I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 8 18:41:33 -12 2021 I: pbuilder-time-stamp: 1631169693 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [crac_2.5.0+dfsg-3.dsc] I: copying [./crac_2.5.0+dfsg.orig.tar.xz] I: copying [./crac_2.5.0+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Sep 13 00:20:36 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./crac_2.5.0+dfsg-3.dsc dpkg-source: info: extracting crac in crac-2.5.0+dfsg dpkg-source: info: unpacking crac_2.5.0+dfsg.orig.tar.xz dpkg-source: info: unpacking crac_2.5.0+dfsg-3.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 fix_includes.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29952/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='29952' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.0Gb2goIZGY/pbuilderrc_FAyn --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0Gb2goIZGY/b1 --logfile b1/build.log crac_2.5.0+dfsg-3.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled9-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 7 02:48 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/29952/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), 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 ... 19168 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgkarrays-dev{a} libgkarrays1{a} libglib2.0-0{a} libgssapi-krb5-2{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts2{a} libicu63{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpopt0{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} lsb-base{a} m4{a} man-db{a} pkg-config{a} po-debconf{a} rsync{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 63 newly installed, 0 to remove and 0 not upgraded. Need to get 27.7 MB of archives. After unpacking 87.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3 [64.7 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3 [122 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3 [353 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3 [150 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1+deb10u1 [69.3 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1+deb10u1 [105 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libldap-2.4-2 arm64 2.4.47+dfsg-3+deb10u2 [216 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libnghttp2-14 arm64 1.36.0-2+deb10u1 [81.9 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libpsl5 arm64 0.20.2-2 [53.6 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [55.7 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 libcurl3-gnutls arm64 7.64.0-4+deb10u1 [310 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libdeflate0 arm64 1.2-1 [51.4 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libgkarrays1 arm64 2.1.0+dfsg-2 [53.4 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libgkarrays-dev arm64 2.1.0+dfsg-2 [81.6 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libgzstream0 arm64 1.5+dfsg-4 [6472 B] Get: 53 http://deb.debian.org/debian buster/main arm64 libgzstream-dev arm64 1.5+dfsg-4 [6800 B] Get: 54 http://deb.debian.org/debian buster/main arm64 libhts2 arm64 1.9-11 [277 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 liblzma-dev arm64 5.2.4-1 [209 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 libhts-dev arm64 1.9-11 [4338 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 libjellyfish-2.0-2 arm64 2.2.10-2 [60.1 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libjellyfish-2.0-dev arm64 2.2.10-2 [132 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libpopt0 arm64 1.16-12 [48.3 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 lsb-base all 10.2019051400 [28.4 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 pkg-config arm64 0.29-6 [62.2 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 rsync arm64 3.1.3-6 [385 kB] Fetched 27.7 MB in 11s (2624 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. 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Setting up libkrb5support0:arm64 (1.17-3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up libjellyfish-2.0-2:arm64 (2.2.10-2) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up libk5crypto3:arm64 (1.17-3) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgzstream0 (1.5+dfsg-4) ... Setting up liblzma-dev:arm64 (5.2.4-1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libssh2-1:arm64 (1.8.0-2.1) ... Setting up libkrb5-3:arm64 (1.17-3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up libpopt0:arm64 (1.16-12) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libjellyfish-2.0-dev:arm64 (2.2.10-2) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:arm64 (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up libgzstream-dev (1.5+dfsg-4) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:arm64 (1.17-3) ... Setting up libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up rsync (3.1.3-6) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libcurl3-gnutls:arm64 (7.64.0-4+deb10u1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libhts2:arm64 (1.9-11) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:arm64 (1.9-11) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/crac-2.5.