Wed Apr 7 06:42:27 UTC 2021 I: starting to build canu/buster/amd64 on jenkins on '2021-04-07 06:42' Wed Apr 7 06:42:27 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_5/10235/console.log Wed Apr 7 06:42:27 UTC 2021 I: Downloading source for buster/canu=1.8+dfsg-2 --2021-04-07 06:42:28-- http://deb.debian.org/debian/pool/main/c/canu/canu_1.8+dfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1980 (1.9K) Saving to: ‘canu_1.8+dfsg-2.dsc’ 0K . 100% 64.6M=0s 2021-04-07 06:42:28 (64.6 MB/s) - ‘canu_1.8+dfsg-2.dsc’ saved [1980/1980] Wed Apr 7 06:42:28 UTC 2021 I: canu_1.8+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: canu Binary: canu Architecture: any Version: 1.8+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Afif Elghraoui Homepage: http://canu.readthedocs.org/en/latest/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/canu Vcs-Git: https://salsa.debian.org/med-team/canu.git Build-Depends: debhelper (>= 11~), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap (>= 2.1.3) Package-List: canu deb science optional arch=any Checksums-Sha1: ecec98038f862eaff77a1f59fac37daaa15e1fbb 1084314 canu_1.8+dfsg.orig.tar.gz cc643355505456260a73b881f7a832630503b45f 5904 canu_1.8+dfsg-2.debian.tar.xz Checksums-Sha256: ac462313aed0d3bfef7fa8420c1ae07a45489584b401a5cfe0b9f43117dc12eb 1084314 canu_1.8+dfsg.orig.tar.gz c4330ca1a683d0168f8521423c76b387625c8a1c8c1cbd53df3c857266db5c39 5904 canu_1.8+dfsg-2.debian.tar.xz Files: e5eb371999f399bf339b0169a134692c 1084314 canu_1.8+dfsg.orig.tar.gz cb4b342031322d4e3c2033556a3fefed 5904 canu_1.8+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlwE+PMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHaTA/+LBeBCR9Xn8MWeuKhOuFJJ5M3LvzRHKQh 0Suv93C6ewe1KNAgApqL78q2e40JPJ/gUIkfE53HR5jb/PB6AEiSlLsNpOTvyNGp d0jvR3mVCx7+A3GSTRZsaIX6FqaY5dv0e1JKVkNvlkf6JpeVFTLFsbu20eC21sWC jLydoUu+qu6YKk45NlGdwRQDloF27XF/YsuPcU2VBa+ox0FM+6e7bCoVije0QvS2 3sm9o0MGisG7yZ/0D+Jcgu/mbOpBiHdZnnt/cE4QB5KWYl54oGsDuLw7rDoFNk9P qtqY6Z2Vh1GqCJ/RXjPT6fXGw6JuH87ic8lZnI+Cf2HcT5811VmquUeeTVofj3nr aMBQ4iBe4b6nCqtPTrP6O0BtWsWIj7f5r2VsiCtRTxcTvEN7nuDFelQe/jNp+soQ 8eMsT9sZT9htcxGm/H9JvBPAjr2CXodSEbMTkabj0xtm6LpqGTB7d/+ZSgqTQrbz 90nW06UdYoT45T07q2qf7rB0JQxrgxKPkZKouYX67tZ1RCT44KsFSgy84Lid56YA hdAj8NxNA8f5vptiz/Q0Gosf+iXEwlBU2Vv3+O3kRhtaDfPB9mInToB5+HPq49dK hbIv66DNtAOmnukIfqAfRmWtBpfVu6XLQKh2CKk93lh6RrWCkAqDSJGYIQdOHDEy z+tBi4JePl4= =xJ9L -----END PGP SIGNATURE----- Wed Apr 7 06:42:28 UTC 2021 I: Checking whether the package is not for us Wed Apr 7 06:42:28 UTC 2021 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed Apr 7 06:42:28 UTC 2021 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed Apr 7 06:45:16 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 6 18:42:29 -12 2021 I: pbuilder-time-stamp: 1617777749 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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 [canu_1.8+dfsg-2.dsc] I: copying [./canu_1.8+dfsg.orig.tar.gz] I: copying [./canu_1.8+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Dec 2 21:35:47 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./canu_1.8+dfsg-2.dsc dpkg-source: info: extracting canu in canu-1.8+dfsg dpkg-source: info: unpacking canu_1.8+dfsg.orig.tar.gz dpkg-source: info: unpacking canu_1.8+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-mhap-at-runtime.patch dpkg-source: info: applying external-mhap.patch dpkg-source: info: applying tell_version_properly.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/52717/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3fac25298d1d4b52b9240e7208263769' 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='52717' 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/tmp.1c9zZcAaaL/pbuilderrc_lKFJ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/b1 --logfile b1/build.log canu_1.8+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Mar 20 20:25 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/52717/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: amd64 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 (>= 11~), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap (>= 2.1.3) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libmeryl-dev; however: Package libmeryl-dev is not installed. pbuilder-satisfydepends-dummy depends on libfilesys-df-perl; however: Package libfilesys-df-perl is not installed. pbuilder-satisfydepends-dummy depends on mhap (>= 2.1.3); however: Package mhap 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} binfmt-support{a} bsdmainutils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} fastjar{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} jaligner{a} jarwrapper{a} java-common{a} libapache-pom-java{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libboost-dev{a} libboost1.67-dev{a} libbsd0{a} libcommons-compress-java{a} libcommons-parent-java{a} libcroco3{a} libcups2{a} libdbus-1-3{a} libelf1{a} libexpat1{a} libfastutil-java{a} libfile-stripnondeterminism-perl{a} libfilesys-df-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0{a} libgssapi-krb5-2{a} libguava-java{a} libicu63{a} libjpeg62-turbo{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libmagic-mgc{a} libmagic1{a} libmeryl-dev{a} libncurses6{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpng16-16{a} libsigsegv2{a} libssl1.1{a} libssw-java{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxrender1{a} libxtst6{a} lsb-base{a} m4{a} man-db{a} mhap{a} openjdk-11-jre-headless{a} openssl{a} po-debconf{a} sensible-utils{a} ucf{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 94.1 MB of archives. After unpacking 423 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 binfmt-support amd64 2.2.0-2 [70.0 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u5 [1539 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u5 [844 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 java-common all 0.71 [14.4 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+deb10u1 [54.4 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+deb10u1 [58.2 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u4 [324 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libasound2-data all 1.1.8-1 [59.6 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libasound2 amd64 1.1.8-1 [361 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u1 [757 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre-headless amd64 11.0.9.1+1-1~deb10u2 [37.7 MB] Get: 59 http://deb.debian.org/debian buster/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 ca-certificates-java all 20190405 [15.7 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 fastjar amd64 2:0.98-6+b1 [81.0 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 jaligner all 1.0+dfsg-6 [131 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 jarwrapper all 0.72.9 [21.0 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libapache-pom-java all 18-1 [4676 B] Get: 81 http://deb.debian.org/debian buster/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 82 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get: 84 http://deb.debian.org/debian buster/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libcommons-compress-java all 1.18-2+deb10u1 [531 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libfastutil-java all 8.2.2-1 [15.4 MB] Get: 87 http://deb.debian.org/debian buster/main amd64 libfilesys-df-perl amd64 0.92-6+b4 [12.6 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libguava-java all 19.0-1 [2028 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libmeryl-dev amd64 0~20150903+r2013-6 [53.6 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libssw-java amd64 1.1-2 [13.8 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 mhap all 2.1.3+dfsg-2 [160 kB] Fetched 94.1 MB in 2s (45.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../11-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../12-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package lsb-base. Preparing to unpack .../18-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../19-binfmt-support_2.2.0-2_amd64.deb ... Unpacking binfmt-support (2.2.0-2) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../20-libssl1.1_1.1.1d-0+deb10u5_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u5) ... Selecting previously unselected package openssl. Preparing to unpack .../21-openssl_1.1.1d-0+deb10u5_amd64.deb ... Unpacking openssl (1.1.1d-0+deb10u5) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../22-ca-certificates_20200601~deb10u2_all.deb ... Unpacking ca-certificates (20200601~deb10u2) ... Selecting previously unselected package java-common. Preparing to unpack .../23-java-common_0.71_all.deb ... Unpacking java-common (0.71) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../24-libavahi-common-data_0.7-4+deb10u1_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.7-4+deb10u1) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../25-libavahi-common3_0.7-4+deb10u1_amd64.deb ... Unpacking libavahi-common3:amd64 (0.7-4+deb10u1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../26-libdbus-1-3_1.12.20-0+deb10u1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.12.20-0+deb10u1) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../27-libavahi-client3_0.7-4+deb10u1_amd64.deb ... Unpacking libavahi-client3:amd64 (0.7-4+deb10u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../28-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../29-libkrb5support0_1.17-3+deb10u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../30-libk5crypto3_1.17-3+deb10u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../31-libkrb5-3_1.17-3+deb10u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../32-libgssapi-krb5-2_1.17-3+deb10u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../33-libcups2_2.2.10-6+deb10u4_amd64.deb ... Unpacking libcups2:amd64 (2.2.10-6+deb10u4) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../34-liblcms2-2_2.9-3_amd64.deb ... Unpacking liblcms2-2:amd64 (2.9-3) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../35-libjpeg62-turbo_1%3a1.5.2-2+deb10u1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../36-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../37-libpng16-16_1.6.36-6_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../38-libfreetype6_2.9.1-3+deb10u2_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3+deb10u2) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../39-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../40-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../41-libfontconfig1_2.13.1-2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-2) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../42-libnspr4_2%3a4.20-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.20-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../43-libnss3_2%3a3.42.1-1+deb10u3_amd64.deb ... Unpacking libnss3:amd64 (2:3.42.1-1+deb10u3) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../44-libasound2-data_1.1.8-1_all.deb ... Unpacking libasound2-data (1.1.8-1) ... Selecting previously unselected package libasound2:amd64. Preparing to unpack .../45-libasound2_1.1.8-1_amd64.deb ... Unpacking libasound2:amd64 (1.1.8-1) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../46-libpcsclite1_1.8.24-1_amd64.deb ... Unpacking libpcsclite1:amd64 (1.8.24-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../47-libxau6_1%3a1.0.8-1+b2_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../48-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../49-libxcb1_1.13.1-2_amd64.deb ... Unpacking libxcb1:amd64 (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../50-libx11-data_2%3a1.6.7-1+deb10u1_all.deb ... Unpacking libx11-data (2:1.6.7-1+deb10u1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../51-libx11-6_2%3a1.6.7-1+deb10u1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.7-1+deb10u1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../52-libxext6_2%3a1.3.3-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1+b2) ... Selecting previously unselected package libxi6:amd64. Preparing to unpack .../53-libxi6_2%3a1.7.9-1_amd64.deb ... Unpacking libxi6:amd64 (2:1.7.9-1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../54-libxrender1_1%3a0.9.10-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../55-x11-common_1%3a7.7+19_all.deb ... Unpacking x11-common (1:7.7+19) ... Selecting previously unselected package libxtst6:amd64. Preparing to unpack .../56-libxtst6_2%3a1.2.3-1_amd64.deb ... Unpacking libxtst6:amd64 (2:1.2.3-1) ... Selecting previously unselected package openjdk-11-jre-headless:amd64. Preparing to unpack .../57-openjdk-11-jre-headless_11.0.9.1+1-1~deb10u2_amd64.deb ... Unpacking openjdk-11-jre-headless:amd64 (11.0.9.1+1-1~deb10u2) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../58-default-jre-headless_2%3a1.11-71_amd64.deb ... Unpacking default-jre-headless (2:1.11-71) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../59-ca-certificates-java_20190405_all.deb ... Unpacking ca-certificates-java (20190405) ... Selecting previously unselected package libtool. Preparing to unpack .../60-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../61-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../62-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../63-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../64-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../65-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../66-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../67-libglib2.0-0_2.58.3-2+deb10u2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../68-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../69-libxml2_2.9.4+dfsg1-7+deb10u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../70-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../71-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../72-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../73-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../74-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../75-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package fastjar. Preparing to unpack .../76-fastjar_2%3a0.98-6+b1_amd64.deb ... Unpacking fastjar (2:0.98-6+b1) ... Selecting previously unselected package jaligner. Preparing to unpack .../77-jaligner_1.0+dfsg-6_all.deb ... Unpacking jaligner (1.0+dfsg-6) ... Selecting previously unselected package jarwrapper. Preparing to unpack .../78-jarwrapper_0.72.9_all.deb ... Unpacking jarwrapper (0.72.9) ... 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Setting up libfilesys-df-perl (0.92-6+b4) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libssw-java (1.1-2) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u1) ... Setting up libasound2-data (1.1.8-1) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up libx11-data (2:1.6.7-1+deb10u1) ... Setting up libnspr4:amd64 (2:4.20-1) ... Setting up libapache-pom-java (18-1) ... Setting up libavahi-common-data:amd64 (0.7-4+deb10u1) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:amd64 (1.12.20-0+deb10u1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up libmeryl-dev (0~20150903+r2013-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up binfmt-support (2.2.0-2) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up fonts-dejavu-core (2.37-1) ... Setting up libpcsclite1:amd64 (1.8.24-1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libasound2:amd64 (1.1.8-1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u1) ... Setting up libboost-dev:amd64 (1.67.0.1) ... Setting up openssl (1.1.1d-0+deb10u5) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up jarwrapper (0.72.9) ... Setting up libtool (2.4.6-9) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:amd64 (0.7-4+deb10u1) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libfreetype6:amd64 (2.9.1-3+deb10u2) ... Setting up libguava-java (19.0-1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u1) ... Setting up libavahi-client3:amd64 (0.7-4+deb10u1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libcommons-compress-java (1.18-2+deb10u1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libcups2:amd64 (2.2.10-6+deb10u4) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Taiwan_GRCA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up default-jre-headless (2:1.11-71) ... Setting up debhelper (12.1.1) ... Setting up jaligner (1.0+dfsg-6) ... Setting up mhap (2.1.3+dfsg-2) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Setting up openjdk-11-jre-headless:amd64 (11.0.9.1+1-1~deb10u2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/canu-1.8+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 1.8+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=src/ dh_auto_clean -O--sourcedirectory=src/ cd src && make -j15 clean make[1]: Entering directory '/build/canu-1.8+dfsg/src' WARNING: WARNING: g++ 8 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: Building for 'Linux' '4.19.0-16-amd64' as 'amd64' into '/build/canu-1.8+dfsg/Linux-amd64/{bin,obj}'. Using '/usr/bin/g++' version '8'. rm -f /build/canu-1.8+dfsg/Linux-amd64/lib/libcanu.a /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreEncode.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStorePartition.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-applyAlignment.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-baseCall.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/dumpBlob /build/canu-1.8+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreBuild /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreConfig /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreBucketizer /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreSorter /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreIndexer /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreDump /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreStats /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/sqStoreCreate /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/sqStoreCreatePartition /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreatePartition/stores/sqStoreCreatePartition.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/sqStoreDumpFASTQ /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/sqStoreDumpMetaData /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/tgStoreCompress /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/tgStoreDump /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/tgStoreLoad /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/tgStoreFilter /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/tgStoreCoverageStat /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCoverageStat/stores/tgStoreCoverageStat.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/tgTigDisplay /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/loadCorrectedReads /build/canu-1.8+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/loadTrimmedReads /build/canu-1.8+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/loadErates /build/canu-1.8+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/meryl /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/sequence /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/overlapInCore /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/overlapInCorePartition /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/overlapConvert /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/overlapImport /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/overlapPair /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/edalign /build/canu-1.8+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/prefixEditDistance-matchLimitGenerate /build/canu-1.8+dfsg/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/mhapConvert /build/canu-1.8+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/mmapConvert /build/canu-1.8+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/wtdbgConvert /build/canu-1.8+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/filterCorrectionOverlaps /build/canu-1.8+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/generateCorrectionLayouts /build/canu-1.8+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/filterCorrectionLayouts /build/canu-1.8+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/falconsense /build/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/readConsensus /build/canu-1.8+dfsg/Linux-amd64/obj/bin/readConsensus/correction/readConsensus.