitMatrix-sort.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/heavychains-driver.o -c seatac/heavychains-driver.C In file included from seatac/heavychains.H:11, from seatac/heavychains-driver.C:24: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ seatac/heavychains.H: In member function 'double DPTree::matchScore(kd_node, Match&)': seatac/heavychains.H:374:19: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 374 | if ( (flo.X() && node[flo.intv].lo <= p.xlo || | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/heavychains.o -c seatac/heavychains.C In file included from seatac/heavychains.H:11, from seatac/heavychains.C:22: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ seatac/heavychains.C:96:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr,"HeavyChains: filtering strands "uint32FMT" "uint32FMT" "uint32FMT"\n", iid1, iid2, Plen); | ^ seatac/heavychains.C:96:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr,"HeavyChains: filtering strands "uint32FMT" "uint32FMT" "uint32FMT"\n", iid1, iid2, Plen); | ^ seatac/heavychains.C:96:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr,"HeavyChains: filtering strands "uint32FMT" "uint32FMT" "uint32FMT"\n", iid1, iid2, Plen); | ^ seatac/heavychains.C:164:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 164 | fprintf(stderr, "heavychains: out "uint32FMTW(8)" %8d %8d -- "uint32FMTW(8)" %8d %8d\n", | ^ seatac/heavychains.C:164:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 164 | fprintf(stderr, "heavychains: out "uint32FMTW(8)" %8d %8d -- "uint32FMTW(8)" %8d %8d\n", | ^ seatac/heavychains.C:169:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(outF, "M x H"uint64FMT" . %s:"uint32FMT" %d %d %d %s:"uint32FMT" %d %d %d > /hf=%.1f /hr=%.1f\n", | ^ seatac/heavychains.C:169:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(outF, "M x H"uint64FMT" . %s:"uint32FMT" %d %d %d %s:"uint32FMT" %d %d %d > /hf=%.1f /hr=%.1f\n", | ^ seatac/heavychains.C:169:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(outF, "M x H"uint64FMT" . %s:"uint32FMT" %d %d %d %s:"uint32FMT" %d %d %d > /hf=%.1f /hr=%.1f\n", | ^ seatac/heavychains.C:186:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 186 | fprintf(stderr, "HeavyChains: finished strands "uint32FMTW(8)" "uint32FMTW(8)" maxlen1=%f maxlen2=%f maxScoreFwd=%f maxScoreRef=%f\n", | ^ seatac/heavychains.C:186:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 186 | fprintf(stderr, "HeavyChains: finished strands "uint32FMTW(8)" "uint32FMTW(8)" maxlen1=%f maxlen2=%f maxScoreFwd=%f maxScoreRef=%f\n", | ^ seatac/heavychains.H: In member function 'double DPTree::matchScore(kd_node, Match&)': seatac/heavychains.H:374:19: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 374 | if ( (flo.X() && node[flo.intv].lo <= p.xlo || | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seatac/heavychains seatac/heavychains-driver.o seatac/heavychains.o -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/filter-nop.o -c seatac/filter-nop.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seatac/filter-nop.C:9: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seatac/filter-nop.C:10: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seatac/filter-nop.C:67:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C: In function 'void* construct(char*)': seatac/filter-nop.C:116:16: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 116 | char *seq1 = "UNK"; | ^~~~~ seatac/filter-nop.C:117:16: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 117 | char *seq2 = "UNK"; | ^~~~~ rm -f seatac/filter-nop.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o seatac/filter-nop.so seatac/filter-nop.o -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/filter-heavychains.o -c seatac/filter-heavychains.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from seatac/filter-heavychains.C:24: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/filter-heavychains.C:25: seatac/heavychains.H: In member function 'double DPTree::matchScore(kd_node, Match&)': seatac/heavychains.H:374:19: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 374 | if ( (flo.X() && node[flo.intv].lo <= p.xlo || | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seatac/heavychains.H: In function 'void addHit(void*, char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)': seatac/heavychains.H:53:12: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 53 | strncpy(assemblyId1, assemblyid1, 31); | ^ seatac/heavychains.H:54:12: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 54 | strncpy(assemblyId2, assemblyid2, 31); | ^ seatac/heavychains.H:53:12: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 53 | strncpy(assemblyId1, assemblyid1, 31); | ^ seatac/heavychains.H:54:12: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 54 | strncpy(assemblyId2, assemblyid2, 31); | ^ seatac/heavychains.H:53:12: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 53 | strncpy(assemblyId1, assemblyid1, 31); | ^ seatac/heavychains.H:54:12: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 54 | strncpy(assemblyId2, assemblyid2, 31); | ^ rm -f seatac/filter-heavychains.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o seatac/filter-heavychains.so seatac/filter-heavychains.o seatac/heavychains.o -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/leaff.o -c leaff/leaff.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/leaff.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/leaff.C:311:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 311 | fprintf(stderr, "WARNING: Didn't find sequence with iid '"uint32FMT"'\n", sid); | ^ leaff/leaff.C:400:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 400 | fprintf(stdout, "G\tseq\t%s:"uint32FMT"\t"uint32FMT"\t%s\n", | ^ leaff/leaff.C:400:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 400 | fprintf(stdout, "G\tseq\t%s:"uint32FMT"\t"uint32FMT"\t%s\n", | ^ leaff/leaff.C:469:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 469 | sprintf(def, "random"uint32FMTW(06), i); | ^ leaff/leaff.C:727:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 727 | fprintf(stderr, "Couldn't read "uint64FMT" bytes from '%s': %s\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/blocks.o -c leaff/blocks.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/blocks.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/blocks.C:32:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:32:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:32:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:32:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:42:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^ leaff/blocks.C:42:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^ leaff/blocks.C:42:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^ leaff/blocks.C: In function 'void dumpBlocks(char*)': leaff/blocks.C:42:21: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ leaff/blocks.C:7:16: warning: unused variable 'S' [-Wunused-variable] 7 | seqInCore *S = 0L; | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/dups.o -c leaff/dups.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/dups.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/dups.C:26:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stdout, uint32FMT" <-> "uint32FMT"\n", sa->getIID(), sb->getIID()); | ^ leaff/dups.C:28:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 28 | fprintf(stderr, "COLLISION DETECTED BETWEEN %s:"uint32FMT" AND %s:"uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ leaff/dups.C:28:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 28 | fprintf(stderr, "COLLISION DETECTED BETWEEN %s:"uint32FMT" AND %s:"uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ leaff/dups.C:52:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 52 | fprintf(stderr, "Internal error: found two copies of the same sequence iid ("uint32FMT")!\n", result[idx].i); | ^ leaff/dups.C:60:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stdout, uint32FMT":%s\n"uint32FMT":%s\n\n", | ^ leaff/dups.C:64:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(stderr, "COLLISION DETECTED BETWEEN IID "uint32FMT" AND "uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ leaff/dups.C:64:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(stderr, "COLLISION DETECTED BETWEEN IID "uint32FMT" AND "uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/gc.o -c leaff/gc.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/gc.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/gc.C:68:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/partition.o -c leaff/partition.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/partition.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/partition.C:55:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "ERROR: Failed to partition "uint32FMT"\n", i); | ^ leaff/partition.C:62:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | sprintf(filename, "%s-"uint32FMTW(03)".fasta", prefix, o); | ^ leaff/partition.C:77:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 77 | fprintf(stderr, "Huh? '%s' "uint32FMT" != "uint32FMT"\n", S->header(), S->sequenceLength(), p[i].length); | ^ leaff/partition.C:77:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 77 | fprintf(stderr, "Huh? '%s' "uint32FMT" != "uint32FMT"\n", S->header(), S->sequenceLength(), p[i].length); | ^ leaff/partition.C:96:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stdout, uint32FMT"]("uint32FMT")", o, sizeP); | ^ leaff/partition.C:99:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 99 | fprintf(stdout, " "uint32FMT"("uint32FMT")", p[i].index, p[i].length); | ^ leaff/partition.C:99:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 99 | fprintf(stdout, " "uint32FMT"("uint32FMT")", p[i].index, p[i].length); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/simseq.o -c leaff/simseq.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from leaff/simseq.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/stats.o -c leaff/stats.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/stats.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/stats.C:110:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "numSeqs "uint32FMT"\n", numSeq); | ^ leaff/stats.C:112:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 112 | fprintf(stdout, "SPAN (smallest "uint32FMT" largest "uint32FMT")\n", Ls[numSeq-1], Ls[0]); | ^ leaff/stats.C:112:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 112 | fprintf(stdout, "SPAN (smallest "uint32FMT" largest "uint32FMT")\n", Ls[numSeq-1], Ls[0]); | ^ leaff/stats.C:114:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50s[i], l50s[i]); | ^ leaff/stats.C:114:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50s[i], l50s[i]); | ^ leaff/stats.C:114:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50s[i], l50s[i]); | ^ leaff/stats.C:115:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(stdout, "totLen "uint64FMTW(10)"\n", Ss); | ^ leaff/stats.C:116:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stdout, "refLen "uint64FMTW(10)"\n", Rs); | ^ leaff/stats.C:118:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 118 | fprintf(stdout, "BASES (smallest "uint32FMT" largest "uint32FMT")\n", Lb[numSeq-1], Lb[0]); | ^ leaff/stats.C:118:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 118 | fprintf(stdout, "BASES (smallest "uint32FMT" largest "uint32FMT")\n", Lb[numSeq-1], Lb[0]); | ^ leaff/stats.C:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50b[i], l50b[i]); | ^ leaff/stats.C:120:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50b[i], l50b[i]); | ^ leaff/stats.C:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50b[i], l50b[i]); | ^ leaff/stats.C:121:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(stdout, "totLen "uint64FMTW(10)"\n", Sb); | ^ leaff/stats.C:122:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 122 | fprintf(stdout, "refLen "uint64FMTW(10)"\n", Rb); | ^ g++ -Wl,-z,relro -Wl,-z,now -o leaff/leaff leaff/leaff.o leaff/blocks.o leaff/dups.o leaff/gc.o leaff/partition.o leaff/simseq.o leaff/stats.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/meryl.o -c meryl/meryl.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/args.o -c meryl/args.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/args.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/args.C:26:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "writeString()-- Failed to write string of length "uint32FMT": %s\n", len, strerror(errno)); | ^ meryl/args.C: In function 'char* readString(FILE*)': meryl/args.C:40:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 40 | fread(&len, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/args.C:50:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 50 | fread(str, sizeof(char), len, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/args.C: In constructor 'merylArgs::merylArgs(const char*)': meryl/args.C:513:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 513 | fread(magic, sizeof(char), 16, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/args.C:521:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 521 | fread(this, sizeof(merylArgs), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/binaryOp.o -c meryl/binaryOp.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/binaryOp.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/binaryOp.C:43:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stderr, "ERROR - mersize of '%s' is "uint32FMT"\n", args->mergeFiles[0], A->merSize()); | ^ meryl/binaryOp.C:44:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 44 | fprintf(stderr, "ERROR - mersize of '%s' is "uint32FMT"\n", args->mergeFiles[1], B->merSize()); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build.o -c meryl/build.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/build.