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.0+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf aclocal: warning: couldn't open directory 'config/m4': No such file or directory libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config/m4'. libtoolize: copying file 'config/m4/libtool.m4' libtoolize: copying file 'config/m4/ltoptions.m4' libtoolize: copying file 'config/m4/ltsugar.m4' libtoolize: copying file 'config/m4/ltversion.m4' libtoolize: copying file 'config/m4/lt~obsolete.m4' configure.ac:147: installing 'config/compile' configure.ac:139: installing 'config/config.guess' configure.ac:139: installing 'config/config.sub' configure.ac:137: installing 'config/install-sh' configure.ac:137: installing 'config/missing' src/Makefile.am: installing 'config/depcomp' test_f/Makefile.am:109: warning: shell find . -name "*.should_get": non-POSIX variable name test_f/Makefile.am:109: (probably a GNU make extension) test_f/Makefile.am:110: warning: shell find . -name "*.fasta" -o -name "*.fa": non-POSIX variable name test_f/Makefile.am:110: (probably a GNU make extension) test_f/Makefile.am:111: warning: shell find . -name "*.fastq" -o -name "*.fq": non-POSIX variable name test_f/Makefile.am:111: (probably a GNU make extension) parallel-tests: installing 'config/test-driver' dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --libexecdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe 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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for gawk... (cached) mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes 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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for 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 ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.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 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... no checking whether to build static libraries... yes 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 whether sys/types.h defines makedev... no checking sys/mkdev.h usability... no checking sys/mkdev.h presence... no checking for sys/mkdev.h... no checking sys/sysmacros.h usability... yes checking sys/sysmacros.h presence... yes checking for sys/sysmacros.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking libintl.h usability... yes checking libintl.h presence... yes checking for libintl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking for memory.h... (cached) 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 sys/file.h usability... yes checking sys/file.h presence... yes checking for sys/file.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no 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... no checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) 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 gzread in -lz... yes checking for hts_open in -lhts... 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 -j8 make[1]: Entering directory '/build/crac-2.5.0+dfsg' Making all in src make[2]: Entering directory '/build/crac-2.5.0+dfsg/src' Making all in libReadsInfo make[3]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsInfo' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-bamUtils.o `test -f 'bamUtils.cpp' || echo './'`bamUtils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo './'`tagInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo './'`undeterminedErrorInfo.cpp samHeader.cpp: In member function 'bam_hdr_t* SamHeader::writeBamHeader(samFile*)': samHeader.cpp:160:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(out,h); ~~~~~~~~~~~~~^~~~~~~ In file included from ../libReadsReader/readsReader.h:57, from ../Read.h:55, from ../ReadIndex.h:52, from ../Support.h:59, from tagInfo.h:71, from tagInfo.cpp:53: ../libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ ../libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ ../libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ 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-2.5.0+dfsg/src/libReadsInfo' Making all in libSSA make[3]: Entering directory '/build/crac-2.5.0+dfsg/src/libSSA' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cracIndex.o cracIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitarray.o bitarray.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitrankw32int.o bitrankw32int.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o chrPosition.o chrPosition.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o HuffAlphabetRank.o HuffAlphabetRank.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Huffman_Codes.o Huffman_Codes.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateOnGenome.o locateOnGenome.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateTags.o locateTags.cpp cracIndex.cpp:85:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] cerr << "\tCompiled on " <<__DATE__ << endl << endl; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SSA.o SSA.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GenomeInfo.o GenomeInfo.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] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ /usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ /usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ In file included from ./seqan/basic.h:64, from ./seqan/sequence.h:27, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': ./seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': ./seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': ./seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^~~~~~~~~~ In file included from ./seqan/sequence.h:38, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': ./seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^~~~~~~~~~ In file included from ./seqan/sequence.h:51, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': ./seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': ./seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': ./seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': ./seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': ./seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': ./seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': ./seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': ./seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': ./seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': ./seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': ./seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': ./seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ In file included from ./seqan/sequence.h:53, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': ./seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./seqan/sequence.h:57, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./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:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^~~~~~~~~ ./seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': ./seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./seqan/sequence.h:62, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': ./seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^~~ In file included from ./seqan/index.h:82, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11, from cracIndex.cpp:67: ./seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': ./seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ ./seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': ./seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^~~~~~~ ./seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< Shape > >::Type TSize; ^~~~~ ./seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': ./seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ ./seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': ./seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ ./seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': ./seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ In file included from ./seqan/index.h:83, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11, from cracIndex.cpp:67: ./seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': ./seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ ./seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': ./seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^~~~~~~ ./seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': ./seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^~~~~~~ In file included from ./seqan/file.h:66, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13, from cracIndex.cpp:67: ./seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': ./seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^~~~ ./seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': ./seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^~~~~~~~~ In file included from ./seqan/file.h:69, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13, from cracIndex.cpp:67: ./seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': ./seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^~~~ In file included from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13, from cracIndex.cpp:67: /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from cracIndex.cpp:67: /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^~~~~~~~~ /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:745:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^~~~~~~~~ In file included from ./seqan/sequence.h:57, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': ./seqan/sequence/string_packed.h:906:43: required from 'typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]' ./seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]' ./seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]' /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:354:32: required from here ./seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] 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:958:50: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Iter >&) [with TContainer = seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::GetValue > >::Type = seqan::SimpleType]' ./seqan/basic/basic_proxy.h:242:17: required from 'typename seqan::GetValue >::Type seqan::getValue(const seqan::Proxy&) [with TSpec = seqan::IteratorProxy, seqan::Packed<> >, seqan::Packed<> > >; typename seqan::GetValue >::Type = seqan::SimpleType]' ./seqan/basic/basic_proxy.h:272:34: required from 'typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Packed<> >, seqan::Packed<> > > >; TSpec = seqan::IteratorProxy, seqan::Packed<> >, seqan::Packed<> > >; typename seqan::Convert >::Type = char]' ./seqan/basic/basic_converter.h:111:20: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy, seqan::Packed<> >, seqan::Packed<> > > >; typename seqan::Convert::Type = char]' cracIndex.cpp:224:50: required from here ./seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] In file included from ./seqan/basic.h:101, from ./seqan/sequence.h:27, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': ./seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' ./seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' ./seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' ./seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' ./seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; TExpand = const seqan::Tag; typename seqan::Size::Type = long unsigned int]' ./seqan/sequence/string_base.h:1459:52: required from 'typename seqan::Size >::Type seqan::resize(seqan::String&, TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc; TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' ./seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]' ./seqan/file/file_format_fasta.h:269:8: required from 'void seqan::read(TFile&, TData&, TSize, Fasta) [with TFile = std::basic_ifstream; TData = seqan::String, seqan::Alloc >; TSize = long unsigned int; seqan::Fasta = const seqan::Tag]' ./seqan/file/file_format_fasta.h:309:6: required from 'void seqan::read(TFile&, TData&, Fasta) [with TFile = std::basic_ifstream; TData = seqan::String, seqan::Alloc >; seqan::Fasta = const seqan::Tag]' cracIndex.cpp:142:40: required from here ./seqan/basic/basic_alphabet_trait_basic.h:207:9: 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] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./seqan/basic.h:106, from ./seqan/sequence.h:27, from /build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ rm -f libSSA.a ar cru libSSA.a bitarray.o bitrankw32int.o chrPosition.o HuffAlphabetRank.o Huffman_Codes.o locateOnGenome.o locateTags.o SSA.o utils.o GenomeInfo.