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/errorEstimate /build/canu-1.8+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/splitHaplotype /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/trimReads /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-quality.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/splitReads /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/findErrors /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/findErrors-Dump /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/correctOverlaps /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/bogart /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/bogus /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogus.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogusUtil.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/utgcns /build/canu-1.8+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/utgcns.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/alignGFA /build/canu-1.8+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/fastqAnalyze /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqAnalyze/fastq-utilities/fastqAnalyze.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/fastqSample /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSample/fastq-utilities/fastqSample.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/fastqSimulate /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate/fastq-utilities/fastqSimulate.[doP] rm -f /build/canu-1.8+dfsg/Linux-amd64/bin/fastqSimulate-sort /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate-sort/fastq-utilities/fastqSimulate-sort.[doP] make[1]: Leaving directory '/build/canu-1.8+dfsg/src' dh_autoreconf_clean -O--sourcedirectory=src/ dh_clean -O--sourcedirectory=src/ debian/rules build dh build --sourcedirectory=src/ dh_update_autotools_config -O--sourcedirectory=src/ dh_autoreconf -O--sourcedirectory=src/ dh_auto_configure -O--sourcedirectory=src/ debian/rules override_dh_auto_build make[1]: Entering directory '/build/canu-1.8+dfsg' dh_auto_build cd src && make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/canu-1.8+dfsg/src' WARNING: WARNING: g++ 8 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: Building for 'Linux' '4.19.0-16-amd64' as 'amd64' into '/build/canu-1.8+dfsg/Linux-amd64/{bin,obj}'. Using '/usr/bin/g++' version '8'. g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-compressed.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-buffered.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-memoryMapped.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/strings.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/system.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/system-stackTrace.C Building release v1.8 g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/sequence.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-reader.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer-block.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer-stream.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-statistics.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-exact.C utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] #warning how to set prefix size for streaming operations? ^~~~~~~ utility/files-memoryMapped.C: In constructor 'memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)': utility/files-memoryMapped.C:76:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] read(_fd, _data, _length); ~~~~^~~~~~~~~~~~~~~~~~~~~ utility/files-memoryMapped.C: In destructor 'memoryMappedFile::~memoryMappedFile()': utility/files-memoryMapped.C:102:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] write(_fd, _data, _length), close(_fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from utility/sequence.H:29, from utility/sequence.C:30: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = dnaSeqIndexEntry; LL = long unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:131:15: required from 'void increaseArray(TT*&, uint64, LL&, uint64) [with TT = dnaSeqIndexEntry; LL = long unsigned int; uint64 = long unsigned int]' utility/sequence.C:301:56: required from here utility/arrays.H:109:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class dnaSeqIndexEntry'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(copy, array, sizeof(TT) * arrayLen); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utility/sequence.C:154:7: note: 'class dnaSeqIndexEntry' declared here class dnaSeqIndexEntry { ^~~~~~~~~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from utility/sequence.H:29, from utility/sequence.C:30: utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class dnaSeqIndexEntry'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utility/sequence.C:154:7: note: 'class dnaSeqIndexEntry' declared here class dnaSeqIndexEntry { ^~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/bits.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/hexDump.C utility/kmers-writer.C: In destructor 'kmerCountFileWriter::~kmerCountFileWriter()': utility/kmers-writer.C:136:29: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from utility/kmers.H:29, from utility/kmers-writer.C:26: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/md5.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/mt19937ar.C utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': utility/kmers-reader.C:39:29: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from utility/kmers.H:29, from utility/kmers-reader.C:26: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)', declared with attribute warn_unused_result [-Wunused-result] symlink(pathToFile, pathToLink); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector&)': utility/files.C:509:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, FILENAME_MAX, F); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ utility/files.C:515:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, FILENAME_MAX, F); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/objectStore.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/speedCounter.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/sweatShop.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/computeGlobalScore.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/falconConsensus.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqLibrary.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStore.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreConstructor.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreInfo.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreEncode.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreEncode.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStorePartition.C correction/computeGlobalScore.C: In member function 'uint16 globalScore::compute(uint32, ovOverlap*, uint32, uint32, uint16*)': correction/computeGlobalScore.C:150:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (logFile) ^ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovOverlap.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStore.C stores/ovOverlap.C:184:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING ^~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreWriter.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreFilter.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from stores/sqStore.H:37, from stores/sqStore.C:38: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = sqLibrary; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:131:15: required from 'void increaseArray(TT*&, uint64, LL&, uint64) [with TT = sqLibrary; LL = unsigned int; uint64 = long unsigned int]' stores/sqStore.C:582:78: required from here utility/arrays.H:109:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class sqLibrary'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(copy, array, sizeof(TT) * arrayLen); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/sqStore.H:86, from stores/sqStore.C:38: stores/sqLibrary.H:66:7: note: 'class sqLibrary' declared here class sqLibrary { ^~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from stores/sqStore.H:37, from stores/sqStore.C:38: utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class sqLibrary'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/sqStore.H:86, from stores/sqStore.C:38: stores/sqLibrary.H:66:7: note: 'class sqLibrary' declared here class sqLibrary { ^~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from stores/sqStore.H:37, from stores/sqStore.C:38: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = sqRead; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:131:15: required from 'void increaseArray(TT*&, uint64, LL&, uint64) [with TT = sqRead; LL = unsigned int; uint64 = long unsigned int]' stores/sqStore.C:631:88: required from here utility/arrays.H:109:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class sqRead'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(copy, array, sizeof(TT) * arrayLen); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/sqStore.H:87, from stores/sqStore.C:38: stores/sqRead.H:206:7: note: 'class sqRead' declared here class sqRead { ^~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from stores/sqStore.H:37, from stores/sqStore.C:38: utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class sqRead'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/sqStore.H:87, from stores/sqStore.C:38: stores/sqRead.H:206:7: note: 'class sqRead' declared here class sqRead { ^~~~~~ stores/ovStoreWriter.C:69:2: warning: #warning not failing if a valid store [-Wcpp] #warning not failing if a valid store ^~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreFile.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreHistogram.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgStore.C stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:252:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V); In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 13 and 4109 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:260:32: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(No, FILENAME_MAX, "%s/libraries", _storePath); ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:261:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/libraries", _storePath, V); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:264:32: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(No, FILENAME_MAX, "%s/reads", _storePath); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:265:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads", _storePath, V); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 19 and 4122 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:268:32: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(No, FILENAME_MAX, "%s/info", _storePath); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:269:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info", _storePath, V); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 18 and 4121 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:272:32: warning: '/info.txt' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(No, FILENAME_MAX, "%s/info.txt", _storePath); ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 10 and 4106 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:273:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info.txt", _storePath, V); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4125 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:255:34: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V); stores/sqStoreConstructor.C:255:34: note: using the range [0, 4294967295] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 13 and 4116 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_deletePartitions()': stores/sqStoreConstructor.C:399:32: warning: '/partitions/map' directive output may be truncated writing 15 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s/partitions/map", _storePath); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4112 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:417:34: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s/partitions/reads.%04u", _storePath, ii+1); AS_UTL_unlink(path); ^~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:417:34: note: using the range [0, 4294967295] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:418:34: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s/partitions/blobs.%04u", _storePath, ii+1); AS_UTL_unlink(path); ^~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:418:34: note: using the range [0, 4294967295] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:423:32: warning: '/partitions' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s/partitions", _storePath); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:385:32: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s/info", _storePath); AS_UTL_unlink(path); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:386:32: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s/libraries", _storePath); AS_UTL_unlink(path); ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:387:32: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s/reads", _storePath); AS_UTL_unlink(path); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:388:32: warning: '/blobs' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s/blobs", _storePath); AS_UTL_unlink(path); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/sqStore.H:89, from stores/sqStore.C:38: stores/sqStoreBlobWriter.H: In member function 'void sqStore::sqStore_stashReadData(sqReadData*)': stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount); stores/sqStoreBlobWriter.H:68:39: note: using the range [0, 4294967295] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStore.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStorePartition.C: In member function 'void sqStore::sqStore_buildPartitions(uint32*)': stores/sqStorePartition.C:93:32: warning: '/partitions' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/partitions", _clonePath); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStorePartition.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStorePartition.C:106:34: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i); ^~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStorePartition.C:106:34: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStorePartition.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStorePartition.C:110:34: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i); ^~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStorePartition.C:110:34: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStorePartition.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/sqStore.H:88, from stores/sqStorePartition.C:38: stores/sqStoreBlobReader.H:66:33: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s/blobs.%04u", storePath, file); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStorePartition.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStorePartition.C:197:34: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i); ^~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStorePartition.C:197:34: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStorePartition.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStorePartition.C:200:34: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i); ^~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStorePartition.C:200:34: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStorePartition.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In constructor 'sqStore::sqStore(const char*, const char*, sqStore_mode, uint32)': stores/sqStoreConstructor.C:109:33: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(nameI, FILENAME_MAX, "%s/info", _storePath); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:202:33: warning: '/partitions/map' directive output may be truncated writing 15 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(nameI, FILENAME_MAX, "%s/partitions/map", _storePath); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4112 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:221:33: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(nameL, FILENAME_MAX, "%s/libraries", _storePath); ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:222:33: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(nameR, FILENAME_MAX, "%s/partitions/reads.%04" F_U32P, _storePath, partID); stores/sqStoreConstructor.C:222:33: note: directive argument in the range [0, 4294967294] In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C:223:33: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(nameB, FILENAME_MAX, "%s/partitions/blobs.%04" F_U32P, _storePath, partID); stores/sqStoreConstructor.C:223:33: note: directive argument in the range [0, 4294967294] In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/sqStore.H:89, from stores/sqStoreConstructor.C:38: stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount); In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/sqStore.H:89, from stores/sqStoreConstructor.C:38: stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount); In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTig.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc In file included from stores/ovStore.C:55: stores/ovStore.H: In constructor 'ovStore::ovStore(const char*, sqStore*)': stores/ovStore.H:77:36: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/info", path); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStore.C:55: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStore.C:105:32: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/evalues", _storePath); ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStore.C:55: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapErrorAdjustment/analyzeAlignment.C stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': stores/ovStoreWriter.C:226:34: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C:235:34: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)': stores/ovStoreWriter.C:258:32: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': stores/ovStoreWriter.C:342:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/ovStoreWriter.C:54: stores/ovStore.H:104:36: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index); ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C stores/ovStoreHistogram.C: In member function 'void ovStoreHistogram::mergeScores(ovStoreHistogram*)': stores/ovStoreHistogram.C:303:80: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class oSH_ovlSco'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] sizeof(oSH_ovlSco) * (other->_scoresLastID - other->_scoresBaseID + 1)); ^ In file included from stores/ovStoreHistogram.C:30: stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here class oSH_ovlSco { ^~~~~~~~~~ In file included from stores/ovStoreWriter.C:54: stores/ovStore.H: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': stores/ovStore.H:79:36: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index); ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C:402:39: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/ovStoreWriter.C:54: stores/ovStore.H:102:36: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/info", path); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from stores/ovStoreHistogram.H:33, from stores/ovStoreHistogram.C:30: utility/arrays.H: In instantiation of 'void allocateArray(TT*&, LL, uint32) [with TT = oSH_ovlSco; LL = unsigned int; uint32 = unsigned int]': stores/ovStoreHistogram.C:282:62: required from here utility/arrays.H:54:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class oSH_ovlSco'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array, 0, sizeof(TT) * arrayMax); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/ovStoreHistogram.C:30: stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here class oSH_ovlSco { ^~~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from stores/ovStoreHistogram.H:33, from stores/ovStoreHistogram.C:30: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = oSH_ovlSco; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:145:15: required from 'void resizeArray(TT*&, uint64, LL&, uint64, uint32) [with