Tue May 23 22:43:34 UTC 2023 I: starting to build crac/bookworm/armhf on jenkins on '2023-05-23 22:43' Tue May 23 22:43:34 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_6/995/console.log Tue May 23 22:43:34 UTC 2023 I: Downloading source for bookworm/crac=2.5.2+dfsg-5 --2023-05-23 22:43:34-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/crac/crac_2.5.2%2bdfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2081 (2.0K) [text/prs.lines.tag] Saving to: ‘crac_2.5.2+dfsg-5.dsc’ 0K .. 100% 159M=0s 2023-05-23 22:43:34 (159 MB/s) - ‘crac_2.5.2+dfsg-5.dsc’ saved [2081/2081] Tue May 23 22:43:34 UTC 2023 I: crac_2.5.2+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: crac Binary: crac Architecture: any Version: 2.5.2+dfsg-5 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), 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 f58c67f600cbece333557be64a2556a09b8fd509 15060 crac_2.5.2+dfsg-5.debian.tar.xz Checksums-Sha256: 66198b60f8bebb4d923a1230231949f8c7dc1adce92176b45f041726496c69fd 658188 crac_2.5.2+dfsg.orig.tar.xz 5acd56ec96ecffcefe04b31ec8a940565544b5e633db302e56ca8eb691e1957c 15060 crac_2.5.2+dfsg-5.debian.tar.xz Files: a58db6dc3a449b7dd4bea567bbb7233a 658188 crac_2.5.2+dfsg.orig.tar.xz 55b2051e000b1fe2ec859733b8b7f64b 15060 crac_2.5.2+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmGIRjERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEILg//Zi3ThK7zxGQ8eKs4PKS+n7jmpPrK40ZX xex16NyKXWTXFPMjIl4aisza1E5q9xEpxO8zqOzgzWlY6+ooneOIR3/XS6NOnNG/ 2QzoNA6R5e5UXrynVaDOTOg97YZNzuTG7KU1hdFAr0MYJ0S2Eaww67xN5aWqWMLD qmP7hvTMYXX1oVZ4kUzLSl/n6za8vcgLHzQ7uhh6C6SZJ5kiJgYsTr/v64WK2Rtt fRFTlscqype4m27L859mUHtUvPPSYc9kA4j5EAYO+pJajeLaLJ7F+EedLYMssgjn zCQGNQmdimFCOEdhzwvwPRRQG3NmpeFlZscc/vW8joUbuazlllw5oTrYzrqCBrHV A55xRAxG0/BO35HbLKNminu5cavwT0TPs8i6blFOUpsXe/CW9BVZdhvrjTyAyTDp iWw0p8wFYj5fclPmbDdyP0vYYyIvFcRMOyqZ60zT4dEXLd8lQ+PTl3ohR1LPePT3 5CB2aoJIu4FK/9NKED0I73Jwt2f8Tbd7i0bogrVAakOQhT8OlOtpASN7PXx88zRz tEHWrKF0DBOZHqAUZzdAPnl5DQPF0kF64+6f0uuIJEQ050ss6nidEdZ8Zh6yDtW6 Zqw4jFL6Tx5jifQlCti5tc+IEUrVVsM++Cszvo1dBckhwCIzMm4KD+cvzukleYYw CcH6lofYf8k= =woPT -----END PGP SIGNATURE----- Tue May 23 22:43:34 UTC 2023 I: Checking whether the package is not for us Tue May 23 22:43:34 UTC 2023 I: Starting 1st build on remote node virt64b-armhf-rb.debian.net. Tue May 23 22:43:34 UTC 2023 I: Preparing to do remote build '1' on virt64b-armhf-rb.debian.net. Tue May 23 22:51:00 UTC 2023 I: Deleting $TMPDIR on virt64b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 23 10:43:49 -12 2023 I: pbuilder-time-stamp: 1684881829 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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-5.dsc] I: copying [./crac_2.5.2+dfsg.orig.tar.xz] I: copying [./crac_2.5.2+dfsg-5.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 7 09:33:37 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./crac_2.5.2+dfsg-5.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-5.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/8891/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='5fddbf245fe74d97acc3bc62a6040b0e' 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='8891' 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.TND2GIaZ/pbuilderrc_KEJu --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TND2GIaZ/b1 --logfile b1/build.log crac_2.5.2+dfsg-5.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64b 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/8891/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19329 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 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: 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} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgkarrays-dev{a} libgkarrays1{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpopt0{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 23.7 MB of archives. After unpacking 81.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libpopt0 armhf 1.19+dfsg-1 [40.2 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf rsync armhf 3.2.7-1 [395 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 23 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 25 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libcurl3-gnutls armhf 7.88.1-9 [343 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libcurl4-gnutls-dev armhf 7.88.1-9 [448 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libdeflate-dev armhf 1.14-1 [48.7 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libgkarrays1 armhf 2.1.0+dfsg-4 [51.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libgkarrays-dev armhf 2.1.0+dfsg-4 [81.5 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libgzstream0 armhf 1.5+git20171107.9a20658-1+b2 [6900 B] Get: 48 http://deb.debian.org/debian bookworm/main armhf libgzstream-dev armhf 1.5+git20171107.9a20658-1+b2 [7180 B] Get: 49 http://deb.debian.org/debian bookworm/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libhts3 armhf 1.16+ds-3 [375 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf liblzma-dev armhf 5.4.1-0.2 [248 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libhts-dev armhf 1.16+ds-3 [1517 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libjellyfish-2.0-2 armhf 2.3.0-15+b3 [55.3 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libjellyfish-2.0-dev armhf 2.3.0-15+b3 [130 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] Fetched 23.7 MB in 3s (6794 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpopt0:armhf. (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 ... 19329 files and directories currently installed.) Preparing to unpack .../00-libpopt0_1.19+dfsg-1_armhf.deb ... Unpacking libpopt0:armhf (1.19+dfsg-1) ... Selecting previously unselected package rsync. Preparing to unpack .../01-rsync_3.2.7-1_armhf.deb ... Unpacking rsync (3.2.7-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... 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Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. 