I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 28 03:44:01 +14 2024 I: pbuilder-time-stamp: 1714225441 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [segemehl_0.3.4-5.dsc] I: copying [./segemehl_0.3.4.orig.tar.xz] I: copying [./segemehl_0.3.4-5.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Aug 24 16:51:21 2021 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./segemehl_0.3.4-5.dsc: no acceptable signature found dpkg-source: info: extracting segemehl in segemehl-0.3.4 dpkg-source: info: unpacking segemehl_0.3.4.orig.tar.xz dpkg-source: info: unpacking segemehl_0.3.4-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying rpath.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying arm64.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/73462/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 27 13:44 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/73462/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/73462/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=ee11b82adaaa41bea78472e25ce307c1 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=73462 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Cwxekbj5/pbuilderrc_9tPF --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Cwxekbj5/b2 --logfile b2/build.log segemehl_0.3.4-5.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 27 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/73462/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkg-config, libhts-dev, libncurses-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19694 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses-dev; however: Package libncurses-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 25.7 MB of archives. After unpacking 95.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-7 [93.0 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.7.1-3 [432 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.7.1-3 [537 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.4+20240414-1 [349 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Fetched 25.7 MB in 2s (16.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19694 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3+b1_amd64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-7_amd64.deb ... Unpacking bsdextrautils (2.40-7) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../30-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../31-libcom-err2_1.47.0-2.4_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.0-2.4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../32-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../33-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../34-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../35-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../36-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../37-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../38-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../39-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../40-libnghttp2-14_1.61.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../41-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../42-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../43-libssh2-1t64_1.11.0-4.1+b2_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. 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Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libncurses-dev:amd64 (6.4+20240414-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up pkgconf:amd64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up pkg-config:amd64 (1.8.1-1+b2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.7.1-3) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libhts-dev:amd64 (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-18) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/73462/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/73462/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/segemehl-0.3.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../segemehl_0.3.4-5_source.changes dpkg-buildpackage: info: source package segemehl dpkg-buildpackage: info: source version 0.3.4-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j20 clean make[1]: Entering directory '/build/reproducible-path/segemehl-0.3.4' Cleaning... rm -f -r build segemehl haarz make[1]: Leaving directory '/build/reproducible-path/segemehl-0.3.4' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/segemehl-0.3.4' dh_auto_build -- all make -j20 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/build/reproducible-path/segemehl-0.3.4' Building... library for source build/nw.o Building... library for source build/bgzip.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/nw.o libs/nw.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bgzip.o libs/bgzip.c Building... library for source build/pigeon.o Building... library for source build/biofiles.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/pigeon.o libs/pigeon.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/biofiles.o libs/biofiles.c Building... library for source build/gzip.o Building... library for source build/fileBins.o Building... library for source build/locus.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/gzip.o libs/gzip.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileBins.o libs/fileBins.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/locus.o libs/locus.c Building... library for source build/vstack.o Building... library for source build/aluruSort.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vstack.o libs/vstack.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/aluruSort.o libs/aluruSort.c Building... library for source build/splitalign.