TT = oSH_ovlSco; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]' stores/ovStoreHistogram.C:318:112: required from here utility/arrays.H:109:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class oSH_ovlSco'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(copy, array, sizeof(TT) * arrayLen); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/ovStoreHistogram.C:30: stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here class oSH_ovlSco { ^~~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from stores/ovStoreHistogram.H:33, from stores/ovStoreHistogram.C:30: utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class oSH_ovlSco'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/ovStoreHistogram.C:30: stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here class oSH_ovlSco { ^~~~~~~~~~ In file included from stores/ovStore.H:43, from stores/ovStoreFile.C:47: stores/ovStoreFile.H: In member function 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)': stores/ovStoreFile.H:89:37: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_name, FILENAME_MAX, "%s.oc", prefix); ^~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreFile.C:47: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::insertTig(tgTig*, bool)': stores/tgStore.C:336:71: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct tgStore::tgStoreEntry'; use assignment or value-initialization instead [-Wclass-memaccess] memset(nr + _tigLen, 0, sizeof(tgStoreEntry) * (_tigMax - _tigLen)); ^ In file included from stores/tgStore.C:44: stores/tgStore.H:134:10: note: 'struct tgStore::tgStoreEntry' declared here struct tgStoreEntry { ^~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)': stores/tgStore.C:634:42: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct tgStore::tgStoreEntry'; use assignment or value-initialization instead [-Wclass-memaccess] memset(R, 0, sizeof(tgStoreEntry) * M); ^ In file included from stores/tgStore.C:44: stores/tgStore.H:134:10: note: 'struct tgStore::tgStoreEntry' declared here struct tgStoreEntry { ^~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeOverlapSlice()': stores/ovStoreWriter.C:484:34: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum); ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::checkSortingIsComplete()': stores/ovStoreWriter.C:503:35: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(nameF, FILENAME_MAX, "%s/%04u.info", _storePath, i); ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C:504:35: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(nameI, FILENAME_MAX, "%s/%04u.index", _storePath, i); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:535:34: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C:538:34: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/%04u.info", _storePath, ss); ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C:555:34: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, bb); ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C:559:36: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, ss); ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C:563:34: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u", _storePath, bb); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, from stores/ovStoreWriter.C:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from stores/tgTig.H:33, from stores/tgTig.C:34: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:145:15: required from 'void resizeArray(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]' stores/tgTig.C:455:87: required from here utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class tgPosition'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.C:34: stores/tgTig.H:87:7: note: 'class tgPosition' declared here class tgPosition { ^~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)': stores/tgStore.C:191:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); ^~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:191:33: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/tgStore.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:192:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); ^~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:192:33: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/tgStore.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:193:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); ^~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:193:33: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/tgStore.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStore::tgStoreEntry*&, uint32&, uint32)': stores/tgStore.C:594:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); ^~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:594:33: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/tgStore.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)': stores/tgStore.C:626:37: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i); ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/tgStore.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:637:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); ^~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:637:33: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/tgStore.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:641:35: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); ^~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:641:35: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/tgStore.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': stores/tgTig.C:560:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(LINE, LINEmax, F); LINEnum++; ~~~~~^~~~~~~~~~~~~~~~~~ stores/tgTig.C:687:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(LINE, LINEmax, F); LINEnum++; ~~~~~^~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)': stores/tgStore.C:695:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); ^~~~~~~~~~~~~~~~~~~~ stores/tgStore.C:695:33: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/tgStore.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/libedlib/edlib.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-addRead.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-appendBases.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-applyAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-applyAlignment.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-baseCall.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-baseCall.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-mergeRefine.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-refine.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-refreshMultiAlign.C utgcns/libcns/abAbacus-refine.C:1326:2: warning: #warning SKIPPING ALL REFINEMENTS [-Wcpp] #warning SKIPPING ALL REFINEMENTS ^~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abColumn.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abMultiAlign.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from utgcns/libcns/abAbacus.H:60, from utgcns/libcns/abAbacus-applyAlignment.C:65: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = abBead; LL = short unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:131:15: required from 'void increaseArray(TT*&, uint64, LL&, uint64) [with TT = abBead; LL = short unsigned int; uint64 = long unsigned int]' utgcns/libcns/abAbacus-applyAlignment.C:440:48: required from here utility/arrays.H:109:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class abBead'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(copy, array, sizeof(TT) * arrayLen); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from utgcns/libcns/abAbacus.H:94, from utgcns/libcns/abAbacus-applyAlignment.C:65: utgcns/libcns/abBead.H:61:7: note: 'class abBead' declared here class abBead { ^~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from utgcns/libcns/abAbacus.H:60, from utgcns/libcns/abAbacus-applyAlignment.C:65: utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class abBead'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from utgcns/libcns/abAbacus.H:94, from utgcns/libcns/abAbacus-applyAlignment.C:65: utgcns/libcns/abBead.H:61:7: note: 'class abBead' declared here class abBead { ^~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/unitigConsensus.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from utgcns/libcns/abAbacus.H:60, from utgcns/libcns/abAbacus-mergeRefine.C:65: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = abBead; LL = short unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:131:15: required from 'void increaseArray(TT*&, uint64, LL&, uint64) [with TT = abBead; LL = short unsigned int; uint64 = long unsigned int]' utgcns/libcns/abAbacus-mergeRefine.C:74:48: required from here utility/arrays.H:109:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class abBead'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(copy, array, sizeof(TT) * arrayLen); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from utgcns/libcns/abAbacus.H:94, from utgcns/libcns/abAbacus-mergeRefine.C:65: utgcns/libcns/abBead.H:61:7: note: 'class abBead' declared here class abBead { ^~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from utgcns/libcns/abAbacus.H:60, from utgcns/libcns/abAbacus-mergeRefine.C:65: utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class abBead'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from utgcns/libcns/abAbacus.H:94, from utgcns/libcns/abAbacus-mergeRefine.C:65: utgcns/libcns/abBead.H:61:7: note: 'class abBead' declared here class abBead { ^~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap gfa/gfa.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap gfa/bed.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/dumpBlob.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/ovStoreBuild.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/ovStoreConfig.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/ovStoreBucketizer.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/ovStoreSorter.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/ovStoreIndexer.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/ovStoreDump.