Sat Jun 15 01:06:29 UTC 2024 I: starting to build crac/trixie/arm64 on jenkins on '2024-06-15 01:06' Sat Jun 15 01:06:29 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/47374/console.log Sat Jun 15 01:06:29 UTC 2024 I: Downloading source for trixie/crac=2.5.2+dfsg-6 --2024-06-15 01:06:29-- http://deb.debian.org/debian/pool/main/c/crac/crac_2.5.2%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2080 (2.0K) [text/prs.lines.tag] Saving to: ‘crac_2.5.2+dfsg-6.dsc’ 0K .. 100% 268M=0s 2024-06-15 01:06:29 (268 MB/s) - ‘crac_2.5.2+dfsg-6.dsc’ saved [2080/2080] Sat Jun 15 01:06:29 UTC 2024 I: crac_2.5.2+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: crac Binary: crac Architecture: any Version: 2.5.2+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Nilesh Patra Homepage: https://crac.gforge.inria.fr/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/crac Vcs-Git: https://salsa.debian.org/med-team/crac.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, zlib1g-dev, libhts-dev, libjellyfish-2.0-dev, libgzstream-dev, libgkarrays-dev, pkg-config, rsync Package-List: crac deb science optional arch=any Checksums-Sha1: 3a29c15452fb1337fc2d5336a0a00ff72512e21f 658188 crac_2.5.2+dfsg.orig.tar.xz ae172330244046ea69775241ae2a3aefcc47ff81 15152 crac_2.5.2+dfsg-6.debian.tar.xz Checksums-Sha256: 66198b60f8bebb4d923a1230231949f8c7dc1adce92176b45f041726496c69fd 658188 crac_2.5.2+dfsg.orig.tar.xz 7535c1ad0e4267058e13931d2967f7ce72c39a88fe41c3c055e7ce446d0bb067 15152 crac_2.5.2+dfsg-6.debian.tar.xz Files: a58db6dc3a449b7dd4bea567bbb7233a 658188 crac_2.5.2+dfsg.orig.tar.xz 03c0fec9a98c32f7dc81800088df77c5 15152 crac_2.5.2+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmX5y7cACgkQPCZ2P2xn 5uKrug//VHQQhwxx60sOQDctxZuGdqKHR/i2u82vag5cmRd73/T7PCcHG/XYVEjg a/OMM2CQ1zWYP9V8e4bluyw5+w8N+w5N4kSTeUYeSiAomr8lHLbPiREE0oka2y7x nB6fjX2+vEEm3ZOpjtG9JLsdg0nMxK5TRD+Ig8PdYmae+WmGy79O/Vs/E83IdeHv pBRZtPIYqMCzTol7chVwVFo5GzrpQ3G7GQFD0qHBHrmuy7Qt68+VIEX38aG8/CvW yyG6IhXRUDKOUnH6BdFHZ8Lred5DRA8a6xINYrrYh7tygOgIXVESul6moeXTqZBW ij4c2zGl4y4qwlsj9WkbkIx576GYyloOhxoqa/ohOMb8T65xFOnWMPHmwwG0HS8K Unp6RrSgAKfof1Nu0vCQARTblylruQ4J49SSvCuTEXq/1Tn74BnLPEugeVNNRe2Q nmiJwDCEb8dzMZPAcOtKHd+W4oAUE+E+cfmixjtuNNGuxk8FJSwmAy2pdATs850g HGeKrCUKkSOVPCUMeVNGi5ZT7lYL2iu8uR1t9T9WhzOd+S1HHGUoVHbr5ofpQYGP J+ukgyq9rdTtBtXO4l0c7YrcnwuOMuJvHRX6F4suHj7bIFtGE/7McV7ObD0pSQbH SGqFOQROt44iZF9S4F5piOHTo481xTUcpWVQSOERrn4QtGZVJvg= =ekT8 -----END PGP SIGNATURE----- Sat Jun 15 01:06:29 UTC 2024 I: Checking whether the package is not for us Sat Jun 15 01:06:29 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sat Jun 15 01:06:29 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sat Jun 15 01:08:52 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Jun 14 13:06:32 -12 2024 I: pbuilder-time-stamp: 1718413592 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [crac_2.5.2+dfsg-6.dsc] I: copying [./crac_2.5.2+dfsg.orig.tar.xz] I: copying [./crac_2.5.2+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Mar 19 17:30:31 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./crac_2.5.2+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting crac in crac-2.5.2+dfsg dpkg-source: info: unpacking crac_2.5.2+dfsg.orig.tar.xz dpkg-source: info: unpacking crac_2.5.2+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libgzstream.patch dpkg-source: info: applying use_debian_packaged_libjellyfish.patch dpkg-source: info: applying skip_failed_test_bug-14958.patch dpkg-source: info: applying use_debian_packages_libgtarrays.patch dpkg-source: info: applying reproducible_build.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying bashism.patch dpkg-source: info: applying tempfile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2699121/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='3f9401cfd07c443ba0d01813bf2c4836' 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='2699121' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.NgF2U0zw/pbuilderrc_BP2B --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NgF2U0zw/b1 --logfile b1/build.log crac_2.5.2+dfsg-6.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 22:35 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2699121/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), architecture-is-64-bit, zlib1g-dev, libhts-dev, libjellyfish-2.0-dev, libgzstream-dev, libgkarrays-dev, pkg-config, rsync dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19743 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libjellyfish-2.0-dev; however: Package libjellyfish-2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libgzstream-dev; however: Package libgzstream-dev is not installed. pbuilder-satisfydepends-dummy depends on libgkarrays-dev; however: Package libgkarrays-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on rsync; however: Package rsync 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgkarrays-dev{a} libgkarrays1t64{a} libgssapi-krb5-2{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpopt0{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} rsync{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 65 newly installed, 0 to remove and 0 not upgraded. Need to get 25.4 MB of archives. After unpacking 98.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpopt0 arm64 1.19+dfsg-1+b1 [42.6 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 rsync arm64 3.3.0-1 [401 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.1-8.1 [95.1 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 architecture-properties arm64 0.1.1+b1 [1880 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 25 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 38 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.62.1-1 [71.2 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-5 [207 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.8.0-1 [405 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.8.0-1 [526 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libgkarrays1t64 arm64 2.1.0+dfsg-4.2 [53.3 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libgkarrays-dev arm64 2.1.0+dfsg-4.2 [82.4 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libgzstream0 arm64 1.5+git20171107.9a20658-2 [7288 B] Get: 54 http://deb.debian.org/debian trixie/main arm64 libgzstream-dev arm64 1.5+git20171107.9a20658-2 [7488 B] Get: 55 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.20+ds-1 [1613 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libjellyfish-2.0-2 arm64 2.3.1-3+b4 [62.0 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libjellyfish-2.0-dev arm64 2.3.1-3+b4 [136 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Fetched 25.4 MB in 1s (33.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpopt0:arm64. (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 ... 19743 files and directories currently installed.) Preparing to unpack .../00-libpopt0_1.19+dfsg-1+b1_arm64.deb ... Unpacking libpopt0:arm64 (1.19+dfsg-1+b1) ... Selecting previously unselected package rsync. Preparing to unpack .../01-rsync_3.3.0-1_arm64.deb ... Unpacking rsync (3.3.0-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.1-8.1_arm64.deb ... Unpacking bsdextrautils (2.40.1-8.1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../10-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package architecture-properties:arm64. Preparing to unpack .../12-architecture-properties_0.1.1+b1_arm64.deb ... Unpacking architecture-properties:arm64 (0.1.1+b1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. 