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/build.C:153:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | sprintf(cmd, "qsub -t 1-"uint64FMT" -cwd -b n -j y -o %s-count-\\$TASK_ID.err %s -N mc%s %s-count.sh", | ^ meryl/build.C:156:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 156 | sprintf(cmd, "qsub -t 1-"uint64FMT" -cwd -b n -j y -o %s-count-\\$TASK_ID.err -N mc%s %s-count.sh", | ^ meryl/build.C:238:2: warning: #warning not submitting prepareBatch to grid [-Wcpp] 238 | #warning not submitting prepareBatch to grid | ^~~~~~~ meryl/build.C:293:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 293 | fprintf(stderr, " numMersActual = "uint64FMT"\n", args->numMersActual); | ^ meryl/build.C:294:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 294 | fprintf(stderr, " mersPerBatch = "uint64FMT"\n", args->mersPerBatch); | ^ meryl/build.C:295:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stderr, " basesPerBatch = "uint64FMT"\n", args->basesPerBatch); | ^ meryl/build.C:296:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:296:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:297:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 297 | fprintf(stderr, " bucketPointerWidth = "uint32FMT"\n", args->bucketPointerWidth); | ^ meryl/build.C:298:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 298 | fprintf(stderr, " merDataWidth = "uint32FMT"\n", args->merDataWidth); | ^ meryl/build.C:305:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:305:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:305:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:305:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:314:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 314 | fprintf(stderr, " numMersActual = "uint64FMT"\n", args->numMersActual); | ^ meryl/build.C:315:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 315 | fprintf(stderr, " mersPerBatch = "uint64FMT"\n", args->mersPerBatch); | ^ meryl/build.C:316:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 316 | fprintf(stderr, " basesPerBatch = "uint64FMT"\n", args->basesPerBatch); | ^ meryl/build.C:317:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 317 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:317:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 317 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:318:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 318 | fprintf(stderr, " bucketPointerWidth = "uint32FMT"\n", args->bucketPointerWidth); | ^ meryl/build.C:319:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 319 | fprintf(stderr, " merDataWidth = "uint32FMT"\n", args->merDataWidth); | ^ meryl/build.C:342:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 342 | sprintf(filename, "%s.batch"uint64FMT".mcdat", args->outputFile, segment); | ^ meryl/build.C:346:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | fprintf(stderr, "Found result for batch "uint64FMT" in %s.\n", segment, filename); | ^ meryl/build.C:352:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 352 | fprintf(stderr, "Computing segment "uint64FMT" of "uint64FMT".\n", segment+1, args->segmentLimit); | ^ meryl/build.C:352:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 352 | fprintf(stderr, "Computing segment "uint64FMT" of "uint64FMT".\n", segment+1, args->segmentLimit); | ^ meryl/build.C:365:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, " Allocating "uint64FMT"MB for mer storage ("uint32FMT" bits wide).\n", | ^ meryl/build.C:365:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, " Allocating "uint64FMT"MB for mer storage ("uint32FMT" bits wide).\n", | ^ meryl/build.C:384:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 384 | fprintf(stderr, " Allocating "uint64FMT"MB for mer position storage.\n", | ^ meryl/build.C:390:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " Allocating "uint64FMT"MB for bucket pointer table ("uint32FMT" bits wide).\n", | ^ meryl/build.C:390:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " Allocating "uint64FMT"MB for bucket pointer table ("uint32FMT" bits wide).\n", | ^ meryl/build.C:396:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 396 | fprintf(stderr, " Allocating "uint64FMT"MB for counting the size of each bucket.\n", args->numBuckets >> 18); | ^ meryl/build.C:477:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 477 | fprintf(stderr, " Releasing "uint64FMT"MB from counting the size of each bucket.\n", args->numBuckets >> 18); | ^ meryl/build.C:532:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 532 | sprintf(batchOutputFile, "%s.batch"uint64FMT, args->outputFile, segment); | ^ meryl/build.C:552:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 552 | fprintf(stderr, "ERROR: In segment "uint64FMT"\n", segment); | ^ meryl/build.C:553:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 553 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") ends before it starts!\n", | ^ meryl/build.C:553:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 553 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") ends before it starts!\n", | ^ meryl/build.C:555:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 555 | fprintf(stderr, "ERROR: start="uint64FMT"\n", st); | ^ meryl/build.C:556:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 556 | fprintf(stderr, "ERROR: end ="uint64FMT"\n", ed); | ^ meryl/build.C:561:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 561 | fprintf(stderr, "ERROR: In segment "uint64FMT"\n", segment); | ^ meryl/build.C:562:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 562 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") is HUGE!\n", | ^ meryl/build.C:562:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 562 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") is HUGE!\n", | ^ meryl/build.C:564:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 564 | fprintf(stderr, "ERROR: start="uint64FMT"\n", st); | ^ meryl/build.C:565:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 565 | fprintf(stderr, "ERROR: end ="uint64FMT"\n", ed); | ^ meryl/build.C:667:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 667 | fprintf(stderr, "Segment "uint64FMT" finished.\n", segment); | ^ meryl/build.C:705:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 705 | fprintf(stdout, "%s -countbatch "uint64FMT" -o %s\n", args->execName, s, args->outputFile); | ^ meryl/build.C:783:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 783 | sprintf(argv[argc], "%s.batch"uint32FMT, args->outputFile, i); | ^ meryl/build.C:807:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 807 | sprintf(filename, "%s.batch"uint32FMT".mcidx", args->outputFile, i); | ^ meryl/build.C:809:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 809 | sprintf(filename, "%s.batch"uint32FMT".mcdat", args->outputFile, i); | ^ meryl/build.C:811:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 811 | sprintf(filename, "%s.batch"uint32FMT".mcpos", args->outputFile, i); | ^ meryl/build.C: In function 'void prepareBatch(merylArgs*)': meryl/build.C:310:23: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 311 | estimateMemory(args->merSize, args->mersPerBatch, args->positionsEnabled) * args->numThreads, 312 | estimateMemory(args->merSize, args->numMersActual, args->positionsEnabled)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/build.C:310:23: warning: format '%llu' expects a matching 'long long unsigned int' argument [-Wformat=] meryl/build.C:310:23: warning: format '%llu' expects a matching 'long long unsigned int' argument [-Wformat=] meryl/build.C: In function 'void runSegment(merylArgs*, uint64)': meryl/build.C:412:8: warning: unused variable 'mstring' [-Wunused-variable] 412 | char mstring[256]; | ^~~~~~~ meryl/build.C: In function 'void build(merylArgs*)': meryl/build.C:769:41: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 769 | arga[argc] = false; argv[argc++] = "meryl-build-merge"; | ^~~~~~~~~~~~~~~~~~~ meryl/build.C:770:41: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 770 | arga[argc] = false; argv[argc++] = "-M"; | ^~~~ meryl/build.C:771:41: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 771 | arga[argc] = false; argv[argc++] = "merge"; | ^~~~~~~ meryl/build.C:775:22: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 775 | argv[argc++] = "-v"; | ^~~~ meryl/build.C:780:22: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 780 | argv[argc++] = "-s"; | ^~~~ meryl/build.C:787:41: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] 787 | arga[argc] = false; argv[argc++] = "-o"; | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build-threads.o -c meryl/build-threads.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/build-threads.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/dump.o -c meryl/dump.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/dump.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/dump.C:17:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | fprintf(stdout, ">"uint64FMT"\n%s\n", | ^ meryl/dump.C:35:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(stdout, ">"uint64FMT, M->theCount()); | ^ meryl/dump.C:37:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, " "uint32FMT, M->getPosition(i)); | ^ meryl/dump.C:50:2: warning: #warning make this a test [-Wcpp] 50 | #warning make this a test | ^~~~~~~ meryl/dump.C:72:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 72 | fprintf(stdout, "Found "uint64FMT" mers.\n", M->numberOfTotalMers()); | ^ meryl/dump.C:73:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 73 | fprintf(stdout, "Found "uint64FMT" distinct mers.\n", M->numberOfDistinctMers()); | ^ meryl/dump.C:74:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stdout, "Found "uint64FMT" unique mers.\n", M->numberOfUniqueMers()); | ^ meryl/dump.C:87:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Found "uint64FMT" mers.\n", M->numberOfTotalMers()); | ^ meryl/dump.C:88:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 88 | fprintf(stderr, "Found "uint64FMT" distinct mers.\n", M->numberOfDistinctMers()); | ^ meryl/dump.C:89:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "Found "uint64FMT" unique mers.\n", M->numberOfUniqueMers()); | ^ meryl/dump.C:91:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "Largest mercount is "uint64FMT"; "uint64FMT" mers are too big for histogram.\n", | ^ meryl/dump.C:91:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "Largest mercount is "uint64FMT"; "uint64FMT" mers are too big for histogram.\n", | ^ meryl/dump.C:101:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, uint32FMT"\t"uint64FMT"\t%.4f\t%.4f\n", | ^ meryl/dump.C:148:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, uint32FMT"\t"uint64FMT"\n", d, hist[d]); | ^ meryl/dump.C:151:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stderr, "huge\t"uint64FMT"\n", histHuge); | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/estimate.o -c meryl/estimate.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/estimate.C:4: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/estimate.C:54:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "Can fit "uint64FMT" mers into table with prefix of "uint64FMT" bits, using %.3fMB (%.3fMB for positions)\n", | ^ meryl/estimate.C:54:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "Can fit "uint64FMT" mers into table with prefix of "uint64FMT" bits, using %.3fMB (%.3fMB for positions)\n", | ^ meryl/estimate.C:162:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 162 | fprintf(stderr, uint64FMT" "uint32FMT"-mers can be computed using "uint64FMT"MB memory.\n", | ^ meryl/estimate.C:162:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 162 | fprintf(stderr, uint64FMT" "uint32FMT"-mers can be computed using "uint64FMT"MB memory.\n", | ^ meryl/estimate.C: In function 'uint64 estimateMemory(uint32, uint64, bool)': meryl/estimate.C:77:13: warning: unused variable 'N' [-Wunused-variable] 77 | uint64 N = logBaseTwo64(numMers); // Width of the bucket pointer table | ^ meryl/estimate.C:73:11: warning: variable 'tMin' set but not used [-Wunused-but-set-variable] 73 | uint64 tMin = tMax; | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/merge.o -c meryl/merge.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/merge.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/merge.C:14:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 14 | fprintf(stderr, "ERROR - must have at least two databases (you gave "uint32FMT")!\n", args->mergeFilesLen); | ^ meryl/merge.C: In function 'void multipleOperations(merylArgs*)': meryl/merge.C:237:10: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 237 | delete R; | ^ meryl/merge.C:37:71: note: returned from 'void* operator new [](std::size_t)' 37 | merylStreamReader **R = new merylStreamReader* [args->mergeFilesLen]; | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/unaryOp.o -c meryl/unaryOp.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/unaryOp.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ rm -f meryl/libmerylguts.a && ar ruvs meryl/libmerylguts.a meryl/args.o meryl/binaryOp.o meryl/build.o meryl/build-threads.o meryl/dump.o meryl/estimate.o meryl/merge.o meryl/unaryOp.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating meryl/libmerylguts.a a - meryl/args.o a - meryl/binaryOp.o a - meryl/build.o a - meryl/build-threads.o a - meryl/dump.o a - meryl/estimate.o a - meryl/merge.o a - meryl/unaryOp.o g++ -Wl,-z,relro -Wl,-z,now -o meryl/meryl meryl/meryl.o meryl/libmerylguts.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/simple.o -c meryl/simple.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/simple.C:8: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/simple.C:98:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 98 | fprintf(stderr, "Guessing "uint64FMT" mers in input '%s'\n", numMers, inName); | ^ meryl/simple.C:99:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 99 | fprintf(stderr, "Allocating "uint64FMT"MB for mer storage.\n", numMers * 8 >> 20); | ^ meryl/simple.C:129:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "Found "uint64FMT" mers in input '%s'\n", theMersLen, inName); | ^ g++ -Wl,-z,relro -Wl,-z,now -o meryl/simple meryl/simple.o /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers.o -c meryl/mapMers.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/mapMers.