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/ovStoreStats.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/sqStoreCreate.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreatePartition/stores/sqStoreCreatePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/sqStoreCreatePartition.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/sqStoreDumpMetaData.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreCompress.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreDump.C stores/sqStoreCreate.C: In function 'uint32 loadFASTA(char*, char*, char*, uint32&, uint8*, compressedFileReader*, FILE*, uint32&)': stores/sqStoreCreate.C:99:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, AS_MAX_READLEN+1, F->file()); nLines++; ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreCreate.C:154:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, AS_MAX_READLEN+1, F->file()); nLines++; ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreCreate.C: In function 'uint32 loadFASTQ(char*, char*, char*, uint32&, uint8*, compressedFileReader*, FILE*, uint32&)': stores/sqStoreCreate.C:212:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(S, AS_MAX_READLEN+1, F->file()); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreCreate.C:225:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(overflow, 1048576, F->file()); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreCreate.C:278:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, AS_MAX_READLEN+1, F->file()); // NOTE: Using L, not Q, since L is char and Q is uint8 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreCreate.C:279:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, AS_MAX_READLEN+1, F->file()); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreCreate.C:291:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(overflow, 1048576, F->file()); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreCreate.C: In function 'void loadReads(sqStore*, sqLibrary*, uint32, uint32, FILE*, FILE*, FILE*, char*, uint32&, uint32&, uint64&, uint32&, uint64&)': stores/sqStoreCreate.C:410:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, AS_MAX_READLEN+1, F->file()); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreCreate.C:483:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, AS_MAX_READLEN+1, F->file()); lineNumber++; ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C: In function 'int main(int, char**)': stores/sqStoreDumpFASTQ.C:498:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (dumpFASTA) // Dear GCC: I'm NOT ambiguous ^ stores/sqStoreDumpFASTQ.C:508:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (dumpFASTQ) // Dear GCC: I'm NOT ambiguous ^ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgTigSizeAnalysis.C stores/tgStoreDump.C:677:2: warning: #warning replace this with genericStatistics [-Wcpp] #warning replace this with genericStatistics ^~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreLoad.C stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTQ()': stores/sqStoreDumpFASTQ.C:88:33: warning: '.fastq' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s.fastq%s", _p, _s); ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStoreDumpFASTQ.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 8197 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C:86:33: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s.%s.fastq%s", _p, _n, _s); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStoreDumpFASTQ.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 8 and 12293 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTA()': stores/sqStoreDumpFASTQ.C:118:33: warning: '.fasta' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s.fasta%s", _p, _s); ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStoreDumpFASTQ.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 8197 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C:116:33: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s.%s.fasta%s", _p, _n, _s); ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStoreDumpFASTQ.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 8 and 12293 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreDump.C: In member function 'void dumpParameters::loadBogartStatus(const char*, uint32)': stores/ovStoreDump.C:283:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(NN, FILENAME_MAX, E); ~~~~~^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreDump.C:299:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(NN, FILENAME_MAX, E); ~~~~~^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreDump.C:305:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(NN, FILENAME_MAX, S); ~~~~~^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreDump.C:321:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(NN, FILENAME_MAX, S); ~~~~~^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreDump.C:327:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(NN, FILENAME_MAX, G); ~~~~~^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreDump.C:343:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(NN, FILENAME_MAX, G); ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreFilter.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCoverageStat/stores/tgStoreCoverageStat.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreCoverageStat.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgTigDisplay.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/loadCorrectedReads.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/loadErates.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/meryl.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylCountArray.C meryl/meryl.C:265:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] #warning HARD CODED NUMBER OF FILES! ^~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylInput.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-count.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp.C meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp] #warning "need to decide whic direction we're going?" ^~~~~~~ meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp] #warning "rounding issues in word-frequency!" ^~~~~~~ meryl/meryl.C: In member function 'void merylOpStack::addPrinter(char*)': meryl/meryl.C:197:35: warning: '%0*d' directive output may be truncated writing 1 or more bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s%0*d%s", pre, len, ff, suf); ^~~~~~~~~~ meryl/meryl.C:197:35: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from meryl/meryl.H:49, from meryl/meryl.C:46: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output 2 or more bytes (assuming 4098) into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Isequence -I/build/canu-1.8+dfsg/src -Iutility sequence/sequence.C meryl/meryl.C: In function 'int main(int, char**)': meryl/meryl.C:415:27: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 1006 [-Wformat-truncation=] snprintf(s, 1024, "Requested memory '%s' (GB) is more than physical memory %.2f GB.", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ optString, physMemory / 1024.0 / 1024.0 / 1024.0); ~~~~~~~~~ meryl/meryl.C:415:27: note: assuming directive output of 4 bytes In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from meryl/meryl.H:49, from meryl/meryl.C:46: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 62 and 4468 bytes into a destination of size 1024 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/meryl.C:594:25: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 996 [-Wformat-truncation=] snprintf(s, 1024, "Don't know what to do with '%s'.", optString); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from meryl/meryl.H:49, from meryl/meryl.C:46: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector&)': stores/loadErates.C:85:38: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath); ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/loadErates.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 17 and 4113 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/loadErates.C:86:38: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(evalueName, FILENAME_MAX, "%s/evalues", _storePath); ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/loadErates.C:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()': overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 1024, F); ~~~~~^~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C overlapInCore/overlapPair.C:479:2: warning: #warning do we need to check for contained too? [-Wcpp] #warning do we need to check for contained too? ^~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C overlapInCore/overlapImport.C: In function 'int main(int, char**)': overlapInCore/overlapImport.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(S, 1024, in->file()); ~~~~~^~~~~~~~~~~~~~~~~~~~~ overlapInCore/overlapImport.C:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(S, 1024, in->file()); ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)': overlapInCore/edalign.C:37:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, lineMax, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from wtdbg/wtdbgConvert.C:30: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:145:15: required from 'void resizeArray(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]' wtdbg/wtdbgConvert.C:51:110: required from here utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class tgPosition'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgStore.H:43, from wtdbg/wtdbgConvert.C:33: stores/tgTig.H:87:7: note: 'class tgPosition' declared here class tgPosition { ^~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/readConsensus/correction/readConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/readConsensus.