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Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:arm64 (0.1.1+b1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.62.1-1) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libgkarrays1t64 (2.1.0+dfsg-4.2) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up libjellyfish-2.0-2:arm64 (2.3.1-3+b4) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.1-1+b2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libgzstream0:arm64 (1.5+git20171107.9a20658-2) ... Setting up liblzma-dev:arm64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libssh2-1t64:arm64 (1.11.0-5) ... Setting up libdeflate-dev:arm64 (1.20-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up libpopt0:arm64 (1.19+dfsg-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libjellyfish-2.0-dev (2.3.1-3+b4) ... Setting up libgkarrays-dev (2.1.0+dfsg-4.2) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libgzstream-dev:arm64 (1.5+git20171107.9a20658-2) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up pkg-config:arm64 (1.8.1-1+b2) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up rsync (3.3.0-1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.8.0-1) ... Setting up libcurl4-gnutls-dev:arm64 (8.8.0-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:arm64 (1.20+ds-1) ... Setting up libhts-dev:arm64 (1.20+ds-1) ... Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-13) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/crac-2.5.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../crac_2.5.2+dfsg-6_source.changes dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.2+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf aclocal: warning: couldn't open directory 'config/m4': No such file or directory libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config/m4'. libtoolize: copying file 'config/m4/libtool.m4' libtoolize: copying file 'config/m4/ltoptions.m4' libtoolize: copying file 'config/m4/ltsugar.m4' libtoolize: copying file 'config/m4/ltversion.m4' libtoolize: copying file 'config/m4/lt~obsolete.m4' configure.ac:147: installing 'config/compile' configure.ac:139: installing 'config/config.guess' configure.ac:139: installing 'config/config.sub' configure.ac:137: installing 'config/install-sh' configure.ac:137: installing 'config/missing' src/Makefile.am: installing 'config/depcomp' test_f/Makefile.am:109: warning: shell find . -name "*.should_get": non-POSIX variable name test_f/Makefile.am:109: (probably a GNU make extension) test_f/Makefile.am:110: warning: shell find . -name "*.fasta" -o -name "*.fa": non-POSIX variable name test_f/Makefile.am:110: (probably a GNU make extension) test_f/Makefile.am:111: warning: shell find . -name "*.fastq" -o -name "*.fq": non-POSIX variable name test_f/Makefile.am:111: (probably a GNU make extension) parallel-tests: installing 'config/test-driver' dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for gawk... (cached) mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C preprocessor... gcc -E checking whether make sets $(MAKE)... (cached) yes checking whether ln -s works... yes checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for ld used by gcc... (cached) /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... (cached) yes checking for dpkg... /usr/bin/dpkg checking for rpmbuild... no checking for sqrt in -lm... yes checking for pthread_join in -lpthread... yes checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking for sys/mkdev.h... no checking for sys/sysmacros.h... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking for libintl.h... yes checking for limits.h... yes checking for locale.h... yes checking for memory.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for sys/file.h... yes checking for sys/param.h... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for utime.h... yes checking for _Bool... no checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for int64_t... yes checking for off_t... yes checking for size_t... (cached) yes checking for struct stat.st_blksize... yes checking for uint32_t... yes checking for uint8_t... yes checking for ptrdiff_t... yes yes checking for GNU libc compatible realloc... yes checking for floor... yes checking for gettimeofday... yes checking for memchr... yes checking for memmove... yes checking for memset... yes checking for mkfifo... yes checking for pow... yes checking for select... yes checking for sqrt... yes checking for strrchr... yes checking for strstr... yes checking for strtol... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for libProgressBar... yes checking for gzread in -lz... yes checking for hts_hopen in -lhts... yes checking for libGkArrays... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating control config.status: creating crac.spec config.status: creating Makefile config.status: creating src/Makefile config.status: creating scripts/Makefile config.status: creating src/libReadsInfo/Makefile config.status: creating src/libSSA/Makefile config.status: creating src/libReadsReader/Makefile config.status: creating src/libReadsReader/kseq/Makefile config.status: creating man/Makefile config.status: creating man/crac.1 config.status: creating scripts/crac-client config.status: creating test_f/Makefile config.status: creating test_f/bug/Makefile config.status: creating test_f/causes/Makefile config.status: creating test_f/cigar/Makefile config.status: creating test_f/splices_adjust/Makefile config.status: creating config/config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' Making all in src make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' Making all in libReadsInfo make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-BioTagIndelInfo.o `test -f 'BioTagIndelInfo.cpp' || echo './'`BioTagIndelInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-BioUndeterminedInfo.o `test -f 'BioUndeterminedInfo.cpp' || echo './'`BioUndeterminedInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-cigarTypes.o `test -f 'cigarTypes.cpp' || echo './'`cigarTypes.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-Cigar.o `test -f 'Cigar.cpp' || echo './'`Cigar.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-DuplicationInfo.o `test -f 'DuplicationInfo.cpp' || echo './'`DuplicationInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-genericInfo.o `test -f 'genericInfo.cpp' || echo './'`genericInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-IndelInfo.o `test -f 'IndelInfo.cpp' || echo './'`IndelInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-repetitionInfo.o `test -f 'repetitionInfo.cpp' || echo './'`repetitionInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-SeqErrInfo.o `test -f 'SeqErrInfo.cpp' || echo './'`SeqErrInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-SNPInfo.o `test -f 'SNPInfo.cpp' || echo './'`SNPInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-SpliceInfo.o `test -f 'SpliceInfo.cpp' || echo './'`SpliceInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-SpliceInterInfo.o `test -f 'SpliceInterInfo.cpp' || echo './'`SpliceInterInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-SpliceIntraInfo.o `test -f 'SpliceIntraInfo.cpp' || echo './'`SpliceIntraInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-SpliceNoCoverInfo.o `test -f 'SpliceNoCoverInfo.cpp' || echo './'`SpliceNoCoverInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-SplicingInfo.o `test -f 'SplicingInfo.cpp' || echo './'`SplicingInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-samLine.o `test -f 'samLine.cpp' || echo './'`samLine.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-samHeader.o `test -f 'samHeader.cpp' || echo './'`samHeader.