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/splitalign.o libs/splitalign.c Building... library for source build/mathematics.o Building... library for source build/mappingqual.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mathematics.o libs/mathematics.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mappingqual.o libs/mappingqual.c Building... library for source build/segemehl_helper.o Building... library for source build/haarz.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/segemehl_helper.o libs/segemehl_helper.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/haarz.o libs/haarz.c Building... library for source build/sw.o Building... library for source build/bamio.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sw.o libs/sw.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bamio.o libs/bamio.c In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/bitvectoralg.h:32, from include/splitalign.h:29, from libs/splitalign.c:32: libs/splitalign.c: In function 'bl_fixSplitAlignHoffmann': Building... library for source build/charsequence.o include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1323:25: note: in expansion of macro 'FREEMEMORY' 1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); | ^~~~~~~~~~ libs/splitalign.c:1323:7: note: some parts of macro expansion are not guarded by this 'if' clause 1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1324:25: note: in expansion of macro 'FREEMEMORY' 1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); | ^~~~~~~~~~ libs/splitalign.c:1324:7: note: some parts of macro expansion are not guarded by this 'if' clause 1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1325:26: note: in expansion of macro 'FREEMEMORY' 1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); | ^~~~~~~~~~ libs/splitalign.c:1325:7: note: some parts of macro expansion are not guarded by this 'if' clause 1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1326:26: note: in expansion of macro 'FREEMEMORY' 1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); | ^~~~~~~~~~ libs/splitalign.c:1326:7: note: some parts of macro expansion are not guarded by this 'if' clause 1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); | ^~ libs/splitalign.c: In function 'bl_fixSplitAlignBrendel': Building... library for source build/samio.o include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1565:27: note: in expansion of macro 'FREEMEMORY' 1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); | ^~~~~~~~~~ In file included from libs/fileBins.c:51: libs/fileBins.c: In function 'bl_fileBinsSortLine': libs/splitalign.c:1565:9: note: some parts of macro expansion are not guarded by this 'if' clause 1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1566:27: note: in expansion of macro 'FREEMEMORY' 1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); | ^~~~~~~~~~ libs/splitalign.c:1566:9: note: some parts of macro expansion are not guarded by this 'if' clause 1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1567:28: note: in expansion of macro 'FREEMEMORY' 1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); | ^~~~~~~~~~ libs/splitalign.c:1567:9: note: some parts of macro expansion are not guarded by this 'if' clause 1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/fileBins.c:901:18: note: in expansion of macro 'FREEMEMORY' 901 | if(fileSort) FREEMEMORY(space, line); | ^~~~~~~~~~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1568:28: note: in expansion of macro 'FREEMEMORY' 1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); | ^~~~~~~~~~ libs/fileBins.c:901:5: note: some parts of macro expansion are not guarded by this 'if' clause 901 | if(fileSort) FREEMEMORY(space, line); | ^~ libs/splitalign.c:1568:9: note: some parts of macro expansion are not guarded by this 'if' clause 1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); | ^~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/charsequence.o libs/charsequence.c In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/segemehl.h:44, from libs/pigeon.c:35: libs/pigeon.c: In function 'pigeon': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/pigeon.c:352:13: note: in expansion of macro 'FREEMEMORY' 352 | if(check) FREEMEMORY(space, check); | ^~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samio.o libs/samio.c libs/pigeon.c:352:3: note: some parts of macro expansion are not guarded by this 'if' clause 352 | if(check) FREEMEMORY(space, check); | ^~ Building... library for source build/mapfrag.o In file included from include/mathematics.h:117, from libs/mathematics.c:38: libs/mathematics.c: In function 'destructVector': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/mathematics.c:251:26: note: in expansion of macro 'FREEMEMORY' 251 | if (v->elements) FREEMEMORY(space, v->elements); | ^~~~~~~~~~ libs/mathematics.c:251:9: note: some parts of macro expansion are not guarded by this 'if' clause 251 | if (v->elements) FREEMEMORY(space, v->elements); | ^~ Building... library for source build/md5.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mapfrag.o libs/mapfrag.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/md5.o libs/md5.c Building... library for source build/filebuffer.o Building... library for source build/segemehl.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/filebuffer.o libs/filebuffer.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/segemehl.o libs/segemehl.c In file included from libs/charsequence.c:26: libs/charsequence.c: In function 'destructSequence': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/charsequence.c:467:9: note: in expansion of macro 'FREEMEMORY' 467 | FREEMEMORY(space, sequence->sequence); | ^~~~~~~~~~ libs/charsequence.c:466:3: note: some parts of macro expansion are not guarded by this 'if' clause 466 | if (sequence->sequence != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/charsequence.c:470:5: note: in expansion of macro 'FREEMEMORY' 470 | FREEMEMORY(space, sequence->alphabetname); | ^~~~~~~~~~ libs/charsequence.c:469:9: note: some parts of macro expansion are not guarded by this 'if' clause 469 | if (sequence->alphabetname != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/charsequence.c:472:9: note: in expansion of macro 'FREEMEMORY' 472 | FREEMEMORY(space, sequence->url); | ^~~~~~~~~~ libs/charsequence.c:471:5: note: some parts of macro expansion are not guarded by this 'if' clause 471 | if (sequence->url != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/charsequence.c:474:9: note: in expansion of macro 'FREEMEMORY' 474 | FREEMEMORY(space, sequence->info); | ^~~~~~~~~~ libs/charsequence.c:473:5: note: some parts of macro expansion are not guarded by this 'if' clause 473 | if (sequence->info != NULL) | ^~ Building... library for source build/junctions.o libs/charsequence.c: In function 'loadSequence': libs/charsequence.c:296:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 296 | fread(s, sizeof(CharSequence), 1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/charsequence.c:304:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | fread(s->description, sizeof(char), s->descrlen+1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/charsequence.c:305:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread(s->alphabetname, sizeof(char), s->namelen+1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/charsequence.c:306:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 306 | fread(s->url, sizeof(char), s->urllen+1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/charsequence.c:307:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 307 | fread(sequence, sizeof(char), s->length, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/junctions.o libs/junctions.c Building... library for source build/sufarray.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sufarray.o libs/sufarray.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: libs/samio.c: In function 'bl_samDestructTag': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:102:15: note: in expansion of macro 'FREEMEMORY' 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); | ^~~~~~~~~~ libs/samio.c:102:3: note: some parts of macro expansion are not guarded by this 'if' clause 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:103:15: note: in expansion of macro 'FREEMEMORY' 103 | if(kv->val) FREEMEMORY(NULL, kv->val); | ^~~~~~~~~~ libs/samio.c:103:3: note: some parts of macro expansion are not guarded by this 'if' clause 103 | if(kv->val) FREEMEMORY(NULL, kv->val); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:104:16: note: in expansion of macro 'FREEMEMORY' 104 | if(kv->type) FREEMEMORY(NULL, kv->type); | ^~~~~~~~~~ libs/samio.c:104:3: note: some parts of macro expansion are not guarded by this 'if' clause 104 | if(kv->type) FREEMEMORY(NULL, kv->type); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:105:15: note: in expansion of macro 'FREEMEMORY' 105 | if(kv->key) FREEMEMORY(NULL, kv->key); | ^~~~~~~~~~ libs/samio.c:105:3: note: some parts of macro expansion are not guarded by this 'if' clause 105 | if(kv->key) FREEMEMORY(NULL, kv->key); | ^~ libs/samio.c: In function 'bl_samDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:112:21: note: in expansion of macro 'FREEMEMORY' 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); | ^~~~~~~~~~ libs/samio.c:112:3: note: some parts of macro expansion are not guarded by this 'if' clause 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:113:21: note: in expansion of macro 'FREEMEMORY' 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); | ^~~~~~~~~~ libs/samio.c:113:3: note: some parts of macro expansion are not guarded by this 'if' clause 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:114:21: note: in expansion of macro 'FREEMEMORY' 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); | ^~~~~~~~~~ libs/samio.c:114:3: note: some parts of macro expansion are not guarded by this 'if' clause 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:115:21: note: in expansion of macro 'FREEMEMORY' 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); | ^~~~~~~~~~ libs/samio.c:115:3: note: some parts of macro expansion are not guarded by this 'if' clause 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:116:21: note: in expansion of macro 'FREEMEMORY' 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); | ^~~~~~~~~~ libs/samio.c:116:3: note: some parts of macro expansion are not guarded by this 'if' clause 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:117:21: note: in expansion of macro 'FREEMEMORY' 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); | ^~~~~~~~~~ libs/samio.c:117:3: note: some parts of macro expansion are not guarded by this 'if' clause 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:121:20: note: in expansion of macro 'FREEMEMORY' 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); | ^~~~~~~~~~ libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this 'if' clause 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from include/bamio.h:21, from libs/bamio.c:32: libs/bamio.c: In function 'bl_bamCrossSectionDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/bamio.c:468:20: note: in expansion of macro 'FREEMEMORY' 468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d); | ^~~~~~~~~~ libs/bamio.c:468:5: note: some parts of macro expansion are not guarded by this 