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Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../24-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../26-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-12_armhf.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../32-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../33-libsasl2-modules-db_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../34-libsasl2-2_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../35-libldap-2.5-0_2.5.13+dfsg-5_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../36-libnghttp2-14_1.52.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.52.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../37-libpsl5_0.21.2-1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../38-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. 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Setting up libmagic1:armhf (1:5.44-3) ... Setting up libdeflate0:armhf (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up libjellyfish-2.0-2:armhf (2.3.0-15+b3) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:armhf (1.8.1-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up autopoint (0.21-12) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up libgzstream0:armhf (1.5+git20171107.9a20658-1+b2) ... Setting up liblzma-dev:armhf (5.4.1-0.2) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up libdeflate-dev:armhf (1.14-1) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up libpopt0:armhf (1.19+dfsg-1) ... 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 (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libjellyfish-2.0-dev (2.3.0-15+b3) ... Setting up libtool (2.4.7-5) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Setting up pkgconf:armhf (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libgzstream-dev:armhf (1.5+git20171107.9a20658-1+b2) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:armhf (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up rsync (3.2.7-1) ... 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 libcurl3-gnutls:armhf (7.88.1-9) ... Setting up libcurl4-gnutls-dev:armhf (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:armhf (1.16+ds-3) ... Setting up libhts-dev:armhf (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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/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-5_source.changes dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.2+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf 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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... /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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /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 arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf 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... /bin/dd checking how to truncate binary pipes... /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 -j3 make[1]: Entering directory '/build/crac-2.5.2+dfsg' Making all in src make[2]: Entering directory '/build/crac-2.5.2+dfsg/src' Making all in libReadsInfo make[3]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsInfo' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-BioTagIndelInfo.o `test -f 'BioTagIndelInfo.cpp' || echo './'`BioTagIndelInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-BioUndeterminedInfo.o `test -f 'BioUndeterminedInfo.cpp' || echo './'`BioUndeterminedInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-cigarTypes.o `test -f 'cigarTypes.cpp' || echo './'`cigarTypes.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-Cigar.o `test -f 'Cigar.cpp' || echo './'`Cigar.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-DuplicationInfo.o `test -f 'DuplicationInfo.cpp' || echo './'`DuplicationInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-genericInfo.o `test -f 'genericInfo.cpp' || echo './'`genericInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-IndelInfo.o `test -f 'IndelInfo.cpp' || echo './'`IndelInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-repetitionInfo.o `test -f 'repetitionInfo.cpp' || echo './'`repetitionInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SeqErrInfo.o `test -f 'SeqErrInfo.cpp' || echo './'`SeqErrInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SNPInfo.o `test -f 'SNPInfo.cpp' || echo './'`SNPInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceInfo.o `test -f 'SpliceInfo.cpp' || echo './'`SpliceInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceInterInfo.o `test -f 'SpliceInterInfo.cpp' || echo './'`SpliceInterInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceIntraInfo.o `test -f 'SpliceIntraInfo.cpp' || echo './'`SpliceIntraInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceNoCoverInfo.o `test -f 'SpliceNoCoverInfo.cpp' || echo './'`SpliceNoCoverInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SplicingInfo.o `test -f 'SplicingInfo.cpp' || echo './'`SplicingInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-samLine.o `test -f 'samLine.cpp' || echo './'`samLine.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-samHeader.o `test -f 'samHeader.cpp' || echo './'`samHeader.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-bamUtils.o `test -f 'bamUtils.cpp' || echo './'`bamUtils.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); | ~~~~~~~~~~~~~^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo './'`tagInfo.cpp samLine.cpp: In constructor 'OptionalField::OptionalField(const char*, char)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, 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*, 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*, 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*, 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*, 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*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo './'`undeterminedErrorInfo.cpp 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 member function 'void SamLine::addOptionalField(const char*, char)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, 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*, 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*, 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*, 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*, 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/crac-2.5.2+dfsg/src/libReadsInfo' Making all in libSSA make[3]: Entering directory '/build/crac-2.5.2+dfsg/src/libSSA' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cracIndex.o cracIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitarray.o bitarray.