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-bamUtils.o `test -f 'bamUtils.cpp' || echo './'`bamUtils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo './'`tagInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo './'`undeterminedErrorInfo.cpp samHeader.cpp: In member function 'bam_hdr_t* SamHeader::writeBamHeader(samFile*)': samHeader.cpp:160:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 160 | sam_hdr_write(out,h); | ~~~~~~~~~~~~~^~~~~~~ In file included from ../libReadsReader/readsReader.h:57, from ../Read.h:55, from ../ReadIndex.h:52, from ../Support.h:59, from tagInfo.h:71, from tagInfo.cpp:53: ../libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ ../libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ ../libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ samLine.cpp: In constructor 'OptionalField::OptionalField(const char*, char)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] 60 | strncpy(tag,tag_name,2); | ^ samLine.cpp: In constructor 'CharOptionalField::CharOptionalField(const char*, char)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In constructor 'IntOptionalField::IntOptionalField(const char*, int)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In constructor 'IntOptionalField::IntOptionalField(const char*, uint)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In constructor 'StringOptionalField::StringOptionalField(const char*, std::string)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In constructor 'StringOptionalField::StringOptionalField(const char*, char*)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In member function 'void SamLine::addOptionalField(const char*, char)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In member function 'void SamLine::addOptionalField(const char*, int)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In member function 'void SamLine::addOptionalField(const char*, uint)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In member function 'void SamLine::addOptionalField(const char*, const std::string&)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In member function 'void SamLine::addOptionalField(const char*, const char*)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] rm -f libReadsInfo.a ar cru libReadsInfo.a libReadsInfo_a-BioTagIndelInfo.o libReadsInfo_a-BioUndeterminedInfo.o libReadsInfo_a-cigarTypes.o libReadsInfo_a-Cigar.o libReadsInfo_a-DuplicationInfo.o libReadsInfo_a-genericInfo.o libReadsInfo_a-IndelInfo.o libReadsInfo_a-repetitionInfo.o libReadsInfo_a-SeqErrInfo.o libReadsInfo_a-SNPInfo.o libReadsInfo_a-SpliceInfo.o libReadsInfo_a-SpliceInterInfo.o libReadsInfo_a-SpliceIntraInfo.o libReadsInfo_a-SpliceNoCoverInfo.o libReadsInfo_a-SplicingInfo.o libReadsInfo_a-samLine.o libReadsInfo_a-samHeader.o libReadsInfo_a-bamUtils.o libReadsInfo_a-tagInfo.o libReadsInfo_a-undeterminedErrorInfo.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libReadsInfo.a make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' Making all in libSSA make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o cracIndex.o cracIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o bitarray.o bitarray.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o bitrankw32int.o bitrankw32int.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o chrPosition.o chrPosition.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o HuffAlphabetRank.o HuffAlphabetRank.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Huffman_Codes.o Huffman_Codes.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o locateOnGenome.o locateOnGenome.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o locateTags.o locateTags.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o SSA.o SSA.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o GenomeInfo.o GenomeInfo.cpp cracIndex.cpp:85:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 85 | cerr << "\tCompiled on " <<__DATE__ << endl << endl; | ^~~~~~~~ In file included from ./seqan/basic.h:64, from ./seqan/sequence.h:27, from /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/basic/basic_holder.h: In function 'void seqan::setValue(Holder&, TValue&)': ./seqan/basic/basic_holder.h:1001:66: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] 1001 | typedef typename Value >::Type THolderType; | ^~~~~~~~~~~ ./seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(Holder&)': ./seqan/basic/basic_holder.h:1027:66: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] 1027 | typedef typename Value >::Type THolderType; | ^~~~~~~~~~~ ./seqan/basic/basic_holder.h: In function 'void seqan::assignValue(Holder&, const TSource&)': ./seqan/basic/basic_holder.h:1051:66: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] 1051 | typedef typename Value >::Type THostValue; | ^~~~~~~~~~ In file included from ./seqan/sequence.h:38: ./seqan/sequence/lexical.h: In function 'void seqan::compare_(Lexical&, TLeft&, TRight&)': ./seqan/sequence/lexical.h:239:45: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] 239 | typedef typename Value::Type TLeftValue; | ^~~~~~~~~~ In file included from ./seqan/sequence.h:51: ./seqan/sequence/string_base.h: In function 'void seqan::assign(String&, const TSource&, Tag)': ./seqan/sequence/string_base.h:811:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 811 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::assign(String&, const TSource&, TSize, Tag)': ./seqan/sequence/string_base.h:821:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 821 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::assign(String&, const TSourceValue*, Tag)': ./seqan/sequence/string_base.h:834:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 834 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::assign(String&, const TSourceValue*, TSize, Tag)': ./seqan/sequence/string_base.h:844:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 844 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::append(String&, const TSource&, Tag)': ./seqan/sequence/string_base.h:1044:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 1044 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::append(String&, const TSource&, typename Size >::Type, Tag)': ./seqan/sequence/string_base.h:1056:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 1056 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::append(String&, TSourceValue*, Tag)': ./seqan/sequence/string_base.h:1070:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 1070 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::append(String&, TSourceValue*, typename Size >::Type, Tag)': ./seqan/sequence/string_base.h:1082:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 1082 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::replace(String&, typename Size >::Type, typename Size >::Type, const TSource&, Tag)': ./seqan/sequence/string_base.h:1249:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 1249 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::replace(String&, typename Size >::Type, typename Size >::Type, const TSource&, typename Size >::Type, Tag)': ./seqan/sequence/string_base.h:1263:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 1263 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::replace(String&, typename Size >::Type, typename Size >::Type, const TSourceValue*, Tag)': ./seqan/sequence/string_base.h:1279:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 1279 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::replace(String&, typename Size >::Type, typename Size >::Type, const TSourceValue*, typename Size >::Type, Tag)': ./seqan/sequence/string_base.h:1293:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 1293 | typedef String TTarget; | ^~~~~~~ In file included from ./seqan/sequence.h:53: ./seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(String >&, _TSize, Insist)': ./seqan/sequence/string_alloc.h:456:70: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] 456 | typedef typename Size< String > >::Type TSize; | ^~~~~ In file included from /usr/include/libGkArrays/readsReader.h:109, from locateTags.h:60, from locateTags.cpp:53: /usr/include/libGkArrays/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ /usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ /usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from ./seqan/sequence.h:57: ./seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': ./seqan/sequence/string_packed.h:594:62: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] 594 | typedef typename Iterator::Type TIterator; | ^~~~~~~~~ ./seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(String >&, _TSize, Insist)': ./seqan/sequence/string_packed.h:758:70: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] 758 | typedef typename Size< String > >::Type TSize; | ^~~~~ In file included from ./seqan/sequence.h:62: ./seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(StringSet > >&, StringSet > >&, TIds, TLength)': ./seqan/sequence/sequence_multiple.h:1647:55: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] 1647 | typedef typename Id::Type TId; | ^~~ In file included from ./seqan/index.h:82, from /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11: ./seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(Shape >&, TIter)': ./seqan/index/shape_base.h:273:81: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 273 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ ./seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(Shape >&, TIter)': ./seqan/index/shape_base.h:309:81: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 309 | typedef typename Value< Shape > >::Type THValue; | ^~~~~~~ ./seqan/index/shape_base.h:310:81: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] 310 | typedef typename Size< Shape > >::Type TSize; | ^~~~~ ./seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(Shape&, TIter, TSize)': ./seqan/index/shape_base.h:322:73: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 322 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ ./seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(Shape&, TIter, TSize)': ./seqan/index/shape_base.h:424:73: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 424 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ ./seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(Shape&, TIter, TSize)': ./seqan/index/shape_base.h:492:73: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 492 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ In file included from ./seqan/index.h:83: ./seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(Shape > >&, TIter)': ./seqan/index/shape_gapped.h:370:81: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 370 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ ./seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(Shape >&, TIter, TSize)': ./seqan/index/shape_gapped.h:387:89: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 387 | typedef typename Value< Shape > >::Type THValue; | ^~~~~~~ ./seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(Shape >&, TIter, TSize)': ./seqan/index/shape_gapped.h:415:89: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 415 | typedef typename Value< Shape > >::Type THValue; | ^~~~~~~ In file included from ./seqan/file.h:66, from /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, from /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13: ./seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, Align&, FastaAlign)': ./seqan/file/file_format_fasta_align.h:138:44: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] 138 | typedef typename Row::Type TRow; | ^~~~ ./seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, Align&, TStringContainer&, FastaAlign)': ./seqan/file/file_format_fasta_align.h:252:49: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] 252 | typedef typename Position::Type TPosition; | ^~~~~~~~~ In file included from ./seqan/file.h:69: ./seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, Align&, TStringContainer&, CGViz)': ./seqan/file/file_format_cgviz.h:66:44: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] 66 | typedef typename Row::Type TRow; | ^~~~ /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 156 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 156 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 157 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 157 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 206 | if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample | ^~ /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 206 | if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample | ^~~ /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:380:44: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] 380 | typedef typename Value::Type TAlphabet; | ^~~~~~~~~ /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:745:44: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] 745 | typedef typename Value::Type TAlphabet; | ^~~~~~~~~ ./seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': ./seqan/sequence/string_packed.h:906:72: required from 'typename seqan::Position > >::Type seqan::position(const Iter >&) [with TContainer = const String, Packed<> >; THostspec = Alloc; typename Position > >::Type = long unsigned int]' ./seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference > >::Type seqan::operator-(const Iter >&, const Iter >&) [with TContainer = const String, Packed<> >; THostspec = Alloc; typename Difference > >::Type = long int]' ./seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size >::Type seqan::length(const String&) [with TValue = SimpleType; TSpec = Packed<>; typename Size >::Type = long unsigned int]' /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:354:30: required from here ./seqan/sequence/string_packed.h:294:51: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] 294 | VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ ./seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': ./seqan/sequence/string_packed.h:958:79: required from 'typename seqan::GetValue > >::Type seqan::getValue(const Iter >&) [with TContainer = String, Packed<> >; THostspec = Alloc; typename GetValue > >::Type = SimpleType]' ./seqan/basic/basic_proxy.h:242:17: required from 'typename seqan::GetValue >::Type seqan::getValue(const Proxy&) [with TSpec = IteratorProxy, Packed<> >, Packed<> > >; typename GetValue >::Type = SimpleType]' ./seqan/basic/basic_proxy.h:272:34: required from 'typename seqan::Convert >::Type seqan::convertImpl(Convert, const Proxy&) [with TTarget = char; T = Proxy, Packed<> >, Packed<> > > >; TSpec = IteratorProxy, Packed<> >, Packed<> > >; typename Convert >::Type = char]' ./seqan/basic/basic_converter.h:111:20: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = Proxy, Packed<> >, Packed<> > > >; typename Convert::Type = char]' cracIndex.cpp:224:29: required from here ./seqan/sequence/string_packed.h:294:51: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] In file included from ./seqan/basic.h:101: ./seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]': ./seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = SimpleType]' ./seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, True) [with TValue = SimpleType]' ./seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = SimpleType]' ./seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(String >&, _TSize, Tag) [with TValue = SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = TagExact_; typename Size > >::Type = long unsigned int]' ./seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; TExpand = const seqan::Tag; typename seqan::Size::Type = long unsigned int]' ./seqan/sequence/string_base.h:1459:52: required from 'typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = SimpleType; TSpec = Alloc; TSize = long unsigned int; TExpand = TagExact_; typename Size >::Type = long unsigned int]' ./seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc >; TSize = long unsigned int; typename Size::Type = long unsigned int]' ./seqan/file/file_format_fasta.h:269:8: required from 'void seqan::read(TFile&, TData&, TSize, Fasta) [with TFile = std::basic_ifstream; TData = String, Alloc >; TSize = long unsigned int; Fasta = const Tag]' ./seqan/file/file_format_fasta.h:309:6: required from 'void seqan::read(TFile&, TData&, Fasta) [with TFile = std::basic_ifstream; TData = String, Alloc >; Fasta = const Tag]' cracIndex.cpp:142:13: required from here ./seqan/basic/basic_alphabet_trait_basic.h:207:16: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 207 | memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./seqan/basic.h:106: ./seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here 57 | struct SimpleType | ^~~~~~~~~~ rm -f libSSA.a ar cru libSSA.a bitarray.o bitrankw32int.o chrPosition.o HuffAlphabetRank.o Huffman_Codes.o locateOnGenome.o locateTags.o SSA.o utils.o GenomeInfo.