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/mapMers.C:135:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 135 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:135:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 135 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:137:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:165:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:165:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:165:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:171:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "%s\t"uint64FMT"\tuncovered\n", S->header(), MS->thePositionInSequence()); | ^ meryl/mapMers.C:176:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:176:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:176:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:178:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "numCovReg: "uint64FMT"\n", numCovReg); | ^ meryl/mapMers.C:179:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 179 | fprintf(stderr, "lenCovReg: "uint64FMT"\n", lenCovReg); | ^ meryl/mapMers.C:193:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C: In function 'int main(int, char**)': meryl/mapMers.C:21:13: warning: variable 'beVerbose' set but not used [-Wunused-but-set-variable] 21 | bool beVerbose = false; | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o meryl/mapMers meryl/mapMers.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers-depth.o -c meryl/mapMers-depth.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/mapMers-depth.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o meryl/mapMers-depth meryl/mapMers-depth.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/kmer-mask.o -c meryl/kmer-mask.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from meryl/kmer-mask.C:4: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/kmer-mask.C:754:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 754 | fprintf(stderr, "aClean "FW"\n", g->thresholdCounts[0][0]); | ^ meryl/kmer-mask.C:755:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 755 | fprintf(stderr, "aMurky "FW"\n", g->thresholdCounts[1][0]); | ^ meryl/kmer-mask.C:756:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 756 | fprintf(stderr, "aMatch "FW"\n", g->thresholdCounts[2][0]); | ^ meryl/kmer-mask.C:757:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 757 | fprintf(stderr, "aMixed "FW"\n", g->thresholdCounts[3][0]); | ^ meryl/kmer-mask.C:760:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:760:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:760:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:760:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:761:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:761:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:761:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:761:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:762:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:762:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:762:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:762:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:763:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C:763:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C:763:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C:763:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C: In member function 'bool fastqRecord::load(FILE*, FILE*)': meryl/kmer-mask.C:69:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets(a1, 1024, FASTQ1); chomp(a1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:70:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | fgets(a2, maxLength, FASTQ1); chomp(a2); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:71:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 71 | fgets(a3, 1024, FASTQ1); chomp(a3); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:72:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | fgets(a4, maxLength, FASTQ1); chomp(a4); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:83:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | fgets(b1, 1024, FASTQ2); chomp(b1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:84:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 84 | fgets(b2, maxLength, FASTQ2); chomp(b2); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:85:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 85 | fgets(b3, 1024, FASTQ2); chomp(b3); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:86:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | fgets(b4, maxLength, FASTQ2); chomp(b4); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o meryl/kmer-mask meryl/kmer-mask.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitMatrix.o -c seagen/hitMatrix.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/hitMatrix.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.C:642:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:107: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seagen/hitMatrix.H:126:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/searchGENOME.o -c seagen/searchGENOME.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/searchGENOME.C:4: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seagen/hitMatrix.H:126:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/configuration.o -c seagen/configuration.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/configuration.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/configuration.C:84:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "\n"uint32FMTW(7)" sequences in %5.2f seconds, %8.3f per second.\n", nq, tm, nq/tm); | ^ seagen/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seagen/hitMatrix.H:126:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/encodedQuery.o -c seagen/encodedQuery.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seagen/encodedQuery.H:6, from seagen/encodedQuery.C:3: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/encodedQuery.C:142:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "encodedQuery::test()-- mersAvail incorrect: Recomputed:"uint32FMT" Real:"uint32FMT"\n", _mersAvail, _r_mersAvail); | ^ seagen/encodedQuery.C:142:88: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "encodedQuery::test()-- mersAvail incorrect: Recomputed:"uint32FMT" Real:"uint32FMT"\n", _mersAvail, _r_mersAvail); | ^ seagen/encodedQuery.C:152:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 152 | fprintf(stderr, "encodedQuery::test()-- skip["uint32FMTW(4)"] incorrect: Acc:%d Real:%d\n", i, getSkip(i, true), _r_skip[i]); | ^ seagen/encodedQuery.C:160:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | fprintf(stderr, "encodedQuery::test()-- mers["uint32FMTW(4)"] incorrect: Acc:"uint64HEX" %s Real:"uint64HEX" %s\n", | ^ seagen/encodedQuery.C:160:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | fprintf(stderr, "encodedQuery::test()-- mers["uint32FMTW(4)"] incorrect: Acc:"uint64HEX" %s Real:"uint64HEX" %s\n", | ^ seagen/encodedQuery.C:160:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | fprintf(stderr, "encodedQuery::test()-- mers["uint32FMTW(4)"] incorrect: Acc:"uint64HEX" %s Real:"uint64HEX" %s\n", | ^ seagen/encodedQuery.C:209:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 209 | fprintf(stderr, "encodedQuery::addOutput()-- from "uint32FMT" to "uint32FMT" bytes.\n", | ^ seagen/encodedQuery.C:209:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 209 | fprintf(stderr, "encodedQuery::addOutput()-- from "uint32FMT" to "uint32FMT" bytes.\n", | ^ seagen/encodedQuery.C: In member function 'void encodedQuery::addOutput(void*, uint32)': seagen/encodedQuery.C:207:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 207 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-deadlock.o -c seagen/thr-deadlock.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-deadlock.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seagen/hitMatrix.H:126:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-loader.o -c seagen/thr-loader.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-loader.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seagen/hitMatrix.H:126:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ seagen/thr-loader.C: In function 'void* loaderThread(void*)': seagen/thr-loader.C:14:17: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 14 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-search.o -c seagen/thr-search.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-search.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seagen/hitMatrix.H:126:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-output.o -c seagen/thr-output.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-output.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seagen/hitMatrix.H:126:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ seagen/thr-output.C: In function 'void* writerThread(void*, void*)': seagen/thr-output.C:48:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 48 | write(config._outputFile, query->theOutput(), query->theOutputLength()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seagen/thr-output.C:62:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | write(config._matchCountsFile, str, strlen(str)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitMatrix-sort.o -c seagen/hitMatrix-sort.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from seagen/hitMatrix.H:8, from seagen/hitMatrix-sort.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/hitMatrix.H:9: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64)': seagen/hitMatrix.H:126:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/aHit.o -c seagen/aHit.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/aHit.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/aHit.C:20:14: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:98: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C: In function 'void ahit_readBinary(aHit*, FILE*)': seagen/aHit.C:12:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 12 | fread(a, sizeof(aHit), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/seagen seagen/hitMatrix.o seagen/searchGENOME.o seagen/configuration.o seagen/encodedQuery.o seagen/thr-deadlock.o seagen/thr-loader.o seagen/thr-search.o seagen/thr-output.o seagen/hitMatrix-sort.o seagen/aHit.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitConverter.o -c seagen/hitConverter.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/hitConverter.C:3: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/hitConverter.C: In function 'void asc2bin(FILE*, FILE*)': seagen/hitConverter.C:39:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | fgets(b, 1024, I); | ~~~~~^~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/hitConverter seagen/hitConverter.o seagen/aHit.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterEST.o -c seagen/filterEST.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterEST.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterEST.C:7: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/filterEST.C:76:11: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 76 | " hits saved:"uint32FMTW(8)"/"uint32FMTW(8)" = %6.3f%%\r", | ^ seagen/filterEST.C:76:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 76 | " hits saved:"uint32FMTW(8)"/"uint32FMTW(8)" = %6.3f%%\r", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterEST-complicated.o -c seagen/filterEST-complicated.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterEST-complicated.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterEST-complicated.C:7: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/filterEST-complicated.C:67:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | fprintf(logFile, uint32FMT"] unique: aggressively filtered to "uint32FMT" hits out of "uint32FMT" hits.\n", | ^ seagen/filterEST-complicated.C:67:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | fprintf(logFile, uint32FMT"] unique: aggressively filtered to "uint32FMT" hits out of "uint32FMT" hits.\n", | ^ seagen/filterEST-complicated.C:115:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(logFile, uint32FMT"] knee: filtered "uint32FMT" hits down to "uint32FMT" hits using threshold %f\n", | ^ seagen/filterEST-complicated.C:115:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(logFile, uint32FMT"] knee: filtered "uint32FMT" hits down to "uint32FMT" hits using threshold %f\n", | ^ seagen/filterEST-complicated.C:139:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(logFile, uint32FMT"] uniform: uniform signal strength, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:139:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(logFile, uint32FMT"] uniform: uniform signal strength, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:174:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(logFile, uint32FMT"] diff: has no clear signal knee, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f, largestdiff=%f\n", | ^ seagen/filterEST-complicated.C:174:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(logFile, uint32FMT"] diff: has no clear signal knee, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f, largestdiff=%f\n", | ^ seagen/filterEST-complicated.C:228:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(logFile, uint32FMT"] spike: at "uint32FMT", "uint32FMT" hits saved: thresh=%f, "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:228:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(logFile, uint32FMT"] spike: at "uint32FMT", "uint32FMT" hits saved: thresh=%f, "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:228:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(logFile, uint32FMT"] spike: at "uint32FMT", "uint32FMT" hits saved: thresh=%f, "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:277:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 277 | fprintf(logFile, uint32FMT"] is an unclassified signal, "uint32FMT" hits saved out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:277:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 277 | fprintf(logFile, uint32FMT"] is an unclassified signal, "uint32FMT" hits saved out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitReader.o -c seagen/hitReader.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/hitReader.H:7, from seagen/hitReader.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5, from seagen/hitReader.H:8: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterEST seagen/filterEST.o seagen/filterEST-complicated.o seagen/hitReader.o seagen/aHit.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterMRNA.o -c seagen/filterMRNA.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterMRNA.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterMRNA.C:7: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/filterMRNA.C:53:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 53 | fprintf(stderr, " scores at least %4.2f AND at least "uint32FMT" bases covered are always output\n", MC, ML); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterMRNA seagen/filterMRNA.o seagen/hitReader.o seagen/aHit.