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitrankw32int.o bitrankw32int.cpp cracIndex.cpp:85:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 85 | cerr << "\tCompiled on " <<__DATE__ << endl << endl; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o chrPosition.o chrPosition.cpp In file included from ./seqan/basic.h:64, from ./seqan/sequence.h:27, from /build/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; | ^~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o HuffAlphabetRank.o HuffAlphabetRank.cpp 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 ./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; | ^~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Huffman_Codes.o Huffman_Codes.cpp In file included from ./seqan/index.h:82, from /build/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/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, from /build/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/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': /build/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/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/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/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/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': /build/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/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/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': /build/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/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': /build/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 = 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 = 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 = unsigned int]' /build/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 = unsigned int; TExpand = TagExact_; typename Size > >::Type = 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 = 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 = unsigned int; TExpand = TagExact_; typename Size >::Type = unsigned int]' ./seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = String, Alloc >; TSize = unsigned int; typename Size::Type = 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 = 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 | ^~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateOnGenome.o locateOnGenome.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateTags.o locateTags.cpp 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) | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SSA.o SSA.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GenomeInfo.o GenomeInfo.cpp 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 /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lpthread -lSSA -L/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac-index cracIndex.o -lSSA -L/build/crac-2.5.2+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src/libSSA' Making all in libReadsReader make[3]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader' Making all in kseq make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Entering directory '/build/crac-2.5.2+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Classifier.o Classifier.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o classifyTags.o classifyTags.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GkReadIndex.o GkReadIndex.cpp classifyTags.cpp:421:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 421 | headerTemplate << "#Created on " <<__DATE__ << endl << "#" << endl; | ^~~~~~~~ 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); | ^~~~~ 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) | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o JellyReadIndex.o JellyReadIndex.cpp 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 ./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) | ^~~~~~~~~ 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) | ^~~~~~~~~ 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; | ^~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o crac.o crac.cpp crac.cpp:213:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 213 | printf("\tCompiled on %s.\n\n",__DATE__); | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Parameters.o Parameters.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SupportBreak.o SupportBreak.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o BreakList.o BreakList.cpp 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) { | ^~~~~ /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); | ^~~~~ 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) | ^~~~~~~~~ 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) { | ^ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CandidatBreak.o CandidatBreak.cpp 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) | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Support.o Support.