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libSSA.a In file included from ./seqan/basic.h:61: In function 'void seqan::allocate(T&, TValue*&, TSize, Tag) [with T = String >; TValue = unsigned int; TSize = long unsigned int; TUsage = TagAllocateStorage_]', inlined from 'seqan::Value >, 0>::Type* seqan::_allocateStorage(String >&, size_t)' at ./seqan/sequence/string_alloc.h:294:11, inlined from 'typename seqan::Value >::Type* seqan::_reallocateStorage(String&, typename Size >::Type, Exact) [with TValue = unsigned int; TSpec = Alloc]' at ./seqan/sequence/string_base.h:1353:26, inlined from 'typename seqan::Size > >::Type seqan::reserve(String >&, _TSize, Tag) [with TValue = unsigned int; TSpec = void; _TSize = long unsigned int; TExpand = TagExact_]' at ./seqan/sequence/string_alloc.h:418:88, inlined from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = const seqan::Tag]' at ./seqan/sequence/string_base.h:1433:33, inlined from 'typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = unsigned int; TSpec = Alloc; TSize = long unsigned int; TExpand = TagExact_]' at ./seqan/sequence/string_base.h:1459:52, inlined from 'void DifferenceCoverSample::build() [with TStr = seqan::String, seqan::Packed<> >]' at /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:781:9: ./seqan/basic/basic_allocator_interface.h:159:39: warning: argument 1 value '18446744073709551612' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 159 | data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/new_allocator.h:34, from /usr/include/aarch64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from cracIndex.cpp:52: /usr/include/c++/13/new: In member function 'void DifferenceCoverSample::build() [with TStr = seqan::String, seqan::Packed<> >]': /usr/include/c++/13/new:126:26: note: in a call to allocation function 'void* operator new(std::size_t)' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In function 'void seqan::allocate(T&, TValue*&, TSize, Tag) [with T = String >; TValue = unsigned int; TSize = long unsigned int; TUsage = TagAllocateStorage_]', inlined from 'seqan::Value >, 0>::Type* seqan::_allocateStorage(String >&, size_t)' at ./seqan/sequence/string_alloc.h:294:11, inlined from 'typename seqan::Value >::Type* seqan::_reallocateStorage(String&, typename Size >::Type, Exact) [with TValue = unsigned int; TSpec = Alloc]' at ./seqan/sequence/string_base.h:1353:26, inlined from 'typename seqan::Size > >::Type seqan::reserve(String >&, _TSize, Tag) [with TValue = unsigned int; TSpec = void; _TSize = long unsigned int; TExpand = TagExact_]' at ./seqan/sequence/string_alloc.h:418:88, inlined from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String >; TExpand = const seqan::Tag]' at ./seqan/sequence/string_base.h:1433:33, inlined from 'typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = unsigned int; TSpec = Alloc; TSize = long unsigned int; TExpand = TagExact_]' at ./seqan/sequence/string_base.h:1459:52, inlined from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String >; TSize = long unsigned int]' at ./seqan/sequence/sequence_interface.h:1360:15, inlined from 'void DifferenceCoverSample::build() [with TStr = seqan::String, seqan::Packed<> >]' at /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:857:8: ./seqan/basic/basic_allocator_interface.h:159:39: warning: argument 1 value '18446744073709551612' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 159 | data = (TValue *) operator new(count * sizeof(TValue)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/new: In member function 'void DifferenceCoverSample::build() [with TStr = seqan::String, seqan::Packed<> >]': /usr/include/c++/13/new:126:26: note: in a call to allocation function 'void* operator new(std::size_t)' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -lm -lpthread -lSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac-index cracIndex.o -lSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' Making all in libReadsReader make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' Making all in kseq make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libReadsReader_a-readsReader.o `test -f 'readsReader.cpp' || echo './'`readsReader.cpp rm -f libReadsReader.a ar cru libReadsReader.a libReadsReader_a-readsReader.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libReadsReader.a make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Classifier.o Classifier.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o classifyTags.o classifyTags.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o GkReadIndex.o GkReadIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o JellyReadIndex.o JellyReadIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o crac.o crac.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Parameters.o Parameters.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o SupportBreak.o SupportBreak.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o BreakList.o BreakList.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o CandidatBreak.o CandidatBreak.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Support.o Support.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o locateServer.o locateServer.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o utils.o utils.cpp classifyTags.cpp:421:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 421 | headerTemplate << "#Created on " <<__DATE__ << endl << "#" << endl; | ^~~~~~~~ crac.cpp:213:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 213 | printf("\tCompiled on %s.\n\n",__DATE__); | ^~~~~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 119 | LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:120:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 120 | LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:121:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:127:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 127 | inline LargeBinVect &operator=(const LargeBinVect &v) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 155 | inline LargeBinVect operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:158:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 158 | inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:161:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 161 | inline bool operator[](const CountWordSize i) const throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:177:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 177 | inline bool GetBit(const CountWordSize i) const throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:179:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 179 | inline LargeBinVect &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:182:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 182 | inline LargeBinVect &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:191:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 191 | inline LargeBinVect &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:194:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | inline LargeBinVect &Append(const bool value) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:197:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 197 | inline LargeBinVect &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:200:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 200 | inline LargeBinVect &operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:203:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 203 | inline LargeBinVect &operator++() throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:205:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 205 | inline LargeBinVect operator++(int) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:208:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 208 | inline LargeBinVect &operator--() throw (BinVectOverflow); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 210 | inline LargeBinVect operator--(int) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 214 | inline LargeBinVect Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc); | ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241: /usr/include/libGkArrays/largebinvect.