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterNULL.o -c seagen/filterNULL.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterNULL.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterNULL.C:2: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterNULL seagen/filterNULL.o seagen/hitReader.o seagen/aHit.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filtertest.o -c seagen/filtertest.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/filtertest.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ seagen/filtertest.C:180:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "reading hits "uint32FMT"\r", hitsLen); | ^ seagen/filtertest.C:186:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 186 | fprintf(stderr, "reading hits "uint32FMT"\n", hitsLen); | ^ seagen/filtertest.C:308:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C:308:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C:308:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C:308:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C: In function 'void ahit_printASCII(aHit*, FILE*)': seagen/filtertest.C:57:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint32' {aka 'unsigned int'} [-Wformat=] 57 | fprintf(F, "-%c -e %lu -D %lu %lu %lu -M %lu %lu %lu %s %lu %lu\n", | ~~^ | | | long unsigned int | %u 58 | a->_forward ? 'f' : 'r', 59 | a->_qsIdx, | ~~~~~~~~~ | | | uint32 {aka unsigned int} seagen/filtertest.C:57:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint32' {aka 'unsigned int'} [-Wformat=] 57 | fprintf(F, "-%c -e %lu -D %lu %lu %lu -M %lu %lu %lu %s %lu %lu\n", | ~~^ | | | long unsigned int | %u ...... 60 | a->_dsIdx, | ~~~~~~~~~ | | | uint32 {aka unsigned int} seagen/filtertest.C:57:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint32' {aka 'unsigned int'} [-Wformat=] 57 | fprintf(F, "-%c -e %lu -D %lu %lu %lu -M %lu %lu %lu %s %lu %lu\n", | ~~^ | | | long unsigned int | %u ...... 61 | a->_dsLo, | ~~~~~~~~ | | | uint32 {aka unsigned int} seagen/filtertest.C:57:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint32' {aka 'unsigned int'} [-Wformat=] 57 | fprintf(F, "-%c -e %lu -D %lu %lu %lu -M %lu %lu %lu %s %lu %lu\n", | ~~^ | | | long unsigned int | %u ...... 62 | a->_dsHi, | ~~~~~~~~ | | | uint32 {aka unsigned int} seagen/filtertest.C:57:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint32' {aka 'unsigned int'} [-Wformat=] 57 | fprintf(F, "-%c -e %lu -D %lu %lu %lu -M %lu %lu %lu %s %lu %lu\n", | ~~^ | | | long unsigned int | %u ...... 63 | a->_covered, | ~~~~~~~~~~~ | | | uint32 {aka unsigned int} seagen/filtertest.C:57:50: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'uint32' {aka 'unsigned int'} [-Wformat=] 57 | fprintf(F, "-%c -e %lu -D %lu %lu %lu -M %lu %lu %lu %s %lu %lu\n", | ~~^ | | | long unsigned int | %u ...... 64 | a->_matched, | ~~~~~~~~~~~ | | | uint32 {aka unsigned int} seagen/filtertest.C:57:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'uint32' {aka 'unsigned int'} [-Wformat=] 57 | fprintf(F, "-%c -e %lu -D %lu %lu %lu -M %lu %lu %lu %s %lu %lu\n", | ~~^ | | | long unsigned int | %u ...... 65 | a->_numMers, | ~~~~~~~~~~~ | | | uint32 {aka unsigned int} seagen/filtertest.C:57:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 12 has type 'uint32' {aka 'unsigned int'} [-Wformat=] 57 | fprintf(F, "-%c -e %lu -D %lu %lu %lu -M %lu %lu %lu %s %lu %lu\n", | ~~^ | | | long unsigned int | %u ...... 67 | a->_identity, | ~~~~~~~~~~~~ | | | uint32 {aka unsigned int} seagen/filtertest.C:57:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 13 has type 'uint32' {aka 'unsigned int'} [-Wformat=] 57 | fprintf(F, "-%c -e %lu -D %lu %lu %lu -M %lu %lu %lu %s %lu %lu\n", | ~~^ | | | long unsigned int | %u ...... 68 | a->_coverage); | ~~~~~~~~~~~~ | | | uint32 {aka unsigned int} seagen/filtertest.C: In function 'void ahit_readBinary(aHit*, FILE*)': seagen/filtertest.C:39:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | fread(a, sizeof(aHit), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ seagen/filtertest.C: In function 'int main(int, char**)': seagen/filtertest.C:162:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 162 | fgets(hitLine, 1024, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filtertest seagen/filtertest.o -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/sortHits.o -c seagen/sortHits.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/sortHits.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/sortHits.C: In member function 'bool aHitReader::readHit(aHit&)': seagen/sortHits.C:52:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | fgets(buffer, 1024, theFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ seagen/sortHits.C: In member function 'void aHitTemporary::nextHit()': seagen/sortHits.C:119:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | fread(&hit, sizeof(aHit), 1, theFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/sortHits seagen/sortHits.o seagen/aHit.o /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterESTsimple.o -c seagen/filterESTsimple.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterESTsimple.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterESTsimple.C:12: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterESTsimple seagen/filterESTsimple.o seagen/hitReader.o seagen/aHit.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/cleanPolishes.o -c sim4dbutils/cleanPolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/cleanPolishes.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/cleanPolishes.C:8: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/cleanPolishes.C:178:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "A big intron is one that is at least "uint32FMT"bp long.\n", intronLimit); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/cleanPolishes sim4dbutils/cleanPolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/fixPolishesIID.o -c sim4dbutils/fixPolishesIID.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/fixPolishesIID.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/fixPolishesIID.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ In file included from /usr/include/c++/14/map:62, from sim4dbutils/fixPolishesIID.C:9: /usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::_Alloc_node; _Key = std::__cxx11::basic_string; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]': /usr/include/c++/14/bits/stl_tree.h:2267:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 2267 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, const value_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(iterator, const value_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long unsigned int; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]' at /usr/include/c++/14/bits/stl_map.h:913:38, inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long unsigned int; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]' at /usr/include/c++/14/bits/stl_map.h:517:16, inlined from 'void addToDict(std::map, long long unsigned int>&, char*)' at sim4dbutils/fixPolishesIID.C:30:8: /usr/include/c++/14/bits/stl_tree.h:1143:33: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 1143 | return _M_insert_unique_(__pos, __x, __an); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, const value_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(iterator, const value_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long unsigned int; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]' at /usr/include/c++/14/bits/stl_map.h:913:38, inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long unsigned int; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]' at /usr/include/c++/14/bits/stl_map.h:517:16, inlined from 'int main(int, char**)' at sim4dbutils/fixPolishesIID.C:113:23: /usr/include/c++/14/bits/stl_tree.h:1143:33: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 1143 | return _M_insert_unique_(__pos, __x, __an); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(const_iterator, const value_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(iterator, const value_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long unsigned int; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]' at /usr/include/c++/14/bits/stl_map.h:913:38, inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long unsigned int; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]' at /usr/include/c++/14/bits/stl_map.h:517:16, inlined from 'int main(int, char**)' at sim4dbutils/fixPolishesIID.C:120:23: /usr/include/c++/14/bits/stl_tree.h:1143:33: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 1143 | return _M_insert_unique_(__pos, __x, __an); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/fixPolishesIID sim4dbutils/fixPolishesIID.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/comparePolishes.o -c sim4dbutils/comparePolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/comparePolishes.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/comparePolishes.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/comparePolishes.C:308:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:118: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:145: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:158: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:452:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 452 | fprintf(stderr, "ERROR! inA="uint32FMT" inB="uint32FMT"\n", inA, inB); | ^ sim4dbutils/comparePolishes.C:452:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 452 | fprintf(stderr, "ERROR! inA="uint32FMT" inB="uint32FMT"\n", inA, inB); | ^ sim4dbutils/comparePolishes.C:484:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:156: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:520:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C: In function 'int main(int, char**)': sim4dbutils/comparePolishes.C:74:20: warning: variable 'doGFF3' set but not used [-Wunused-but-set-variable] 74 | bool doGFF3; | ^~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/s4p_overlap.o -c sim4dbutils/s4p_overlap.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from sim4dbutils/s4p_overlap.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/s4p_overlap.C:2: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/comparePolishes sim4dbutils/comparePolishes.o sim4dbutils/s4p_overlap.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/convertToAtac.o -c sim4dbutils/convertToAtac.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/convertToAtac.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/convertToAtac.C:279:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:122: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:134: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:122: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:134: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:330:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 330 | fprintf(stderr, "Fixed "uint32FMT" indel/mismatches.\n", totalFixed); | ^ sim4dbutils/convertToAtac.C: In function 'int main(int, char**)': sim4dbutils/convertToAtac.C:241:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 241 | if (e->_estAlignment[aPos] != '-') | ^ sim4dbutils/convertToAtac.C:310:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 310 | if (e->_estAlignment[aPos] != '-') | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/convertToAtac sim4dbutils/convertToAtac.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/convertToExtent.o -c sim4dbutils/convertToExtent.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/convertToExtent.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/convertToExtent.C:43:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:88: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:118: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C: In function 'int main(int, char**)': sim4dbutils/convertToExtent.C:59:8: warning: variable 'beVerbose' set but not used [-Wunused-but-set-variable] 59 | bool beVerbose = false; | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/convertToExtent sim4dbutils/convertToExtent.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/convertPolishes.o -c sim4dbutils/convertPolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/convertPolishes.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/convertPolishes.C:8: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/convertPolishes sim4dbutils/convertPolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/detectChimera.o -c sim4dbutils/detectChimera.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/detectChimera.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/detectChimera.C:129:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stdout, uint32FMTW(3)"-"uint32FMTW(3)" %s%s ("uint32FMT","uint32FMT")\n", | ^ sim4dbutils/detectChimera.C:129:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stdout, uint32FMTW(3)"-"uint32FMTW(3)" %s%s ("uint32FMT","uint32FMT")\n", | ^ sim4dbutils/detectChimera.C:129:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stdout, uint32FMTW(3)"-"uint32FMTW(3)" %s%s ("uint32FMT","uint32FMT")\n", | ^ sim4dbutils/detectChimera.C:153:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stdout, "first "uint32FMT" alignments.\n", maxPts); | ^ sim4dbutils/detectChimera.C: In function 'int main(int, char**)': sim4dbutils/detectChimera.C:19:10: warning: variable 'beVerbose' set but not used [-Wunused-but-set-variable] 19 | bool beVerbose = false; | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/detectChimera sim4dbutils/detectChimera.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/depthOfPolishes.o -c sim4dbutils/depthOfPolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/depthOfPolishes.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/depthOfPolishes.C:103:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 103 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/depthOfPolishes sim4dbutils/depthOfPolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/filterPolishes.o -c sim4dbutils/filterPolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/filterPolishes.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/filterPolishes.C:8: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/filterPolishes.C:178:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "Filtering at "uint32FMT"%% coverage and "uint32FMT"%% identity and "uint32FMT"bp.