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateServer.o locateServer.cpp 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) | ^~~~~~~~~ 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) | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Bitset.o Bitset.cpp ln -s -f /build/crac-2.5.2+dfsg/src/libSSA/crac-index crac-index /bin/bash ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-2.5.2+dfsg/src/libSSA -L/build/crac-2.5.2+dfsg/src/libReadsInfo -L/build/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/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/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/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/crac-2.5.2+dfsg/src/libSSA -L/build/crac-2.5.2+dfsg/src/libReadsInfo -L/build/crac-2.5.2+dfsg/src/libReadsReader /usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so -lGkArrays -lProgressBar /build/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/src' Making all in man make[2]: Entering directory '/build/crac-2.5.2+dfsg/man' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/crac-2.5.2+dfsg/man' Making all in scripts make[2]: Entering directory '/build/crac-2.5.2+dfsg/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/crac-2.5.2+dfsg/scripts' Making all in test_f make[2]: Entering directory '/build/crac-2.5.2+dfsg/test_f' Making all in causes make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f/causes' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/causes' Making all in bug make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f/bug' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/bug' Making all in cigar make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f/cigar' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/cigar' Making all in splices_adjust make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/test_f' make[2]: Entering directory '/build/crac-2.5.2+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/crac-2.5.2+dfsg' make[1]: Leaving directory '/build/crac-2.5.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/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/crac-2.5.2+dfsg' Making check in src make[3]: Entering directory '/build/crac-2.5.2+dfsg/src' Making check in libReadsInfo make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsInfo' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsInfo' Making check in libSSA make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libSSA' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libSSA' Making check in libReadsReader make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader' Making check in kseq make[5]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader' make[5]: Nothing to be done for 'check-am'. make[5]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader' make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader' make[4]: Entering directory '/build/crac-2.5.2+dfsg/src' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src' Making check in man make[3]: Entering directory '/build/crac-2.5.2+dfsg/man' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/man' Making check in scripts make[3]: Entering directory '/build/crac-2.5.2+dfsg/scripts' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/scripts' Making check in test_f make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f' Making check in causes make[4]: Entering directory '/build/crac-2.5.2+dfsg/test_f/causes' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/causes' Making check in bug make[4]: Entering directory '/build/crac-2.5.2+dfsg/test_f/bug' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/bug' Making check in cigar make[4]: Entering directory '/build/crac-2.5.2+dfsg/test_f/cigar' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/cigar' Making check in splices_adjust make[4]: Entering directory '/build/crac-2.5.2+dfsg/test_f/splices_adjust' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/splices_adjust' make[4]: Entering directory '/build/crac-2.5.2+dfsg/test_f' make check-TESTS make[5]: Entering directory '/build/crac-2.5.2+dfsg/test_f' make[6]: Entering directory '/build/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/crac-2.5.2+dfsg/test_f' make[5]: Leaving directory '/build/crac-2.5.2+dfsg/test_f' make[4]: Leaving directory '/build/crac-2.5.2+dfsg/test_f' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f' make[3]: Entering directory '/build/crac-2.5.2+dfsg' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg' make[2]: Leaving directory '/build/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/crac-2.5.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/crac/ make -j1 install DESTDIR=/build/crac-2.5.2\+dfsg/debian/crac AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/crac-2.5.2+dfsg' Making install in src make[2]: Entering directory '/build/crac-2.5.2+dfsg/src' Making install in libReadsInfo make[3]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsInfo' make[4]: Entering directory '/build/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/crac-2.5.2+dfsg/src/libReadsInfo' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsInfo' Making install in libSSA make[3]: Entering directory '/build/crac-2.5.2+dfsg/src/libSSA' make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libSSA' /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac-index /build/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/crac-2.5.2+dfsg/src/libSSA' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src/libSSA' Making install in libReadsReader make[3]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader' Making install in kseq make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' /usr/bin/install -c -m 644 kseq.h '/build/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' make[5]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader' make[5]: Entering directory '/build/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/crac-2.5.2+dfsg/src/libReadsReader' make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Entering directory '/build/crac-2.5.2+dfsg/src' make[4]: Entering directory '/build/crac-2.5.2+dfsg/src' /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c crac '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac /build/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/crac-2.5.2+dfsg/src' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/src' Making install in man make[2]: Entering directory '/build/crac-2.5.2+dfsg/man' make[3]: Entering