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:136:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 136 | LargeBinVect::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc) | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:147:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 147 | LargeBinVect::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:167:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | LargeBinVect::LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc) | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:184:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 184 | LargeBinVect &LargeBinVect::operator=(const LargeBinVect &v) throw (std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 339 | LargeBinVect LargeBinVect::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:363:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 363 | unsigned long int LargeBinVect::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:397:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 397 | bool LargeBinVect::operator[](const CountWordSize i) const throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:478:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 478 | bool LargeBinVect::GetBit(const CountWordSize i) const throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:493:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 493 | LargeBinVect &LargeBinVect::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:513:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 513 | LargeBinVect &LargeBinVect::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:619:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 619 | LargeBinVect &LargeBinVect::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:653:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 653 | LargeBinVect &LargeBinVect::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:661:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 661 | LargeBinVect &LargeBinVect::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:673:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 673 | LargeBinVect &LargeBinVect::operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:711:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 711 | LargeBinVect &LargeBinVect::operator++() throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:727:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 727 | LargeBinVect LargeBinVect::operator++(int) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:734:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 734 | LargeBinVect &LargeBinVect::operator--() throw (BinVectOverflow) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 750 | LargeBinVect LargeBinVect::operator--(int) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:757:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 757 | LargeBinVect LargeBinVect::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument); | ^~~~~ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 202 | void realloc(uintSA nbElements) throw (logic_error); | ^~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/crac-2.5.2+dfsg -I/build/reproducible-path/crac-2.5.2+dfsg/src -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -I/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o Bitset.o Bitset.cpp In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from GkReadIndex.h:59: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ ln -s -f /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/crac-index crac-index In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from classifyTags.h:53, from classifyTags.cpp:52: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from JellyReadIndex.h:59, from JellyReadIndex.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from Support.h:59, from SupportBreak.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from ./libReadsReader/readsReader.h:57, from ./Read.h:55, from ./ReadIndex.h:52, from ./Classifier.h:56, from Classifier.cpp:52: ./libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ ./libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ ./libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ locateServer.cpp: In function 'void* launchSubServer(void*)': locateServer.cpp:464:8: warning: unused variable 'threshold' [-Wunused-variable] 464 | uint threshold = indexTags->getFactorLength(); | ^~~~~~~~~ locateServer.cpp:466:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] 466 | char *dontCare, *variable, *tag_length, *factor; | ^~~~~~~~ locateServer.cpp: In function 'void locateServer(ClassifyTags*, const char*, const char*)': locateServer.cpp:717:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] 717 | char *dontCare; | ^~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from classifyTags.h:53, from locateServer.cpp:59: libReadsReader/readsReader.h: At global scope: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 119 | LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:120:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 120 | LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:121:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:127:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 127 | inline LargeBinVect &operator=(const LargeBinVect &v) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 155 | inline LargeBinVect operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:158:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 158 | inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:161:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 161 | inline bool operator[](const CountWordSize i) const throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:177:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 177 | inline bool GetBit(const CountWordSize i) const throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:179:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 179 | inline LargeBinVect &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:182:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 182 | inline LargeBinVect &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:191:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 191 | inline LargeBinVect &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:194:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | inline LargeBinVect &Append(const bool value) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:197:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 197 | inline LargeBinVect &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:200:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 200 | inline LargeBinVect &operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:203:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 203 | inline LargeBinVect &operator++() throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:205:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 205 | inline LargeBinVect operator++(int) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:208:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 208 | inline LargeBinVect &operator--() throw (BinVectOverflow); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 210 | inline LargeBinVect operator--(int) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 214 | inline LargeBinVect Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc); | ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241: /usr/include/libGkArrays/largebinvect.