\n", minC, minI, minL); | ^ sim4dbutils/filterPolishes.C:178:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "Filtering at "uint32FMT"%% coverage and "uint32FMT"%% identity and "uint32FMT"bp.\n", minC, minI, minL); | ^ sim4dbutils/filterPolishes.C:178:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "Filtering at "uint32FMT"%% coverage and "uint32FMT"%% identity and "uint32FMT"bp.\n", minC, minI, minL); | ^ sim4dbutils/filterPolishes.C:181:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | fprintf(stderr, "Filtering for cDNA idx "uint32FMT" and genomic idx "uint32FMT"\n", cdna, geno); | ^ sim4dbutils/filterPolishes.C:181:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | fprintf(stderr, "Filtering for cDNA idx "uint32FMT" and genomic idx "uint32FMT"\n", cdna, geno); | ^ sim4dbutils/filterPolishes.C:183:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 183 | fprintf(stderr, "Filtering for cDNA idx "uint32FMT".\n", cdna); | ^ sim4dbutils/filterPolishes.C:185:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 185 | fprintf(stderr, "Filtering for genomic idx "uint32FMT".\n", geno); | ^ sim4dbutils/filterPolishes.C:259:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 259 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\r", | ^ sim4dbutils/filterPolishes.C:259:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 259 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\r", | ^ sim4dbutils/filterPolishes.C:264:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 264 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed)\r", | ^ sim4dbutils/filterPolishes.C:274:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 274 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\n", | ^ sim4dbutils/filterPolishes.C:274:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 274 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\n", | ^ sim4dbutils/filterPolishes.C:279:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed)\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/filterPolishes sim4dbutils/filterPolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/headPolishes.o -c sim4dbutils/headPolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/headPolishes.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/headPolishes sim4dbutils/headPolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/mappedCoverage.o -c sim4dbutils/mappedCoverage.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/mappedCoverage.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/mappedCoverage.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/mappedCoverage.C:94:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 94 | fprintf(stderr, "Found "uint32FMT" sequences in the input file.\n", covMax); | ^ sim4dbutils/mappedCoverage.C:130:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:130:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:153:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:153:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:219:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 219 | fprintf(stderr, "ERROR: range "uint32FMT"-"uint32FMT" out of bounds (seqLen = "uint32FMT")\n", | ^ sim4dbutils/mappedCoverage.C:219:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 219 | fprintf(stderr, "ERROR: range "uint32FMT"-"uint32FMT" out of bounds (seqLen = "uint32FMT")\n", | ^ sim4dbutils/mappedCoverage.C:219:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 219 | fprintf(stderr, "ERROR: range "uint32FMT"-"uint32FMT" out of bounds (seqLen = "uint32FMT")\n", | ^ sim4dbutils/mappedCoverage.C:242:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 242 | fprintf(C, uint32FMT"\t"uint32FMT"\t%5.3f\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/mappedCoverage.C:242:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 242 | fprintf(C, uint32FMT"\t"uint32FMT"\t%5.3f\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/mappedCoverage.C:242:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 242 | fprintf(C, uint32FMT"\t"uint32FMT"\t%5.3f\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/mappedCoverage.C: In function 'int main(int, char**)': sim4dbutils/mappedCoverage.C:106:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | fgets(inLine, 1024, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/mappedCoverage sim4dbutils/mappedCoverage.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/mergePolishes.o -c sim4dbutils/mergePolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/mergePolishes.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/mergePolishes.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/mergePolishes.C: In function 'int main(int, char**)': sim4dbutils/mergePolishes.C:139:10: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 139 | delete inMatch; | ^~~~~~~ sim4dbutils/mergePolishes.C:28:62: note: returned from 'void* operator new [](std::size_t)' 28 | sim4polishReader **inMatch = new sim4polishReader * [argc]; | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/mergePolishes sim4dbutils/mergePolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/parseSNP.o -c sim4dbutils/parseSNP.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/parseSNP.C:9: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/parseSNP.C:10: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/parseSNP.C:229:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:269:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:98: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:113: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:143: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:538:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 538 | fprintf(stderr, "ERROR: Polishes not sorted by SNP idx! this="uint32FMT", looking for "uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:538:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 538 | fprintf(stderr, "ERROR: Polishes not sorted by SNP idx! this="uint32FMT", looking for "uint32FMT"\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/parseSNP sim4dbutils/parseSNP.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/pickBestPolish.o -c sim4dbutils/pickBestPolish.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/pickBestPolish.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/pickBestPolish.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/pickBestPolish.C:35:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(O, uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(4)" "uint32FMTW(4), | ^ sim4dbutils/pickBestPolish.C:35:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(O, uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(4)" "uint32FMTW(4), | ^ sim4dbutils/pickBestPolish.C:35:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(O, uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(4)" "uint32FMTW(4), | ^ sim4dbutils/pickBestPolish.C:39:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:69:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(stderr, "Picking Best for estID="uint32FMT" with %5d choices.\r", p[0]->_estID, pNum); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/pickBestPolish sim4dbutils/pickBestPolish.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/pickBestPair.o -c sim4dbutils/pickBestPair.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/pickBestPair.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/pickBestPair.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/pickBestPair.C:546:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:584:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 584 | fprintf(STA, "alignments: "uint32FMT" "uint32FMT"\n", mr1END, mr2END); | ^ sim4dbutils/pickBestPair.C:584:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 584 | fprintf(STA, "alignments: "uint32FMT" "uint32FMT"\n", mr1END, mr2END); | ^ sim4dbutils/pickBestPair.C: In function 'int main(int, char**)': sim4dbutils/pickBestPair.C:444:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 444 | fprintf(stderr, "Loaded %lu '1' alignments.\n", mr1.size()); | ~~^ ~~~~~~~~~~ | | | | long unsigned int std::vector::size_type {aka unsigned int} | %u sim4dbutils/pickBestPair.C:445:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 445 | fprintf(stderr, "Loaded %lu '2' alignments.\n", mr2.size()); | ~~^ ~~~~~~~~~~ | | | | long unsigned int std::vector::size_type {aka unsigned int} | %u sim4dbutils/pickBestPair.C:266:19: warning: variable 'minIdent' set but not used [-Wunused-but-set-variable] 266 | double minIdent = 0; | ^~~~~~~~ sim4dbutils/pickBestPair.C:267:19: warning: variable 'minLength' set but not used [-Wunused-but-set-variable] 267 | double minLength = 0; | ^~~~~~~~~ sim4dbutils/pickBestPair.C:268:19: warning: variable 'minCoverage' set but not used [-Wunused-but-set-variable] 268 | double minCoverage = 0; | ^~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function 'bool readMR(FILE*, mapResult&)': sim4dbutils/pickBestPair.C:54:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:57:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function 'bool readMRcoords(FILE*, mapResult&)': sim4dbutils/pickBestPair.C:123:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 123 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:124:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 124 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:125:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:126:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 126 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:129:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function 'bool readMRcoords(FILE*, mapResult&, bool&)': sim4dbutils/pickBestPair.C:189:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 189 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:190:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:191:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 191 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:192:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 192 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:195:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 195 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function 'int main(int, char**)': sim4dbutils/pickBestPair.C:354:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 354 | fgets(LL, 10240, IN); | ~~~~~^~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:365:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 365 | fgets(LL, 10240, IN); | ~~~~~^~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/pickBestPair sim4dbutils/pickBestPair.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/pickUniquePolish.o -c sim4dbutils/pickUniquePolish.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/pickUniquePolish.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/pickUniquePolish.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/pickUniquePolish sim4dbutils/pickUniquePolish.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/plotCoverageVsIdentity.o -c sim4dbutils/plotCoverageVsIdentity.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/plotCoverageVsIdentity.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/plotCoverageVsIdentity.C:32:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(S, uint32FMT" "uint32FMT"\n", p->_percentIdentity, p->_querySeqIdentity); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/plotCoverageVsIdentity sim4dbutils/plotCoverageVsIdentity.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/removeDuplicate.o -c sim4dbutils/removeDuplicate.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/removeDuplicate.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/removeDuplicate sim4dbutils/removeDuplicate.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/sortPolishes.o -c sim4dbutils/sortPolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/sortPolishes.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/sortPolishes.C:87:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:125: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C: In function 'sim4polish* savePolish(sim4polish*, uint64*)': sim4dbutils/sortPolishes.C:39:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class sim4polish'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 39 | memcpy(r, q, sizeof(sim4polish)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:99:7: note: 'class sim4polish' declared here 99 | class sim4polish { | ^~~~~~~~~~ sim4dbutils/sortPolishes.C:59:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class sim4polishExon'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 59 | memcpy(r->_exons, q->_exons, sizeof(sim4polishExon) * q->_numExons); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: 'class sim4polishExon' declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/sortPolishes sim4dbutils/sortPolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/summarizePolishes.o -c sim4dbutils/summarizePolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/summarizePolishes.C:4: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/summarizePolishes.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/summarizePolishes.C:167:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 167 | fprintf(stderr, "numSeqs: "uint32FMT"\n", numSeqs); | ^ sim4dbutils/summarizePolishes.C:169:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(stderr, "ids: "uint32FMT" -- ", idLen); | ^ sim4dbutils/summarizePolishes.C:171:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stderr, " "uint32FMT"", id[i]); | ^ sim4dbutils/summarizePolishes.C:173:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 173 | fprintf(stderr, "cvs: "uint32FMT" -- ", cvLen); | ^ sim4dbutils/summarizePolishes.C:175:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 175 | fprintf(stderr, " "uint32FMT"", cv[i]); | ^ sim4dbutils/summarizePolishes.C:244:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:125: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/summarizePolishes sim4dbutils/summarizePolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/uniqPolishes.o -c sim4dbutils/uniqPolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/uniqPolishes.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/uniqPolishes sim4dbutils/uniqPolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/vennPolishes.o -c sim4dbutils/vennPolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/vennPolishes.