directory '/build/crac-2.5.2+dfsg/man' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' /usr/bin/install -c -m 644 crac.1 '/build/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/man' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/man' Making install in scripts make[2]: Entering directory '/build/crac-2.5.2+dfsg/scripts' make[3]: Entering directory '/build/crac-2.5.2+dfsg/scripts' /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' /usr/bin/install -c crac-client '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/scripts' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/scripts' Making install in test_f make[2]: Entering directory '/build/crac-2.5.2+dfsg/test_f' Making install in causes make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f/causes' make[4]: Entering directory '/build/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/crac-2.5.2+dfsg/test_f/causes' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/causes' Making install in bug make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f/bug' make[4]: Entering directory '/build/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/crac-2.5.2+dfsg/test_f/bug' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/bug' Making install in cigar make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f/cigar' make[4]: Entering directory '/build/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/crac-2.5.2+dfsg/test_f/cigar' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/cigar' Making install in splices_adjust make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f/splices_adjust' make[4]: Entering directory '/build/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/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Entering directory '/build/crac-2.5.2+dfsg/test_f' make[4]: Entering directory '/build/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/crac-2.5.2+dfsg/test_f' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/test_f' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/test_f' make[2]: Entering directory '/build/crac-2.5.2+dfsg' make[3]: Entering directory '/build/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/crac-2.5.2+dfsg' make[2]: Leaving directory '/build/crac-2.5.2+dfsg' make[1]: Leaving directory '/build/crac-2.5.2+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/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/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: debian/crac/usr/bin/crac contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/crac/usr/bin/crac-index contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'crac-dbgsym' in '../crac-dbgsym_2.5.2+dfsg-5_armhf.deb'. dpkg-deb: building package 'crac' in '../crac_2.5.2+dfsg-5_armhf.deb'. dpkg-genbuildinfo --build=binary -O../crac_2.5.2+dfsg-5_armhf.buildinfo dpkg-genchanges --build=binary -O../crac_2.5.2+dfsg-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/8891 and its subdirectories I: Current time: Tue May 23 10:50:42 -12 2023 I: pbuilder-time-stamp: 1684882242 Tue May 23 22:51:03 UTC 2023 I: 1st build successful. Starting 2nd build on remote node virt32b-armhf-rb.debian.net. Tue May 23 22:51:03 UTC 2023 I: Preparing to do remote build '2' on virt32b-armhf-rb.debian.net. Tue May 23 22:55:12 UTC 2023 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. Tue May 23 22:55:15 UTC 2023 I: crac_2.5.2+dfsg-5_armhf.changes: Format: 1.8 Date: Sun, 07 Nov 2021 22:28:49 +0100 Source: crac Binary: crac crac-dbgsym Architecture: armhf Version: 2.5.2+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: crac - integrated RNA-Seq read analysis Closes: 998787 Changes: crac (2.5.2+dfsg-5) unstable; urgency=medium . * Fix bashism in configure script Closes: #998787 * Standards-Version: 4.6.0 (routine-update) * Autopkgtest fails due to tempfile usage - use mktemp instead Checksums-Sha1: d1b80e4e42e99691dacb68b6afd4dc93c21a275c 1791792 crac-dbgsym_2.5.2+dfsg-5_armhf.deb 81b17f21fa60c836e15b846cadb2b03d22bd7cdb 6086 crac_2.5.2+dfsg-5_armhf.buildinfo 6c218af978bc3d42a59adbb546e1027c5784f6ae 425340 crac_2.5.2+dfsg-5_armhf.deb Checksums-Sha256: a9dfb286a9c35b56ea7c38afe3dbcb029e78e1ae288c931ee0d658228720d74d 1791792 crac-dbgsym_2.5.2+dfsg-5_armhf.deb 947165e734c15345d4d079deda371a0a158e2432cca8d4ce41132620e2fe072f 6086 crac_2.5.2+dfsg-5_armhf.buildinfo c2e9e93f2ce3351adb657be01dbdb5b3a82a37c69018d2cc1d6d02898980ca63 425340 crac_2.5.2+dfsg-5_armhf.deb Files: 24063f50e6a587bff7a26a888a9b451c 1791792 debug optional crac-dbgsym_2.5.2+dfsg-5_armhf.deb fd14b7fa46bd26d51dd40b0a699b4fdf 6086 science optional crac_2.5.2+dfsg-5_armhf.buildinfo c57511283a6259848262cbd10d30ed06 425340 science optional crac_2.5.2+dfsg-5_armhf.deb Tue May 23 22:55:16 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.TND2GIaZ/crac_2.5.2+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.TND2GIaZ/crac_2.5.2+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.TND2GIaZ/crac_2.5.2+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.TND2GIaZ/b1/crac_2.5.2+dfsg-5_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.TND2GIaZ/b2/crac_2.5.2+dfsg-5_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.342s) 0.341s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.039s) 0.038s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Tue May 23 22:55:18 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Tue May 23 22:55:18 UTC 2023 I: crac from bookworm built successfully and reproducibly on armhf. Tue May 23 22:55:20 UTC 2023 I: Submitting .buildinfo files to external archives: Tue May 23 22:55:20 UTC 2023 I: Submitting 8.0K b1/crac_2.5.2+dfsg-5_armhf.buildinfo.asc Tue May 23 22:55:21 UTC 2023 I: Submitting 8.0K b2/crac_2.5.2+dfsg-5_armhf.buildinfo.asc Tue May 23 22:55:22 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 23 22:55:22 UTC 2023 I: Done submitting .buildinfo files. Tue May 23 22:55:22 UTC 2023 I: Removing signed crac_2.5.2+dfsg-5_armhf.buildinfo.asc files: removed './b1/crac_2.5.2+dfsg-5_armhf.buildinfo.asc' removed './b2/crac_2.5.2+dfsg-5_armhf.buildinfo.asc'