'if' clause 468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, from libs/sufarray.c:39: libs/sufarray.c: In function 'destructSufArr': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY' 613 | FREEMEMORY(space, arr->lcpctab); | ^~~~~~~~~~ libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause 612 | if (arr->lcpctab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY' 615 | FREEMEMORY(space, arr->inv_suftab); | ^~~~~~~~~~ libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause 614 | if (arr->inv_suftab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY' 619 | FREEMEMORY(space, arr->idvtab); | ^~~~~~~~~~ libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause 618 | if (arr->idvtab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY' 624 | FREEMEMORY(space, arr->suflink); | ^~~~~~~~~~ libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause 620 | if (arr->suflink != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY' 627 | FREEMEMORY(space, arr->chldtab); | ^~~~~~~~~~ libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause 626 | if (arr->chldtab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY' 629 | FREEMEMORY(space, arr->mdfive); | ^~~~~~~~~~ libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause 628 | if (arr->mdfive) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY' 631 | FREEMEMORY(space, arr->llvtab); | ^~~~~~~~~~ libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause 630 | if(arr->llvtab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY' 636 | FREEMEMORY(space, arr->id); | ^~~~~~~~~~ libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause 632 | if(arr->id != NULL) | ^~ libs/sufarray.c: In function 'readSuffixarray': libs/sufarray.c:428:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 428 | fread(&nmemb, sizeof(Uint), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:430:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 430 | fread(suftab, sizeof(Uint), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:431:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 431 | fread(&flags, sizeof(char), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:436:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 436 | fread(lcpctab, sizeof(unsigned char), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:438:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 438 | fread(&llvmemb, sizeof(Uint), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:440:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 440 | fread(llvtab, sizeof(PairUint), llvmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:446:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 446 | fread(chldtab, sizeof(childtab), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:484:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | fread(suflink, sizeof(Uint), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:508:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 508 | fread(id, sizeof(signed char), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:511:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 511 | fread(&idvmemb, sizeof(Uint), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:515:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 515 | fread(idvtab, sizeof(PairLSint), idvmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:519:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 519 | fread(idvutab, sizeof(PairUint), idvmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:530:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(mdfive, sizeof(unsigned char), 16, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Building... library for source build/iupac.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/iupac.o libs/iupac.c Building... library for source build/stack.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stack.o libs/stack.c Building... library for source build/vtprogressbar.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vtprogressbar.o libs/vtprogressbar.c Building... library for source build/bitArray.o Building... library for source build/annotation.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitArray.o libs/bitArray.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/annotation.o libs/annotation.c Building... library for source build/memory.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/memory.o libs/memory.c Building... library for source build/debug.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/debug.o libs/debug.c Building... library for source build/merge.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/merge.o libs/merge.c In file included from include/stringutils.h:27, from libs/annotation.c:29: libs/annotation.c: In function 'bl_annotationitemDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:149:23: note: in expansion of macro 'FREEMEMORY' 149 | if(item->chromname) FREEMEMORY(space, item->chromname); | ^~~~~~~~~~ libs/annotation.c:149:3: note: some parts of macro expansion are not guarded by this 'if' clause 149 | if(item->chromname) FREEMEMORY(space, item->chromname); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:150:18: note: in expansion of macro 'FREEMEMORY' 150 | if(item->name) FREEMEMORY(space, item->name); | ^~~~~~~~~~ libs/annotation.c:150:3: note: some parts of macro expansion are not guarded by this 'if' clause 150 | if(item->name) FREEMEMORY(space, item->name); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:151:21: note: in expansion of macro 'FREEMEMORY' 151 | if(item->itemRgb) FREEMEMORY(space, item->itemRgb); | ^~~~~~~~~~ libs/annotation.c:151:3: note: some parts of macro expansion are not guarded by this 'if' clause 151 | if(item->itemRgb) FREEMEMORY(space, item->itemRgb); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:152:24: note: in expansion of macro 'FREEMEMORY' 152 | if(item->blockSizes) FREEMEMORY(space, item->blockSizes); | ^~~~~~~~~~ libs/annotation.c:152:3: note: some parts of macro expansion are not guarded by this 'if' clause 152 | if(item->blockSizes) FREEMEMORY(space, item->blockSizes); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:153:25: note: in expansion of macro 'FREEMEMORY' 153 | if(item->blockStarts) FREEMEMORY(space, item->blockStarts); | ^~~~~~~~~~ libs/annotation.c:153:3: note: some parts of macro expansion are not guarded by this 'if' clause 153 | if(item->blockStarts) FREEMEMORY(space, item->blockStarts); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:154:26: note: in expansion of macro 'FREEMEMORY' 154 | if(item->blockRefseqs) FREEMEMORY(space, item->blockRefseqs); | ^~~~~~~~~~ libs/annotation.c:154:3: note: some parts of macro expansion are not guarded by this 'if' clause 154 | if(item->blockRefseqs) FREEMEMORY(space, item->blockRefseqs); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:155:26: note: in expansion of macro 'FREEMEMORY' 155 | if(item->blockStrands) FREEMEMORY(space, item->blockStrands); | ^~~~~~~~~~ libs/annotation.c:155:3: note: some parts of macro expansion are not guarded by this 'if' clause 155 | if(item->blockStrands) FREEMEMORY(space, item->blockStrands); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:156:20: note: in expansion of macro 'FREEMEMORY' 156 | if(item->source) FREEMEMORY(space, item->source); | ^~~~~~~~~~ libs/annotation.c:156:3: note: some parts of macro expansion are not guarded by this 'if' clause 156 | if(item->source) FREEMEMORY(space, item->source); | ^~ libs/annotation.c: In function 'bl_annotationtrackDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:409:24: note: in expansion of macro 'FREEMEMORY' 409 | if(track->trackname) FREEMEMORY(space, track->trackname); | ^~~~~~~~~~ libs/annotation.c:409:3: note: some parts of macro expansion are not guarded by this 'if' clause 409 | if(track->trackname) FREEMEMORY(space, track->trackname); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:410:23: note: in expansion of macro 'FREEMEMORY' 410 | if(track->filename) FREEMEMORY(space, track->filename); | ^~~~~~~~~~ libs/annotation.c:410:3: note: some parts of macro expansion are not guarded by this 'if' clause 410 | if(track->filename) FREEMEMORY(space, track->filename); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:411:26: note: in expansion of macro 'FREEMEMORY' 411 | if(track->description) FREEMEMORY(space, track->description); | ^~~~~~~~~~ libs/annotation.c:411:3: note: some parts of macro expansion are not guarded by this 'if' clause 411 | if(track->description) FREEMEMORY(space, track->description); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:418:20: note: in expansion of macro 'FREEMEMORY' 418 | if(track->items) FREEMEMORY(space, track->items) ; | ^~~~~~~~~~ libs/annotation.c:418:3: note: some parts of macro expansion are not guarded by this 'if' clause 418 | if(track->items) FREEMEMORY(space, track->items) ; | ^~ libs/annotation.c: In function 'bl_annotationmultitrackDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:455:20: note: in expansion of macro 'FREEMEMORY' 455 | if(track->items) FREEMEMORY(space, track->items) ; | ^~~~~~~~~~ libs/annotation.c:455:3: note: some parts of macro expansion are not guarded by this 'if' clause 455 | if(track->items) FREEMEMORY(space, track->items) ; | ^~ Building... library for source build/seqclip.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/seqclip.o libs/seqclip.c Building... library for source build/container.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/container.o libs/container.c Building... library for source build/manout.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manout.o libs/manout.c Building... library for source build/radixsort.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/radixsort.o libs/radixsort.c Building... library for source build/bitvectoralg.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitvectoralg.o libs/bitvectoralg.c In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/sw.h:38, from libs/seqclip.c:44: libs/seqclip.c: In function 'bl_Find3PrimeGreedy': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/seqclip.c:529:9: note: in expansion of macro 'FREEMEMORY' 529 | FREEMEMORY(space, adapter); | ^~~~~~~~~~ libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this 'if' clause 528 | if(adapter) | ^~ In file included from include/stringutils.h:27, from libs/merge.c:34: libs/merge.c: In function 'se_mergeWorker': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/merge.c:1096:20: note: in expansion of macro 'FREEMEMORY' 1096 | if(curkey) FREEMEMORY(NULL, curkey); | ^~~~~~~~~~ libs/merge.c:1096:9: note: some parts of macro expansion are not guarded by this 'if' clause 1096 | if(curkey) FREEMEMORY(NULL, curkey); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/merge.c:1216:26: note: in expansion of macro 'FREEMEMORY' 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); | ^~~~~~~~~~ libs/merge.c:1216:5: note: some parts of macro expansion are not guarded by this 'if' clause 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); | ^~ Building... library for source build/match.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/match.o libs/match.c Building... library for source build/vqueue.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vqueue.o libs/vqueue.c Building... library for source build/portable_endian.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/portable_endian.o libs/portable_endian.c Building... library for source build/samheader.