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/vennPolishes.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/vennPolishes.C:115:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(stderr, "WARNING: You gave me "uint32FMT" files! That's pretty big. I don't know\n", numFiles); | ^ sim4dbutils/vennPolishes.C:175:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 175 | fprintf(stdout, " "uint32FMTW(8)" ", counts[index]); | ^ sim4dbutils/vennPolishes.C:183:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 183 | fprintf(stdout, "%c = ("uint32FMTW(8)" total) %s\n", 'A' + (char)i, sizes[i], argv[i+numArgs]); | ^ sim4dbutils/vennPolishes.C:189:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 189 | fprintf(stdout, "] "uint32FMT"\n", counts[index]); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/vennPolishes sim4dbutils/vennPolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/realignPolishes.o -c sim4dbutils/realignPolishes.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/realignPolishes.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/realignPolishes.C:8: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/realignPolishes.C:160:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:160:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:160:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:160:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:161:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:161:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:161:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:161:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:243:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | fprintf(stdout, "WARNING: CHANGED! "uint32FMT" -> "uint32FMT"\n", nm, p->_numMatches); | ^ sim4dbutils/realignPolishes.C:243:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | fprintf(stdout, "WARNING: CHANGED! "uint32FMT" -> "uint32FMT"\n", nm, p->_numMatches); | ^ sim4dbutils/realignPolishes.C:248:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(mergeLog, "MERGED\tEST\t"uint32FMT"\tfrom\t%8.3f\t%8.3f\tto\t%8.3f\t%8.3f\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/realignPolishes sim4dbutils/realignPolishes.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/removeRedundant.o -c sim4dbutils/removeRedundant.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/removeRedundant.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/removeRedundant.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/removeRedundant.C:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "IID="uint32FMTW(8)" -- overlap:"uint32FMT" noOverlap:"uint32FMT"\r", | ^ sim4dbutils/removeRedundant.C:107:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "IID="uint32FMTW(8)" -- overlap:"uint32FMT" noOverlap:"uint32FMT"\r", | ^ sim4dbutils/removeRedundant.C:107:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "IID="uint32FMTW(8)" -- overlap:"uint32FMT" noOverlap:"uint32FMT"\r", | ^ sim4dbutils/removeRedundant.C:212:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "\nNOT A PERFECT CLIQUE! Found "uint32FMT" overlaps, wanted "uint32FMT" in the clique.\n", | ^ sim4dbutils/removeRedundant.C:212:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "\nNOT A PERFECT CLIQUE! Found "uint32FMT" overlaps, wanted "uint32FMT" in the clique.\n", | ^ sim4dbutils/removeRedundant.C:260:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 260 | fprintf(stderr, "\nmatches withOvl:"uint32FMT" withoutOvl:"uint32FMT"\n", | ^ sim4dbutils/removeRedundant.C:260:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 260 | fprintf(stderr, "\nmatches withOvl:"uint32FMT" withoutOvl:"uint32FMT"\n", | ^ sim4dbutils/removeRedundant.C:262:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 262 | fprintf(stderr, "not perfect clique:"uint32FMT"\n", notPerfectClique); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/removeRedundant sim4dbutils/removeRedundant.o sim4dbutils/s4p_overlap.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/reportAlignmentDifferences.o -c sim4dbutils/reportAlignmentDifferences.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/reportAlignmentDifferences.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4dbutils/reportAlignmentDifferences.C: In function 'int main(int, char**)': sim4dbutils/reportAlignmentDifferences.C:155:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 155 | if (e->_estAlignment[aPos] != '-') | ^ sim4dbutils/reportAlignmentDifferences.C:201:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | system(gnuCmd); | ~~~~~~^~~~~~~~ sim4dbutils/reportAlignmentDifferences.C:200:30: warning: '%s' directive writing up to 4095 bytes into a region of size 4086 [-Wformat-overflow=] 200 | sprintf(gnuCmd, "gnuplot < %s", gnuName); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:970, from sim4dbutils/reportAlignmentDifferences.C:1: In function 'int sprintf(char*, const char*, ...)', inlined from 'int main(int, char**)' at sim4dbutils/reportAlignmentDifferences.C:200:10: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 11 and 4106 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/reportAlignmentDifferences sim4dbutils/reportAlignmentDifferences.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4db/sim4th.o -c sim4db/sim4th.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4db/sim4th.C:34: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4db/sim4th.C:35: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ sim4db/sim4th.C:327:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 327 | sprintf(str, "%s -Y "uint32FMT" "uint32FMT"\n", | ^ sim4db/sim4th.C:327:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 327 | sprintf(str, "%s -Y "uint32FMT" "uint32FMT"\n", | ^ sim4db/sim4th.C: In function 'void writer(void*, void*)': sim4db/sim4th.C:316:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 316 | write(fOutput, o, strlen(o) * sizeof(char)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sim4db/sim4th.C:332:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 332 | write(fYesNo, str, strlen(str) * sizeof(char)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4db/sim4db sim4db/sim4th.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/snapper2.o -c snapper/snapper2.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/snapper2.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from snapper/snapper2.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.C:59:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:59:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:59:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:59:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:248:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stderr, "WARNING: Found "uint32FMT" queries shorter than minimum reportable size (-discardexonlength = "uint32FMT")\n", | ^ snapper/snapper2.C:248:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stderr, "WARNING: Found "uint32FMT" queries shorter than minimum reportable size (-discardexonlength = "uint32FMT")\n", | ^ snapper/snapper2.C:254:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 254 | fprintf(stderr, "WARNING: Found "uint32FMT" queries longer than maximum size ("uint32FMT")\n", | ^ snapper/snapper2.C:254:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 254 | fprintf(stderr, "WARNING: Found "uint32FMT" queries longer than maximum size ("uint32FMT")\n", | ^ snapper/snapper2.C:295:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stderr, "Created "uint32FMT" filters (out of "uint32FMT" available) to test/validate.\n", | ^ snapper/snapper2.C:295:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stderr, "Created "uint32FMT" filters (out of "uint32FMT" available) to test/validate.\n", | ^ snapper/snapper2.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64, uint64)': snapper/snapper2.H:419:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ snapper/snapper2.C: In function 'int main(int, char**)': snapper/snapper2.C:254:23: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] 254 | fprintf(stderr, "WARNING: Found "uint32FMT" queries longer than maximum size ("uint32FMT")\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ snapper/snapper2.C: In function 'void writerThread(void*, void*)': snapper/snapper2.C:155:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | write(resultFILE, qry->theOutput, sizeof(char) * qry->theOutputLen); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H: In member function 'void logMsg::write(int, const char*)': /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:85:12: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 85 | ::write(file, _log, sizeof(char) * _logLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/configuration.o -c snapper/configuration.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/configuration.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from snapper/snapper2.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/configuration.C:205:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 205 | fprintf(stderr, "ERROR: Invalid afLength "uint32FMT", should be < 64.\n", _afLength), err++; | ^ snapper/snapper2.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64, uint64)': snapper/snapper2.H:419:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-search.o -c snapper/thr-search.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-search.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from snapper/snapper2.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64, uint64)': snapper/snapper2.H:419:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-filter.o -c snapper/thr-filter.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-filter.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from snapper/snapper2.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64, uint64)': snapper/snapper2.H:419:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-polish.o -c snapper/thr-polish.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-polish.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from snapper/snapper2.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/thr-polish.C:311:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 311 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/thr-polish.C:311:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 311 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/snapper2.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64, uint64)': snapper/snapper2.H:419:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-polish-dp.o -c snapper/thr-polish-dp.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-polish-dp.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from snapper/snapper2.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/thr-polish-dp.C:89:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "dpMatrix-- reallocate to "uint32FMT" x "uint32FMT"\n", aMax, bMax); | ^ snapper/thr-polish-dp.C:89:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "dpMatrix-- reallocate to "uint32FMT" x "uint32FMT"\n", aMax, bMax); | ^ snapper/thr-polish-dp.C:441:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 441 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/thr-polish-dp.C:441:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 441 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/snapper2.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64, uint64)': snapper/snapper2.H:419:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/hitMatrix.o -c snapper/hitMatrix.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/hitMatrix.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from snapper/snapper2.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/hitMatrix.C:385:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 385 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT".\n", theHitsPos, theHitsMax); | ^ snapper/hitMatrix.C:385:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 385 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT".\n", theHitsPos, theHitsMax); | ^ snapper/snapper2.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64, uint64)': snapper/snapper2.H:419:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ snapper/hitMatrix.C: In member function 'void hitMatrix::filter(char, double, uint32, aHit*&, uint32&, uint32&)': snapper/hitMatrix.C:383:23: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 383 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/hitMatrix-sort.o -c snapper/hitMatrix-sort.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/hitMatrix-sort.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4.H:1, from snapper/snapper2.H:22: /build/reproducible-path/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:187:3: warning: this decimal constant is unsigned only in ISO C90 187 | void s4p_copyPolish(sim4polish *orig, uint32 exonNum=2147483648); | ^~~~ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H: In member function 'void hitMatrix::addHits(uint32, uint64*, uint64, uint64)': snapper/snapper2.H:419:19: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o snapper/snapper2 snapper/snapper2.o snapper/configuration.o snapper/thr-search.o snapper/thr-filter.o snapper/thr-polish.o snapper/thr-polish-dp.o snapper/hitMatrix.o snapper/hitMatrix-sort.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tagger.o -c tapper/tagger.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tagger.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tagger.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tagger.