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from correction/generateCorrectionLayouts.C:34: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:145:15: required from 'void resizeArray(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]' correction/generateCorrectionLayouts.C:98:107: required from here utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class tgPosition'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgStore.H:43, from correction/generateCorrectionLayouts.C:37: stores/tgTig.H:87:7: note: 'class tgPosition' declared here class tgPosition { ^~~~~~~~~~ correction/falconsense.C: In function 'void loadReadList(char*, uint32, uint32, std::set&)': correction/falconsense.C:64:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] for (fgets(L, 1024, R); ~~~~~^~~~~~~~~~~~ correction/falconsense.C:66:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, 1024, R)) { ~~~~~^~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-quality.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-quality.C In file included from overlapBasedTrimming/trimReads.C:31: overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)': overlapBasedTrimming/trimStat.H:78:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(N); ~~~~~~^~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/bogart.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C bogart/AS_BAT_BestOverlapGraph.C:858:2: warning: #warning what is the error rate of the 'best contained' overlap? [-Wcpp] #warning what is the error rate of the 'best contained' overlap? ^~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] #warning deviationGraph hard coded ^~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C bogart/AS_BAT_BestOverlapGraph.C: In member function 'void BestOverlapGraph::findEdges()': bogart/AS_BAT_BestOverlapGraph.C:434:57: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class BestOverlaps'; use assignment or value-initialization instead [-Wclass-memaccess] memset(_bestA, 0, sizeof(BestOverlaps) * (fiLimit + 1)); ^ In file included from bogart/AS_BAT_BestOverlapGraph.C:43: bogart/AS_BAT_BestOverlapGraph.H:158:7: note: 'class BestOverlaps' declared here class BestOverlaps { ^~~~~~~~~~~~ bogart/AS_BAT_BestOverlapGraph.C:435:57: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class BestScores'; use assignment or value-initialization instead [-Wclass-memaccess] memset(_scorA, 0, sizeof(BestScores) * (fiLimit + 1)); ^ In file included from bogart/AS_BAT_BestOverlapGraph.C:43: bogart/AS_BAT_BestOverlapGraph.H:166:7: note: 'class BestScores' declared here class BestScores { ^~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C bogart/AS_BAT_Logging.C: In member function 'void logFileInstance::open()': bogart/AS_BAT_Logging.C:91:34: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); ^~~~~~~~~~~~~~~~ bogart/AS_BAT_Logging.C:91:34: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from bogart/AS_BAT_Logging.H:41, from bogart/AS_BAT_Logging.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4115 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from bogart/AS_BAT_ReadInfo.H:29, from bogart/AS_BAT_Outputs.C:42: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': utility/arrays.H:145:15: required from 'void resizeArray(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]' bogart/AS_BAT_Outputs.C:92:112: required from here utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class tgPosition'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgStore.H:43, from bogart/AS_BAT_Outputs.C:51: stores/tgTig.H:87:7: note: 'class tgPosition' declared here class tgPosition { ^~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C bogart/AS_BAT_PlaceContains.C: In function 'void placeUnplacedUsingAllOverlaps(TigVector&, const char*)': bogart/AS_BAT_PlaceContains.C:96:66: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class SeqInterval'; use assignment or value-initialization instead [-Wclass-memaccess] memset(placedPos, 0, sizeof(SeqInterval) * (RI->numReads() + 1)); ^ In file included from bogart/AS_BAT_PlaceContains.C:43: bogart/AS_BAT_Unitig.H:58:7: note: 'class SeqInterval' declared here class SeqInterval { ^~~~~~~~~~~ bogart/AS_BAT_PlaceContains.C:108:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (tigs.inUnitig(fid) == 0) // I'm NOT ambiguous! ^ bogart/AS_BAT_PlaceReadUsingOverlaps.C: In function 'bool placeReadUsingOverlaps(TigVector&, Unitig*, uint32, std::vector&, uint32)': bogart/AS_BAT_PlaceReadUsingOverlaps.C:543:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (logFileFlagSet(LOG_PLACE_READ)) // Nope, not ambiguous. ^ bogart/AS_BAT_PopulateUnitig.C: In function 'void populateUnitig(Unitig*, BestEdgeOverlap*)': bogart/AS_BAT_PopulateUnitig.C:101:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (logFileFlagSet(LOG_BUILD_UNITIG)) ^ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogus/bogus.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogus/bogusUtil.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost utgcns/utgcns.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost utgcns/stashContains.C bogus/bogusUtil.C: In function 'void loadNucmer(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': bogus/bogusUtil.C:125:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(inLine, 1024, inFile); // (file paths) ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:126:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(inLine, 1024, inFile); // NUCMER ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:127:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(inLine, 1024, inFile); // (blank) ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:128:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(inLine, 1024, inFile); // (header) ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:142:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(inLine, 1024, inFile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:200:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(inLine, 1024, inFile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C: In function 'void loadSnapper(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': bogus/bogusUtil.C:226:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(inLine, 1024, inFile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(inLine, 1024, inFile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C: In function 'void loadReferenceSequence(char*, std::vector&, std::map, unsigned int>&)': bogus/bogusUtil.C:300:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(refhdr, 1024, F); chomp(refhdr); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:301:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:326:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(refhdr, 1024, F); chomp(refhdr); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqAnalyze/fastq-utilities/fastqAnalyze.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqAnalyze.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSample/fastq-utilities/fastqSample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqSample.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate/fastq-utilities/fastqSimulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqSimulate.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate-sort/fastq-utilities/fastqSimulate-sort.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqSimulate-sort.C cp -pf pipelines/canu.pl /build/canu-1.8+dfsg/Linux-amd64/bin/canu chmod +x /build/canu-1.8+dfsg/Linux-amd64/bin/canu echo > /build/canu-1.8+dfsg/Linux-amd64/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." chmod -x /build/canu-1.8+dfsg/Linux-amd64/bin/canu.defaults cp -pf pipelines/canu/Consensus.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/CorrectReads.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Configure.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Defaults.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Execution.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/SequenceStore.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_LSF.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_SGE.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Meryl.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Output.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapInCore.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMhap.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMMap.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapStore.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Report.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Unitig.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ fastq-utilities/fastqAnalyze.C: In function 'void doStats(char*, char*)': fastq-utilities/fastqAnalyze.C:185:25: warning: conversion from 'long unsigned int' to 'uint32' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] uint32 minLen = UINT64_MAX; ^~~~~~~~~~ gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': gfa/alignGFA.C:151:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(Pfile); ~~~~~~^~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap AS_global.C gfa/alignGFA.C:129:18: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] sprintf(Pname, "plot-%s-%s", Aname, Bname); ^~~~~~~~~~~~ ~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from gfa/alignGFA.C:26: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 8199 bytes into a destination of size 4097 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gfa/alignGFA.C:130:18: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] sprintf(Pfile, "plot-%s-%s.sh", Aname, Bname); ^~~~~~~~~~~~~~~ ~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from gfa/alignGFA.C:26: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 10 and 8202 bytes into a destination of size 4097 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gfa/alignGFA.C:149:18: warning: '%s' directive writing up to 4096 bytes into a region of size 4089 [-Wformat-overflow=] sprintf(Pfile, "sh plot-%s-%s.sh", Aname, Bname); ^~~~~~~~~~~~~~~~~~ ~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from gfa/alignGFA.C:26: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 13 and 8205 bytes into a destination of size 4097 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:128:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(A, MAX_READ_LEN, F); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:129:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(B, MAX_READ_LEN, F); chomp(B); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:130:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(C, MAX_READ_LEN, F); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:131:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(D, MAX_READ_LEN, F); chomp(D); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C: In function 'void doAnalyzeQV(char*, bool&, bool&, bool&)': fastq-utilities/fastqAnalyze.C:295:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(A, MAX_READ_LEN, F); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:296:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(B, MAX_READ_LEN, F); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:297:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(C, MAX_READ_LEN, F); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:298:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(D, MAX_READ_LEN, F); chomp(D); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C: In function 'void doTransformQV(char*, char*, bool, bool, bool)': fastq-utilities/fastqAnalyze.C:407:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(A, MAX_READ_LEN, F); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:408:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(B, MAX_READ_LEN, F); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:409:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(C, MAX_READ_LEN, F); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqAnalyze.C:410:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(D, MAX_READ_LEN, F); chomp(D); ~~~~~^~~~~~~~~~~~~~~~~~~~ fastq-utilities/fastqSample.C: In member function 'bool aRead::read(FILE*)': fastq-utilities/fastqSample.C:72:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(a, MAXLEN, F); ~~~~~^~~~~~~~~~~~~~ fastq-utilities/fastqSample.C:73:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(b, MAXLEN, F); ~~~~~^~~~~~~~~~~~~~ fastq-utilities/fastqSample.C:74:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(c, MAXLEN, F); ~~~~~^~~~~~~~~~~~~~ fastq-utilities/fastqSample.C:75:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(d, MAXLEN, F); ~~~~~^~~~~~~~~~~~~~ fastq-utilities/fastqSimulate.C: In function 'int main(int, char**)': fastq-utilities/fastqSimulate.C:1097:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(seq + seqLen, seqMax - seqLen, fastaFile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AS_global.C: In function 'int AS_configure(int, char**)': AS_global.C:161:29: warning: '%lu' directive output may be truncated writing between 1 and 20 bytes into a region of size between 0 and 4095 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s/" F_U64 "_%s_" F_U64 "_%s", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AS_global.C:161:29: note: using the range [0, 18446744073709551615] for directive argument In file included from /usr/include/stdio.h:873, from AS_global.H:75, from AS_global.C:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output 7 or more bytes (assuming 5125) into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar rv /build/canu-1.8+dfsg/Linux-amd64/lib/libcanu.a /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreEncode.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStorePartition.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-applyAlignment.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-baseCall.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o ar: creating /build/canu-1.8+dfsg/Linux-amd64/lib/libcanu.a a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreEncode.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStorePartition.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEdfastq-utilities/fastqSimulate-sort.C: In function 'char* readRead(FILE*, uint32&, uint32&, uint32&)': fastq-utilities/fastqSimulate-sort.C:98:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(a, hLen, inFile); al = strlen(a); ~~~~~^~~~~~~~~~~~~~~~~ fastq-utilities/fastqSimulate-sort.C:99:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(b, sLen, inFile); bl = strlen(b); ~~~~~^~~~~~~~~~~~~~~~~ fastq-utilities/fastqSimulate-sort.C:100:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(c, hLen, inFile); cl = strlen(c); ~~~~~^~~~~~~~~~~~~~~~~ fastq-utilities/fastqSimulate-sort.C:101:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(d, sLen, inFile); dl = strlen(d); ~~~~~^~~~~~~~~~~~~~~~~ itDistance-allocateMoreSpace.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-applyAlignment.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-baseCall.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/sqStoreCreatePartition -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreatePartition/stores/sqStoreCreatePartition.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/tgStoreDump -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu g++ -o 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/build/canu-1.8+dfsg/Linux-amd64/bin/bogus -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogus.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogusUtil.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/fastqSimulate-sort -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate-sort/fastq-utilities/fastqSimulate-sort.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/fastqSample -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSample/fastq-utilities/fastqSample.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/utgcns -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/utgcns.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.o -lcanu g++ -o /build/canu-1.8+dfsg/Linux-amd64/bin/bogart -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/build/canu-1.8+dfsg/Linux-amd64/lib /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu Success! canu installed in /build/canu-1.8+dfsg/Linux-amd64/bin/canu make[2]: Leaving directory '/build/canu-1.8+dfsg/src' builddir=*-*/; \ find $builddir \ -name OverlapMhap.pm \ -exec sed -i 's#\(\s*my \$javaPath = \).*#\1 "/usr/lib/jvm/java-8-openjdk-amd64/bin/java";#' {} + make[1]: Leaving directory '/build/canu-1.8+dfsg' dh_auto_test -O--sourcedirectory=src/ create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=src/ dh_testroot -O--sourcedirectory=src/ dh_prep -O--sourcedirectory=src/ dh_auto_install -O--sourcedirectory=src/ debian/rules override_dh_install make[1]: Entering directory '/build/canu-1.8+dfsg' dh_install for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/canu-1.8+dfsg' dh_installdocs -O--sourcedirectory=src/ dh_installchangelogs -O--sourcedirectory=src/ dh_installman -O--sourcedirectory=src/ dh_installinit -O--sourcedirectory=src/ dh_perl -O--sourcedirectory=src/ dh_link -O--sourcedirectory=src/ dh_strip_nondeterminism -O--sourcedirectory=src/ dh_compress -O--sourcedirectory=src/ dh_fixperms -O--sourcedirectory=src/ dh_missing -O--sourcedirectory=src/ dh_strip -O--sourcedirectory=src/ dh_makeshlibs -O--sourcedirectory=src/ dh_shlibdeps -O--sourcedirectory=src/ dh_installdeb -O--sourcedirectory=src/ dh_gencontrol -O--sourcedirectory=src/ dh_md5sums -O--sourcedirectory=src/ dh_builddeb -O--sourcedirectory=src/ dpkg-deb: building package 'canu' in '../canu_1.8+dfsg-2_amd64.deb'. dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_1.8+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../canu_1.8+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/52717 and its subdirectories I: Current time: Tue Apr 6 18:45:15 -12 2021 I: pbuilder-time-stamp: 1617777915 Wed Apr 7 06:45:17 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Wed Apr 7 06:45:17 UTC 2021 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Wed Apr 7 06:47:30 UTC 2021 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Wed Apr 7 06:47:30 UTC 2021 I: canu_1.8+dfsg-2_amd64.changes: Format: 1.8 Date: Mon, 03 Dec 2018 09:55:59 +0100 Source: canu Binary: canu canu-dbgsym Architecture: amd64 Version: 1.8+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: canu - single molecule sequence assembler for genomes Changes: canu (1.8+dfsg-2) unstable; urgency=medium . * Team upload * Properly reporting version number Checksums-Sha1: e4542438b05a675ad7ef9e40979d80cf5302330a 36826464 canu-dbgsym_1.8+dfsg-2_amd64.deb b4c4af22574260c1d9eb5c537668477ba742cd23 6750 canu_1.8+dfsg-2_amd64.buildinfo b1e95e9e9901c40681457f486669088c94c4a8ba 2009936 canu_1.8+dfsg-2_amd64.deb Checksums-Sha256: f729b5be7eafbe9a05eacc38bfd59fedd13d0ffeb10c0d5f16b51474d1e44ad1 36826464 canu-dbgsym_1.8+dfsg-2_amd64.deb 7c10fbeba12b407911031bc3bdd4586f29ea129dd9854f61901d2f8309430ca9 6750 canu_1.8+dfsg-2_amd64.buildinfo be78df4a9dfef377f74835173a4e3b61f8dd96bc905324931bb2f8063aa82a27 2009936 canu_1.8+dfsg-2_amd64.deb Files: 3c489c58c8bb7e7085549cc9cab4fb6f 36826464 debug optional canu-dbgsym_1.8+dfsg-2_amd64.deb f41e22b5c220c35abf0e16208aa0a9e2 6750 science optional canu_1.8+dfsg-2_amd64.buildinfo dd21079278a694869c724c747c90151e 2009936 science optional canu_1.8+dfsg-2_amd64.deb Wed Apr 7 06:47:31 UTC 2021 I: diffoscope 172 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/canu_1.8+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/canu_1.8+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/canu_1.8+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/b1/canu_1.8+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/b2/canu_1.8+dfsg-2_amd64.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: 0.761s) 0.761s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.500s) 0.500s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Apr 7 06:47:34 UTC 2021 I: diffoscope 172 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 7 06:47:34 UTC 2021 I: canu from buster built successfully and reproducibly on amd64. Wed Apr 7 06:47:36 UTC 2021 I: Submitting .buildinfo files to external archives: Wed Apr 7 06:47:36 UTC 2021 I: Submitting 8.0K b1/canu_1.8+dfsg-2_amd64.buildinfo.asc Wed Apr 7 06:47:37 UTC 2021 I: Submitting 8.0K b2/canu_1.8+dfsg-2_amd64.buildinfo.asc Wed Apr 7 06:47:38 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 7 06:47:38 UTC 2021 I: Done submitting .buildinfo files. Wed Apr 7 06:47:38 UTC 2021 I: Removing signed canu_1.8+dfsg-2_amd64.buildinfo.asc files: removed './b1/canu_1.8+dfsg-2_amd64.buildinfo.asc' removed './b2/canu_1.8+dfsg-2_amd64.buildinfo.asc'