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libSSA.a /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lpthread -lSSA -L/build/crac-2.5.0+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-2.5.0+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-2.5.0+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-2.5.0+dfsg/src/libSSA' Making all in libReadsReader make[3]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader' Making all in kseq make[4]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg/src/libReadsReader' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsReader' make[3]: Entering directory '/build/crac-2.5.0+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Classifier.o Classifier.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o classifyTags.o classifyTags.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GkReadIndex.o GkReadIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o JellyReadIndex.o JellyReadIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o crac.o crac.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Parameters.o Parameters.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SupportBreak.o SupportBreak.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o BreakList.o BreakList.cpp classifyTags.cpp:421:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] headerTemplate << "#Created on " <<__DATE__ << endl << "#" << endl; ^~~~~~~~ crac.cpp:213:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] printf("\tCompiled on %s.\n\n",__DATE__); ^~~~~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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] 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] inline LargeBinVect &operator=(const LargeBinVect &v) throw (std::bad_alloc); ^~~~~ 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:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] inline LargeBinVect &operator--() throw (BinVectOverflow); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] inline LargeBinVect Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc); ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241, 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.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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] 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] 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] LargeBinVect &LargeBinVect::operator=(const LargeBinVect &v) throw (std::bad_alloc) { ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241, 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.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] LargeBinVect &LargeBinVect::operator--() throw (BinVectOverflow) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] LargeBinVect LargeBinVect::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) { ^~~~~ In file included from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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, from GkReadIndex.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CandidatBreak.o CandidatBreak.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Support.o Support.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] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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] 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] inline LargeBinVect &operator=(const LargeBinVect &v) throw (std::bad_alloc); ^~~~~ 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:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] inline LargeBinVect &operator--() throw (BinVectOverflow); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] inline LargeBinVect Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc); ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241, 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.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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] 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] 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] LargeBinVect &LargeBinVect::operator=(const LargeBinVect &v) throw (std::bad_alloc) { ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241, 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.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] LargeBinVect &LargeBinVect::operator--() throw (BinVectOverflow) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] LargeBinVect LargeBinVect::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) { ^~~~~ In file included from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 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] 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] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 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=] } catch (bad_alloc e) { ^ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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 ./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] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ ./libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ ./libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 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] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ 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] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.