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:136:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 136 | LargeBinVect::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc) | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:147:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 147 | LargeBinVect::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:167:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | LargeBinVect::LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc) | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:184:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 184 | LargeBinVect &LargeBinVect::operator=(const LargeBinVect &v) throw (std::bad_alloc) { | ^~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from Support.h:59, from Support.cpp:57: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ /usr/include/libGkArrays/largebinvect.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 339 | LargeBinVect LargeBinVect::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:363:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 363 | unsigned long int LargeBinVect::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:397:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 397 | bool LargeBinVect::operator[](const CountWordSize i) const throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:478:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 478 | bool LargeBinVect::GetBit(const CountWordSize i) const throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:493:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 493 | LargeBinVect &LargeBinVect::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:513:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 513 | LargeBinVect &LargeBinVect::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:619:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 619 | LargeBinVect &LargeBinVect::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:653:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 653 | LargeBinVect &LargeBinVect::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:661:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 661 | LargeBinVect &LargeBinVect::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:673:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 673 | LargeBinVect &LargeBinVect::operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:711:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 711 | LargeBinVect &LargeBinVect::operator++() throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:727:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 727 | LargeBinVect LargeBinVect::operator++(int) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:734:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 734 | LargeBinVect &LargeBinVect::operator--() throw (BinVectOverflow) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 750 | LargeBinVect LargeBinVect::operator--(int) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:757:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 757 | LargeBinVect LargeBinVect::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument); | ^~~~~ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 202 | void realloc(uintSA nbElements) throw (logic_error); | ^~~~~ crac.cpp: In function 'int main(int, char**)': crac.cpp:1009:26: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 1009 | } catch (bad_alloc e) { | ^ In member function 'ChrPosition* Support::getLocation(uint)', inlined from 'void Support::checkPairedConnection()' at Support.cpp:1085:38: Support.cpp:470:21: warning: 'best_candidate1' may be used uninitialized [-Wmaybe-uninitialized] 470 | return locations[i]; | ^ Support.cpp: In member function 'void Support::checkPairedConnection()': Support.cpp:1030:8: note: 'best_candidate1' was declared here 1030 | uint best_candidate1, best_candidate2; | ^~~~~~~~~~~~~~~ In member function 'ChrPosition* Support::getLocation(uint)', inlined from 'void Support::checkPairedConnection()' at Support.cpp:1084:20: Support.cpp:470:21: warning: 'best_candidate2' may be used uninitialized [-Wmaybe-uninitialized] 470 | return locations[i]; | ^ Support.cpp: In member function 'void Support::checkPairedConnection()': Support.cpp:1030:25: note: 'best_candidate2' was declared here 1030 | uint best_candidate1, best_candidate2; | ^~~~~~~~~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from classifyTags.h:53, from crac.cpp:66: libReadsReader/readsReader.h: At global scope: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ Classifier.cpp: In member function 'virtual void SingleReadClassifier::classify()': Classifier.cpp:203:40: warning: 'bioundetermined_type' may be used uninitialized [-Wmaybe-uninitialized] 203 | taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | suppoBreak->getPositionStartBreak(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | bioundetermined_type, | ~~~~~~~~~~~~~~~~~~~~~ 206 | message.c_str()); | ~~~~~~~~~~~~~~~~ Classifier.cpp:187:33: note: 'bioundetermined_type' was declared here 187 | BioUndeterminedInfo::Type bioundetermined_type; | ^~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm libtool: link: g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/crac-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo -L/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader /usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so -lGkArrays -lProgressBar /build/reproducible-path/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' Making all in man make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/man' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/man' Making all in scripts make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' Making all in test_f make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' Making all in causes make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' Making all in bug make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' Making all in cigar make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' Making all in splices_adjust make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' make[1]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' # Sequence of tests is important so parallel execution is no option dh_auto_test --no-parallel make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' Making check in src make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' Making check in libReadsInfo make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' Making check in libSSA make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' Making check in libReadsReader make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' Making check in kseq make[5]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[5]: Nothing to be done for 'check-am'. make[5]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' Making check in man make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/man' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/man' Making check in scripts