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tagger.C:151:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stdout, "%s\tlength\t"uint32FMT"\n", tagfile, TF->metaData()->tagSize()); | ^ tapper/tagger.C:152:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 152 | fprintf(stdout, "%s\tnumMates\t"uint64FMT"\n", tagfile, TF->numberOfMatePairs()); | ^ tapper/tagger.C:153:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stdout, "%s\tmean\t"uint32FMT"\n", tagfile, TF->metaData()->mean()); | ^ tapper/tagger.C:154:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 154 | fprintf(stdout, "%s\tstddev\t"uint32FMT"\n", tagfile, TF->metaData()->stddev()); | ^ tapper/tagger.C:157:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | fprintf(stdout, "%s\tlength\t"uint32FMT"\n", tagfile, TF->metaData()->tagSize()); | ^ tapper/tagger.C:158:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 158 | fprintf(stdout, "%s\tnumTags\t"uint64FMT"\n", tagfile, TF->numberOfFragmentTags()); | ^ tapper/tagger.C:182:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:362:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tapperResult.H: In member function 'void tapperResultIndex::print(FILE*)': tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 13 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 14 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 15 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 16 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 17 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 18 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 19 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function 'char* tapperHit::printHit(char*, uint64)': tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int tapper/tagger.C: In function 'bool readTag(uint32, FILE*, FILE*, tapperTag*)': tapper/tagger.C:52:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | fgets(seqhdr, 1024, seq); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:54:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fgets(seqhdr, 1024, seq); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:55:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 55 | fgets(seqseq, 1024, seq); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:57:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fgets(qlthdr, 1024, qlt); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:59:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fgets(qlthdr, 1024, qlt); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:60:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fgets(qltseq, 1024, qlt); | ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o tapper/tagger tapper/tagger.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tapper.o -c tapper/tapper.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tapper.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tapper.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tapper.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tapper.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapper.C:633:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 633 | fprintf(stderr, "Reallocate t->numHappiesMax to "uint32FMT"\n", t->numHappiesMax); | ^ tapper/tapper.C:1048:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1048 | fprintf(stderr, "sizeof(tapperResultIndex) -- "sizetFMT"\n", sizeof(tapperResultIndex)); | ^ tapper/tapper.C:1049:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1049 | fprintf(stderr, "sizeof(tapperResultQV) -- "sizetFMT"\n", sizeof(tapperResultQV)); | ^ tapper/tapper.C:1050:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1050 | fprintf(stderr, "sizeof(tapperResultFragment) -- "sizetFMT"\n", sizeof(tapperResultFragment)); | ^ tapper/tapper.C:1051:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1051 | fprintf(stderr, "sizeof(tapperResultMated) -- "sizetFMT"\n", sizeof(tapperResultMated)); | ^ tapper/tapper.C:1052:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1052 | fprintf(stderr, "sizeof(tapperResultTangled) -- "sizetFMT"\n", sizeof(tapperResultTangled)); | ^ tapper/tapper.C:1053:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1053 | fprintf(stderr, "sizeof(tapperHit) -- "sizetFMT"\n", sizeof(tapperHit)); | ^ tapper/tapper.C:1054:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1054 | fprintf(stderr, "sizeof(tapperTag) -- "sizetFMT"\n", sizeof(tapperTag)); | ^ tapper/tapper.C:1124:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1124 | fprintf(stderr, " all alignments. The default is "uint32FMT".\n", g->repeatThreshold); | ^ tapper/tapperResult.H: In member function 'void tapperResultIndex::print(FILE*)': tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 13 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 14 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 15 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 16 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 17 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 18 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 19 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function 'char* tapperHit::printHit(char*, uint64)': tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int tapper/tapper.C: In member function 'bool tapperHit::alignToReference(tapperGlobalData*, uint32, uint32, char*, uint32)': tapper/tapper.C:399:43: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 399 | if (_colorMismatch + _colorInconsistent > g->maxColorError) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ tapper/tapper.C:415:23: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] 415 | for (uint32 ti=0; ti<_len-1; ti++) { | ~~^~~~~~~ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/recordFile.H:6, from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:39: tapper/tapper.C:468:13: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] 468 | assert(nn == _colorMismatch + _colorInconsistent); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o tapper/tapper tapper/tapper.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tapperconvert.o -c tapper/tapperconvert.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tapperconvert.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tapperconvert.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tapperconvert.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tapperconvert.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperResult.H: In member function 'void tapperResultIndex::print(FILE*)': tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 13 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 14 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 15 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 16 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 17 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 18 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 19 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function 'char* tapperHit::printHit(char*, uint64)': tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int g++ -Wl,-z,relro -Wl,-z,now -o tapper/tapperconvert tapper/tapperconvert.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tappermerge.o -c tapper/tappermerge.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tappermerge.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tappermerge.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tappermerge.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tappermerge.C:5: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperResult.H: In member function 'void tapperResultIndex::print(FILE*)': tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 13 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 14 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 15 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 16 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 17 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 18 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 19 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function 'char* tapperHit::printHit(char*, uint64)': tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int g++ -Wl,-z,relro -Wl,-z,now -o tapper/tappermerge tapper/tappermerge.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tappersort.o -c tapper/tappersort.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from tapper/tappersort.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from tapper/tappersort.C:3: tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tappersort.C:4: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tappersort.C:6: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tappersort.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tappersort.C:148:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | sprintf(filename, "%s."uint32FMTW(03)".tapperAlignment", outputName, outputIndex); | ^ tapper/tappersort.C:150:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 150 | fprintf(stderr, "Writing "uint32FMT" sorted alignments to '%s'\n", aliLen, filename); | ^ tapper/tappersort.C:202:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "Can fit "uint32FMT" alignments into "uint64FMT" bytes memory; "uint32FMT" bytes each.\n", | ^ tapper/tappersort.C:202:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "Can fit "uint32FMT" alignments into "uint64FMT" bytes memory; "uint32FMT" bytes each.\n", | ^ tapper/tappersort.C:202:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "Can fit "uint32FMT" alignments into "uint64FMT" bytes memory; "uint32FMT" bytes each.\n", | ^ tapper/tappersort.C:257:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 257 | sprintf(filename, "%s."uint32FMTW(03)".tapperAlignment", outputName, x); | ^ tapper/tappersort.C:299:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 299 | sprintf(filename, "%s."uint32FMTW(03)".tapperAlignment", outputName, x); | ^ tapper/tapperResult.H: In member function 'void tapperResultIndex::print(FILE*)': tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 13 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 14 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 15 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 16 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 17 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 18 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 19 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function 'char* tapperHit::printHit(char*, uint64)': tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int g++ -Wl,-z,relro -Wl,-z,now -o tapper/tappersort tapper/tappersort.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libkmer/ -I/build/reproducible-path/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tappererrorcorrect.o -c tapper/tappererrorcorrect.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:4, from tapper/tappererrorcorrect.C:1: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from tapper/tappererrorcorrect.C:3: tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tappererrorcorrect.C:4: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tappererrorcorrect.C:6: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tappererrorcorrect.C:7: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tappererrorcorrect.C:25:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", i, alignsLen[i]); | ^ tapper/tappererrorcorrect.C:25:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", i, alignsLen[i]); | ^ tapper/tappererrorcorrect.C:49:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 49 | fprintf(stderr, "block[0] - seq "uint32FMT" pos "uint32FMT"\n", | ^ tapper/tappererrorcorrect.C:49:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 49 | fprintf(stderr, "block[0] - seq "uint32FMT" pos "uint32FMT"\n", | ^ tapper/tappererrorcorrect.C:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", alignsMax-1, alignsLen[alignsMax-1]); | ^ tapper/tappererrorcorrect.C:62:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", alignsMax-1, alignsLen[alignsMax-1]); | ^ tapper/tappererrorcorrect.C:160:2: warning: #warning need the real read size here [-Wcpp] 160 | #warning need the real read size here | ^~~~~~~ tapper/tappererrorcorrect.C:213:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 213 | fprintf(stdout, "\nALIGN "uint32FMT"-"uint32FMT"\n", winLo, winHi); | ^ tapper/tappererrorcorrect.C:213:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 213 | fprintf(stdout, "\nALIGN "uint32FMT"-"uint32FMT"\n", winLo, winHi); | ^ tapper/tapperResult.H: In member function 'void tapperResultIndex::print(FILE*)': tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 13 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 14 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 15 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 16 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 17 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 18 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 19 has type 'int' [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function 'char* tapperHit::printHit(char*, uint64)': tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int tapper/tappererrorcorrect.C: In function 'int main(int, char**)': tapper/tappererrorcorrect.C:102:13: warning: variable 'memoryLimit' set but not used [-Wunused-but-set-variable] 102 | uint64 memoryLimit = 1024 * 1024 * 1024; | ^~~~~~~~~~~ tapper/tappererrorcorrect.C:141:21: warning: unused variable 'id' [-Wunused-variable] 141 | uint16 id[4]; | ^~ g++ -Wl,-z,relro -Wl,-z,now -o tapper/tappererrorcorrect tapper/tappererrorcorrect.o /build/reproducible-path/kmer-0~20150903+r2013/libsim4/libsim4.a /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C:53:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 53 | fprintf(stderr, "mer "uint64HEX" not found : e=%d f=%d g=%d\n", m, ee, ef, eg); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C:56:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | fprintf(stderr, "mer "uint64HEX" count differs : e=%u f=%u g=%u (exists=%d)\n", m, ce, cf, cg, ee); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C:65:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "mer "uint64HEX" : e=%u f=%u g=%u (exists=%d)\n", m, ce, cf, cg, ee); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C:96:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr, "Tried "uint64FMT", didn't find "uint64FMT" merStream mers in the existDB.\n", tried, lost); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C:96:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr, "Tried "uint64FMT", didn't find "uint64FMT" merStream mers in the existDB.\n", tried, lost); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C:128:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "Found "uint64FMT" mers in the meryl database.\n", expected); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C:148:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "Expected to find "uint64FMT" mers, but found "uint64FMT" instead.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.C:148:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "Expected to find "uint64FMT" mers, but found "uint64FMT" instead.