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] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ locateServer.cpp: In function 'void* launchSubServer(void*)': locateServer.cpp:464:8: warning: unused variable 'threshold' [-Wunused-variable] uint threshold = indexTags->getFactorLength(); ^~~~~~~~~ locateServer.cpp:466:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] 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] 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] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.0+dfsg -I/build/crac-2.5.0+dfsg/src -I/build/crac-2.5.0+dfsg/src/libSSA -I/build/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Bitset.o Bitset.cpp Classifier.cpp: In member function 'virtual void SingleReadClassifier::classify()': Classifier.cpp:203:33: warning: 'bioundetermined_type' may be used uninitialized in this function [-Wmaybe-uninitialized] taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ suppoBreak->getPositionStartBreak(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bioundetermined_type, ~~~~~~~~~~~~~~~~~~~~~ message.c_str()); ~~~~~~~~~~~~~~~~ ln -s -f /build/crac-2.5.0+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-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-2.5.0+dfsg/src/libSSA -L/build/crac-2.5.0+dfsg/src/libReadsInfo -L/build/crac-2.5.0+dfsg/src/libReadsReader -ljellyfish-2.0 `pkg-config --libs libGkArrays` `pkg-config --libs libProgressBar` -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-2.5.0+dfsg/src/libSSA/libSSA.a /build/crac-2.5.0+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-2.5.0+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm libtool: link: g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.0+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-2.5.0+dfsg/src/libSSA -L/build/crac-2.5.0+dfsg/src/libReadsInfo -L/build/crac-2.5.0+dfsg/src/libReadsReader /usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so -lGkArrays -lProgressBar /build/crac-2.5.0+dfsg/src/libSSA/libSSA.a /build/crac-2.5.0+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-2.5.0+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-2.5.0+dfsg/src' make[2]: Leaving directory '/build/crac-2.5.0+dfsg/src' Making all in man make[2]: Entering directory '/build/crac-2.5.0+dfsg/man' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/crac-2.5.0+dfsg/man' Making all in scripts make[2]: Entering directory '/build/crac-2.5.0+dfsg/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/crac-2.5.0+dfsg/scripts' Making all in test_f make[2]: Entering directory '/build/crac-2.5.0+dfsg/test_f' Making all in causes make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f/causes' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/causes' Making all in bug make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f/bug' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/bug' Making all in cigar make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f/cigar' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/cigar' Making all in splices_adjust make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f/splices_adjust' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/splices_adjust' make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f' make[2]: Leaving directory '/build/crac-2.5.0+dfsg/test_f' make[2]: Entering directory '/build/crac-2.5.0+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/crac-2.5.0+dfsg' make[1]: Leaving directory '/build/crac-2.5.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/crac-2.5.0+dfsg' # Sequence of tests is important so parallel execution is no option dh_auto_test --no-parallel make -j1 check VERBOSE=1 make[2]: Entering directory '/build/crac-2.5.0+dfsg' Making check in src make[3]: Entering directory '/build/crac-2.5.0+dfsg/src' Making check in libReadsInfo make[4]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsInfo' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsInfo' Making check in libSSA make[4]: Entering directory '/build/crac-2.5.0+dfsg/src/libSSA' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/src/libSSA' Making check in libReadsReader make[4]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader' Making check in kseq make[5]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader' make[5]: Nothing to be done for 'check-am'. make[5]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsReader' make[4]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsReader' make[4]: Entering directory '/build/crac-2.5.0+dfsg/src' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/src' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/src' Making check in man make[3]: Entering directory '/build/crac-2.5.0+dfsg/man' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/crac-2.5.0+dfsg/man' Making check in scripts make[3]: Entering directory '/build/crac-2.5.0+dfsg/scripts' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/crac-2.5.0+dfsg/scripts' Making check in test_f make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f' Making check in causes make[4]: Entering directory '/build/crac-2.5.0+dfsg/test_f/causes' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/causes' Making check in bug make[4]: Entering directory '/build/crac-2.5.0+dfsg/test_f/bug' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/bug' Making check in cigar make[4]: Entering directory '/build/crac-2.5.0+dfsg/test_f/cigar' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/cigar' Making check in splices_adjust make[4]: Entering directory '/build/crac-2.5.0+dfsg/test_f/splices_adjust' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/splices_adjust' make[4]: Entering directory '/build/crac-2.5.0+dfsg/test_f' make check-TESTS make[5]: Entering directory '/build/crac-2.5.0+dfsg/test_f' make[6]: Entering directory '/build/crac-2.5.0+dfsg/test_f' PASS: index_genomes.sh PASS: launch_sg.sh PASS: test_index.sh ============================================================================ Testsuite summary for crac 2.5.0 ============================================================================ # TOTAL: 3 # PASS: 3 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[6]: Leaving directory '/build/crac-2.5.0+dfsg/test_f' make[5]: Leaving directory '/build/crac-2.5.0+dfsg/test_f' make[4]: Leaving directory '/build/crac-2.5.0+dfsg/test_f' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f' make[3]: Entering directory '/build/crac-2.5.0+dfsg' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/crac-2.5.0+dfsg' make[2]: Leaving directory '/build/crac-2.5.0+dfsg' make[1]: Leaving directory '/build/crac-2.5.0+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j1 install DESTDIR=/build/crac-2.5.0\+dfsg/debian/crac AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/crac-2.5.0+dfsg' Making install in src make[2]: Entering directory '/build/crac-2.5.0+dfsg/src' Making install in libReadsInfo make[3]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsInfo' make[4]: Entering directory '/build/crac-2.5.0+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-2.5.0+dfsg/src/libReadsInfo' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsInfo' Making install in libSSA make[3]: Entering directory '/build/crac-2.5.0+dfsg/src/libSSA' make[4]: Entering directory '/build/crac-2.5.0+dfsg/src/libSSA' /bin/mkdir -p '/build/crac-2.5.0+dfsg/debian/crac/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/build/crac-2.5.0+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac-index /build/crac-2.5.0+dfsg/debian/crac/usr/bin/crac-index make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/src/libSSA' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/src/libSSA' Making install in libReadsReader make[3]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader' Making install in kseq make[4]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/crac-2.5.0+dfsg/debian/crac/usr/include/crac-2.5.0/kseq' /usr/bin/install -c -m 644 kseq.h '/build/crac-2.5.0+dfsg/debian/crac/usr/include/crac-2.5.0/kseq' make[5]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/build/crac-2.5.0+dfsg/src/libReadsReader' make[5]: Entering directory '/build/crac-2.5.0+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-2.5.0+dfsg/src/libReadsReader' make[4]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsReader' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/src/libReadsReader' make[3]: Entering directory '/build/crac-2.5.0+dfsg/src' make[4]: Entering directory '/build/crac-2.5.0+dfsg/src' /bin/mkdir -p '/build/crac-2.5.0+dfsg/debian/crac/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c crac '/build/crac-2.5.0+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac /build/crac-2.5.0+dfsg/debian/crac/usr/bin/crac make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-2.5.0+dfsg/src' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/src' make[2]: Leaving directory '/build/crac-2.5.0+dfsg/src' Making install in man make[2]: Entering directory '/build/crac-2.5.0+dfsg/man' make[3]: Entering directory '/build/crac-2.5.0+dfsg/man' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/crac-2.5.0+dfsg/debian/crac/usr/share/man/man1' /usr/bin/install -c -m 644 crac.1 '/build/crac-2.5.0+dfsg/debian/crac/usr/share/man/man1' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/man' make[2]: Leaving directory '/build/crac-2.5.0+dfsg/man' Making install in scripts make[2]: Entering directory '/build/crac-2.5.0+dfsg/scripts' make[3]: Entering directory '/build/crac-2.5.0+dfsg/scripts' /bin/mkdir -p '/build/crac-2.5.0+dfsg/debian/crac/usr/bin' /usr/bin/install -c crac-client '/build/crac-2.5.0+dfsg/debian/crac/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/crac-2.5.0+dfsg/scripts' make[2]: Leaving directory '/build/crac-2.5.0+dfsg/scripts' Making install in test_f make[2]: Entering directory '/build/crac-2.5.0+dfsg/test_f' Making install in causes make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f/causes' make[4]: Entering directory '/build/crac-2.5.0+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-2.5.0+dfsg/test_f/causes' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/causes' Making install in bug make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f/bug' make[4]: Entering directory '/build/crac-2.5.0+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-2.5.0+dfsg/test_f/bug' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/bug' Making install in cigar make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f/cigar' make[4]: Entering directory '/build/crac-2.5.0+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-2.5.0+dfsg/test_f/cigar' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/cigar' Making install in splices_adjust make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f/splices_adjust' make[4]: Entering directory '/build/crac-2.5.0+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-2.5.0+dfsg/test_f/splices_adjust' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f/splices_adjust' make[3]: Entering directory '/build/crac-2.5.0+dfsg/test_f' make[4]: Entering directory '/build/crac-2.5.0+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-2.5.0+dfsg/test_f' make[3]: Leaving directory '/build/crac-2.5.0+dfsg/test_f' make[2]: Leaving directory '/build/crac-2.5.0+dfsg/test_f' make[2]: Entering directory '/build/crac-2.5.0+dfsg' make[3]: Entering directory '/build/crac-2.5.0+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-2.5.0+dfsg' make[2]: Leaving directory '/build/crac-2.5.0+dfsg' make[1]: Leaving directory '/build/crac-2.5.0+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/crac-2.5.0+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-2.5.0+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'crac-dbgsym' in '../crac-dbgsym_2.5.0+dfsg-3_arm64.deb'. dpkg-deb: building package 'crac' in '../crac_2.5.0+dfsg-3_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../crac_2.5.0+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/29952 and its subdirectories I: Current time: Wed Sep 8 18:43:53 -12 2021 I: pbuilder-time-stamp: 1631169833