make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' Making check in test_f make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' Making check in causes make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' Making check in bug make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' Making check in cigar make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' Making check in splices_adjust make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make check-TESTS make[5]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[6]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' PASS: index_genomes.sh PASS: launch_sg.sh PASS: test_index.sh ============================================================================ Testsuite summary for crac 2.5.2 ============================================================================ # TOTAL: 3 # PASS: 3 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[6]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[5]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' find test_f -type f \( -name '*~' -o -name '*.tap' -o -name '*.ssa' -o -name '*.conf' -o -name '*.sam' -o -name '*.valgrind' -o -name '*.log' \) -delete make[1]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/crac/ make -j1 install DESTDIR=/build/reproducible-path/crac-2.5.2\+dfsg/debian/crac AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' Making install in src make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' Making install in libReadsInfo make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsInfo' Making install in libSSA make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' /usr/bin/mkdir -p '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac-index /build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin/crac-index make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libSSA' Making install in libReadsReader make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' Making install in kseq make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' /usr/bin/install -c -m 644 kseq.h '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' make[5]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[5]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/src' /usr/bin/mkdir -p '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c crac '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac /build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin/crac make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/src' Making install in man make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/man' make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/man' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' /usr/bin/install -c -m 644 crac.1 '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/man' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/man' Making install in scripts make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' /usr/bin/mkdir -p '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' /usr/bin/install -c crac-client '/build/reproducible-path/crac-2.5.2+dfsg/debian/crac/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/scripts' Making install in test_f make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' Making install in causes make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/causes' Making install in bug make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/bug' Making install in cigar make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/cigar' Making install in splices_adjust make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[4]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg/test_f' make[2]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' make[3]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' make[2]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' make[1]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/crac-2.5.2+dfsg' mkdir debian/crac/usr/share/doc/crac/examples rsync -a --exclude=Makefile* test_f debian/crac/usr/share/doc/crac/examples sed -i 's+${abs_top_builddir:-\.\./\.\.}/src/crac+crac+' `grep -wRl crac debian/crac/usr/share/doc/crac/examples/*` sed -i 's+$abs_top_builddir/src/crac-index+crac-index+' `grep -wRl crac-index debian/crac/usr/share/doc/crac/examples/*` make[1]: Leaving directory '/build/reproducible-path/crac-2.5.2+dfsg' dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'crac-dbgsym' in '../crac-dbgsym_2.5.2+dfsg-6_arm64.deb'. dpkg-deb: building package 'crac' in '../crac_2.5.2+dfsg-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../crac_2.5.2+dfsg-6_arm64.buildinfo dpkg-genchanges --build=binary -O../crac_2.5.2+dfsg-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2699121 and its subdirectories I: Current time: Fri Jun 14 13:08:50 -12 2024 I: pbuilder-time-stamp: 1718413730 Sat Jun 15 01:08:53 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sat Jun 15 01:08:53 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sat Jun 15 01:10:19 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sat Jun 15 01:10:20 UTC 2024 I: crac_2.5.2+dfsg-6_arm64.changes: Format: 1.8 Date: Tue, 19 Mar 2024 18:27:00 +0100 Source: crac Binary: crac crac-dbgsym Architecture: arm64 Version: 2.5.2+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: crac - integrated RNA-Seq read analysis Changes: crac (2.5.2+dfsg-6) unstable; urgency=medium . * Team upload. * d/control: stop building on 32-bit architectures. Checksums-Sha1: b10b134518bb5d9433796435d00378d92f9553d2 1775204 crac-dbgsym_2.5.2+dfsg-6_arm64.deb d09103310c1dedcc5a13160cce13af1f0ecb7242 6392 crac_2.5.2+dfsg-6_arm64.buildinfo 1938c534c3afb65feb032b3c41ef9dd58d049640 447892 crac_2.5.2+dfsg-6_arm64.deb Checksums-Sha256: e9f4a921bd393c7ec619a097d056faafb71ff46520e4636354d4bac642424269 1775204 crac-dbgsym_2.5.2+dfsg-6_arm64.deb cdd2fc19c8667bf5c3de6b90d303067df8ed205160c03d58e91997ce63160a5c 6392 crac_2.5.2+dfsg-6_arm64.buildinfo 8050d1f217386da45c205e2d559afc0c0d9b9145584fac7418111181bdd4c0f9 447892 crac_2.5.2+dfsg-6_arm64.deb Files: 78c3a61549e4310e00c982910ce63238 1775204 debug optional crac-dbgsym_2.5.2+dfsg-6_arm64.deb e3b416704f394a9ff93c88b24cfa2f37 6392 science optional crac_2.5.2+dfsg-6_arm64.buildinfo a8ffea3640d34d4031989689576dc088 447892 science optional crac_2.5.2+dfsg-6_arm64.deb Sat Jun 15 01:10:22 UTC 2024 I: diffoscope 271 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_12-47374.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.NgF2U0zw/crac_2.5.2+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.NgF2U0zw/crac_2.5.2+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.NgF2U0zw/crac_2.5.2+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.NgF2U0zw/b1/crac_2.5.2+dfsg-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.NgF2U0zw/b2/crac_2.5.2+dfsg-6_arm64.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: 0.451s) 0.451s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.044s) 0.044s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 847ms CPU time consumed: 843ms Sat Jun 15 01:10:23 UTC 2024 I: diffoscope 271 found no differences in the changes files, and a .buildinfo file also exists. Sat Jun 15 01:10:23 UTC 2024 I: crac from trixie built successfully and reproducibly on arm64. Sat Jun 15 01:10:25 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Jun 15 01:10:25 UTC 2024 I: Submitting 8.0K b1/crac_2.5.2+dfsg-6_arm64.buildinfo.asc Sat Jun 15 01:10:26 UTC 2024 I: Submitting 8.0K b2/crac_2.5.2+dfsg-6_arm64.buildinfo.asc Sat Jun 15 01:10:27 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Jun 15 01:10:27 UTC 2024 I: Done submitting .buildinfo files. Sat Jun 15 01:10:27 UTC 2024 I: Removing signed crac_2.5.2+dfsg-6_arm64.buildinfo.asc files: removed './b1/crac_2.5.2+dfsg-6_arm64.buildinfo.asc' removed './b2/crac_2.5.2+dfsg-6_arm64.buildinfo.asc'