\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/existDB /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-existDB.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++03 -I/build/reproducible-path/kmer-0~20150903+r2013/libmeryl/ -I/build/reproducible-path/kmer-0~20150903+r2013/libbio/ -I/build/reproducible-path/kmer-0~20150903+r2013/libseq/ -I/build/reproducible-path/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.o -c /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C In file included from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:6: /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/reproducible-path/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:38: /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libutil/util++.H:43: /build/reproducible-path/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:8: /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:68:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | fprintf(stdout, "Found no matches for mer=%s at pos="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:101:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, "Got a F match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:101:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, "Got a F match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:101:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, "Got a F match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:110:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "Got a R match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:110:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "Got a R match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:110:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "Got a R match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:255:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stderr, "ERROR: merbegin="uint64FMT" and merend="uint64FMT" are incompatible.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:255:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stderr, "ERROR: merbegin="uint64FMT" and merend="uint64FMT" are incompatible.\n", | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:275:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 275 | fprintf(stderr, "Building table with merSize "uint32FMT", merSkip "uint32FMT"\n", mersize, merskip); | ^ /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.C:275:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 275 | fprintf(stderr, "Building table with merSize "uint32FMT", merSkip "uint32FMT"\n", mersize, merskip); | ^ g++ -Wl,-z,relro -Wl,-z,now -o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/positionDB /build/reproducible-path/kmer-0~20150903+r2013/libkmer/driver-posDB.o /build/reproducible-path/kmer-0~20150903+r2013/libkmer/libkmer.a /build/reproducible-path/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wl,-z,relro -Wl,-z,now -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqCache.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wl,-z,relro -Wl,-z,now -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-seqStream.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wl,-z,relro -Wl,-z,now -o /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream /build/reproducible-path/kmer-0~20150903+r2013/libseq/test-merStream.o /build/reproducible-path/kmer-0~20150903+r2013/libseq/libseq.a /build/reproducible-path/kmer-0~20150903+r2013/libbio/libbio.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/test.o -c /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/test.c rm -f /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a && ar ruvs /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/test.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/mt19937ar/test.o rm -f /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a && ar ruvs /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/dict.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/except.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/hash.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/list.o /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/sfx.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/dict.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/except.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/hash.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/list.o a - /build/reproducible-path/kmer-0~20150903+r2013/libutil/kazlib/sfx.o make[2]: Leaving directory '/build/reproducible-path/kmer-0~20150903+r2013' mv installdir/bin/atac.pl installdir/bin/atac mv -v installdir/lib/halignmodule.so installdir/lib/halign.so renamed 'installdir/lib/halignmodule.so' -> 'installdir/lib/halign.so' mv -v installdir/lib/localAlignerInterfacemodule.so installdir/lib/localAlignerInterface.so renamed 'installdir/lib/localAlignerInterfacemodule.so' -> 'installdir/lib/localAlignerInterface.so' make[1]: Leaving directory '/build/reproducible-path/kmer-0~20150903+r2013' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j3 install DESTDIR=/build/reproducible-path/kmer-0\~20150903\+r2013/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kmer-0~20150903+r2013' make[1]: Leaving directory '/build/reproducible-path/kmer-0~20150903+r2013' dh_install debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/kmer-0~20150903+r2013' for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` `grep -l '#!/usr/bin/env \+perl' debian/*/usr/lib/atac/bin/*` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/kmer-0~20150903+r2013' dh_installdocs dh_installchangelogs dh_installman debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/kmer-0~20150903+r2013' dh_python3 --no-ext-rename make[1]: Leaving directory '/build/reproducible-path/kmer-0~20150903+r2013' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: debian/sim4db/usr/bin/sim4db contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: debian/atac/usr/lib/atac/bin/seatac contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libmeryl-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libkmer-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'kmer' in '../kmer_0~20150903+r2013-9_all.deb'. dpkg-deb: building package 'libmeryl-dev' in '../libmeryl-dev_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'sim4db-dbgsym' in '../sim4db-dbgsym_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'libkmer-dev' in '../libkmer-dev_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'leaff' in '../leaff_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'leaff-dbgsym' in '../leaff-dbgsym_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'sim4db' in '../sim4db_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'meryl' in '../meryl_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'meryl-dbgsym' in '../meryl-dbgsym_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'atac' in '../atac_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'atac-dbgsym' in '../atac-dbgsym_0~20150903+r2013-9_armhf.deb'. dpkg-deb: building package 'kmer-examples' in '../kmer-examples_0~20150903+r2013-9_all.deb'. dpkg-genbuildinfo --build=binary -O../kmer_0~20150903+r2013-9_armhf.buildinfo dpkg-genchanges --build=binary -O../kmer_0~20150903+r2013-9_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/23629 and its subdirectories I: Current time: Tue Oct 15 12:21:45 -12 2024 I: pbuilder-time-stamp: 1729038105 Wed Oct 16 00:22:14 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Wed Oct 16 00:22:14 UTC 2024 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Wed Oct 16 00:31:33 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Wed Oct 16 00:31:35 UTC 2024 I: kmer_0~20150903+r2013-9_armhf.changes: Format: 1.8 Date: Tue, 10 Sep 2024 10:35:03 +0200 Source: kmer Binary: atac atac-dbgsym kmer kmer-examples leaff leaff-dbgsym libkmer-dev libmeryl-dev meryl meryl-dbgsym sim4db sim4db-dbgsym Architecture: armhf all Version: 0~20150903+r2013-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: atac - genome assembly-to-assembly comparison kmer - suite of tools for DNA sequence analysis kmer-examples - sample data for kmer suite of tools for DNA sequence analysis leaff - biological sequence library utilities and applications libkmer-dev - suite of tools for DNA sequence analysis (development lib) libmeryl-dev - in- and out-of-core kmer counting and utilities (development lib) meryl - in- and out-of-core kmer counting and utilities sim4db - batch spliced alignment of cDNA sequences to a target genome Closes: 1080608 Changes: kmer (0~20150903+r2013-9) unstable; urgency=medium . * Team upload. * Added patch to replace distutils with stdlib usage. Closes: #1080608 * Standards-Version: 4.6.2 (routine-update) * debhelper-compat 13 (routine-update) * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * No tab in license text (routine-update) * Add missing build dependency on dh-python | dh-sequence-python3 for command dh_python3. * d/rules: set -std=c++03 to reduce warnings Checksums-Sha1: 1c6718223e77cd526fa0cb3e342b94164bb49368 2393496 atac-dbgsym_0~20150903+r2013-9_armhf.deb 71eacbce3f67a090b559ac618b6bc822bfbea335 353420 atac_0~20150903+r2013-9_armhf.deb d6599cd20af73ece16f926b3d408f8305e856f2f 2352256 kmer-examples_0~20150903+r2013-9_all.deb e3bd8210e4572e5c9870136d178f46d0e181edaf 4956 kmer_0~20150903+r2013-9_all.deb 91e063f05a47ac365be6aaf4cab3c72b4af1bbcb 9126 kmer_0~20150903+r2013-9_armhf.buildinfo e93ea118d26b3fa9531f9c43f81275379289ddcf 169944 leaff-dbgsym_0~20150903+r2013-9_armhf.deb 85ec4c5e81744343ffebb19355547dd6ba6ef0c3 63456 leaff_0~20150903+r2013-9_armhf.deb 5a012dd59dd7e1654b6e1545187226a1cabae6da 202244 libkmer-dev_0~20150903+r2013-9_armhf.deb 2dc57559f1ceadbc98cc02973c51eb54c52a194a 60624 libmeryl-dev_0~20150903+r2013-9_armhf.deb e59340f229857aff5fa0f5d5129af841d48e9700 1261512 meryl-dbgsym_0~20150903+r2013-9_armhf.deb b4a6b2587f8ca29cb64d08202170c6d40a44ce72 205316 meryl_0~20150903+r2013-9_armhf.deb 0f9d8bbbd8d21cbd5693a08dbe58a6b317845945 1842404 sim4db-dbgsym_0~20150903+r2013-9_armhf.deb 7f08a0132d117ee6acae1692c9613f537741b9ac 383564 sim4db_0~20150903+r2013-9_armhf.deb Checksums-Sha256: 6d5b2ad9e3a8b7f8fd3f53c3817479bc96d56ab4b6267bcc17c221680225bbc7 2393496 atac-dbgsym_0~20150903+r2013-9_armhf.deb 1764d37dbe7dcfefd6581da22995a5ecc5d7a014f7fe5d839f58a6299df7786e 353420 atac_0~20150903+r2013-9_armhf.deb dc44c95ea3ab9f2af8ed156e3406a8a4d9836d78cf4b92bd74350dd130ed7d2b 2352256 kmer-examples_0~20150903+r2013-9_all.deb c18f3bd97d22ff1ca4acb6ebd36fce334120b57660b66c06f377e52bf15e2849 4956 kmer_0~20150903+r2013-9_all.deb ea8ce4c2187bd9b48c0e4f962a66a8064ed2671e4cff814262c79728a33bbf5e 9126 kmer_0~20150903+r2013-9_armhf.buildinfo e441a390ee56a9d3d1d403664ae77d80e66787e0593271f7efb15914e0f6ca93 169944 leaff-dbgsym_0~20150903+r2013-9_armhf.deb bde34336f36943b9aeb01dfde0d4b59deb2d8f2c220e1fcb3807f44c87bc243e 63456 leaff_0~20150903+r2013-9_armhf.deb 82b7b78d9a5bf269cb34bb40fd08606ff4c2e6d253289701b39edf9885282417 202244 libkmer-dev_0~20150903+r2013-9_armhf.deb 362dd87dcebf2ce80be7c69bae6eacf6a484e7819aeca759e8ee55102c7aed19 60624 libmeryl-dev_0~20150903+r2013-9_armhf.deb c5e855f1d694c33d4e14293b1c4b808ff78aa734d22958ee2dafc68f9ec6d116 1261512 meryl-dbgsym_0~20150903+r2013-9_armhf.deb d70ff36ae7ab0f78db2060ef2e78d5a39286ee1797605fa19da934377aed2d73 205316 meryl_0~20150903+r2013-9_armhf.deb b007f1bb30a71f54a08dafeb99aa388d572c8e42b8dc34a622b1d475165e8cf3 1842404 sim4db-dbgsym_0~20150903+r2013-9_armhf.deb 741e0d21eb61244093198b77ffe2be11bfec9e3effe1336d3ce7255497d513d3 383564 sim4db_0~20150903+r2013-9_armhf.deb Files: ae8db8395e6aec951dde8627ae6f7733 2393496 debug optional atac-dbgsym_0~20150903+r2013-9_armhf.deb d8dafd3bf44e768ff5f278f93a0d3191 353420 science optional atac_0~20150903+r2013-9_armhf.deb f6bc134c89ee377dfcc7b06c933bdd4e 2352256 science optional kmer-examples_0~20150903+r2013-9_all.deb 43e796fca49a5fa103fa0cdbe1a15968 4956 science optional kmer_0~20150903+r2013-9_all.deb 3b85d0b90c7574f74d5ddbd519060db4 9126 science optional kmer_0~20150903+r2013-9_armhf.buildinfo 9c4ba385451b0e0f2c0c1b27e62537f5 169944 debug optional leaff-dbgsym_0~20150903+r2013-9_armhf.deb 1f6044db64153e038abbfb7283967520 63456 science optional leaff_0~20150903+r2013-9_armhf.deb 6e5a7fc357c8a2325912ba2ed5859c64 202244 libdevel optional libkmer-dev_0~20150903+r2013-9_armhf.deb 945bc3ba15f900c3f0e8a3a5e6154d81 60624 libdevel optional libmeryl-dev_0~20150903+r2013-9_armhf.deb 7b9e00506bfb595f29164bdf8aa04be1 1261512 debug optional meryl-dbgsym_0~20150903+r2013-9_armhf.deb 878a8e7d6a5d2a88b52d028150f8c95f 205316 science optional meryl_0~20150903+r2013-9_armhf.deb 3c2f83cea8ba86c5ddc0df3256bdfbbb 1842404 debug optional sim4db-dbgsym_0~20150903+r2013-9_armhf.deb b117d957c5e936b6afcc3bc4a97bd638 383564 science optional sim4db_0~20150903+r2013-9_armhf.deb Wed Oct 16 00:31:36 UTC 2024 I: diffoscope 280 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_34-11286.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.zKLWRx5E/kmer_0~20150903+r2013-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.zKLWRx5E/kmer_0~20150903+r2013-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.zKLWRx5E/kmer_0~20150903+r2013-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.zKLWRx5E/b1/kmer_0~20150903+r2013-9_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.zKLWRx5E/b2/kmer_0~20150903+r2013-9_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.479s) 0.479s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.118s) 0.118s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 818ms CPU time consumed: 819ms Wed Oct 16 00:37:57 UTC 2024 I: diffoscope 280 found no differences in the changes files, and a .buildinfo file also exists. Wed Oct 16 00:37:57 UTC 2024 I: kmer from unstable built successfully and reproducibly on armhf. Wed Oct 16 00:38:00 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Oct 16 00:38:00 UTC 2024 I: Submitting 12K b1/kmer_0~20150903+r2013-9_armhf.buildinfo.asc Wed Oct 16 00:38:09 UTC 2024 I: Submitting 12K b2/kmer_0~20150903+r2013-9_armhf.buildinfo.asc Wed Oct 16 00:38:25 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Oct 16 00:38:25 UTC 2024 I: Done submitting .buildinfo files. Wed Oct 16 00:38:25 UTC 2024 I: Removing signed kmer_0~20150903+r2013-9_armhf.buildinfo.asc files: removed './b1/kmer_0~20150903+r2013-9_armhf.buildinfo.asc' removed './b2/kmer_0~20150903+r2013-9_armhf.buildinfo.asc'