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samheader.o libs/samheader.c Building... library for source build/alignment.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/alignment.o libs/alignment.c Building... library for source build/matealign.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/matealign.o libs/matealign.c Building... library for source build/info.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/info.o libs/info.c In file included from include/mathematics.h:117, from libs/alignment.c:38: libs/alignment.c: In function 'wrapAlignment': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/alignment.c:97:18: note: in expansion of macro 'FREEMEMORY' 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); | ^~~~~~~~~~ libs/alignment.c:97:3: note: some parts of macro expansion are not guarded by this 'if' clause 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/alignment.c:98:18: note: in expansion of macro 'FREEMEMORY' 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); | ^~~~~~~~~~ libs/alignment.c:98:3: note: some parts of macro expansion are not guarded by this 'if' clause 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); | ^~ libs/info.c: In function 'timestr_r': libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~ libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from libs/info.c:41: In function 'sprintf', inlined from 'timestr_r' at libs/info.c:64:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ libs/info.c: In function 'infomsg': libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~ In function 'timestr_r', inlined from 'infomsg' at libs/info.c:93:4: libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'timestr_r' at libs/info.c:64:5, inlined from 'infomsg' at libs/info.c:93:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ libs/info.c: In function 'nfolevel': libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~ In function 'timestr_r', inlined from 'nfolevel' at libs/info.c:139:5: libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'timestr_r' at libs/info.c:64:5, inlined from 'nfolevel' at libs/info.c:139:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/locus.h:41, from include/mapfrag.h:39, from libs/matealign.c:32: libs/matealign.c: In function 'bl_matealign': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/matealign.c:313:15: note: in expansion of macro 'FREEMEMORY' 313 | if(npos[0]) FREEMEMORY(NULL, spos[0]); | ^~~~~~~~~~ libs/matealign.c:313:3: note: some parts of macro expansion are not guarded by this 'if' clause 313 | if(npos[0]) FREEMEMORY(NULL, spos[0]); | ^~ Building... library for source build/bitVector.o include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/matealign.c:314:15: note: in expansion of macro 'FREEMEMORY' 314 | if(npos[1]) FREEMEMORY(NULL, spos[1]); | ^~~~~~~~~~ libs/matealign.c:314:3: note: some parts of macro expansion are not guarded by this 'if' clause 314 | if(npos[1]) FREEMEMORY(NULL, spos[1]); | ^~ Building... library for source build/karlin.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitVector.o libs/bitVector.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/karlin.o libs/karlin.c Building... library for source build/gzidx.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/gzidx.o libs/gzidx.c libs/matealign.c: In function 'bl_greedypairMappingSets': libs/matealign.c:76:15: warning: 'm3' may be used uninitialized [-Wmaybe-uninitialized] 76 | s->elem = bl_concatMapping(m3, m4); | ^~~~~~~~~~~~~~~~~~~~~~~~ libs/matealign.c:56:24: note: 'm3' was declared here 56 | mapping_t *m1, *m2, *m3, *m4; | ^~ libs/matealign.c:76:15: warning: 'm4' may be used uninitialized [-Wmaybe-uninitialized] 76 | s->elem = bl_concatMapping(m3, m4); | ^~~~~~~~~~~~~~~~~~~~~~~~ libs/matealign.c:56:29: note: 'm4' was declared here 56 | mapping_t *m1, *m2, *m3, *m4; | ^~ Building... library for source build/multicharseq.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/multicharseq.o libs/multicharseq.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from libs/multicharseq.c:38: libs/multicharseq.c: In function 'destructMultiCharSeq': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/multicharseq.c:212:7: note: in expansion of macro 'FREEMEMORY' 212 | FREEMEMORY(space, mseq->markpos); | ^~~~~~~~~~ libs/multicharseq.c:211:9: note: some parts of macro expansion are not guarded by this 'if' clause 211 | if (mseq->markpos != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/multicharseq.c:214:7: note: in expansion of macro 'FREEMEMORY' 214 | FREEMEMORY(space, mseq->map); | ^~~~~~~~~~ libs/multicharseq.c:213:9: note: some parts of macro expansion are not guarded by this 'if' clause 213 | if (mseq->map != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/multicharseq.c:216:7: note: in expansion of macro 'FREEMEMORY' 216 | FREEMEMORY(space, mseq->ref); | ^~~~~~~~~~ libs/multicharseq.c:215:5: note: some parts of macro expansion are not guarded by this 'if' clause 215 | if (mseq->ref != NULL) | ^~ Building... library for source build/brendel.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/brendel.o libs/brendel.c Building... library for source build/sort.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sort.o libs/sort.c Building... library for source build/stringutils.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stringutils.o libs/stringutils.c Building... library for source build/fileio.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileio.o libs/fileio.c In file included from include/stringutils.h:27, from libs/stringutils.c:39: libs/stringutils.c: In function 'destructStringset': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY' 274 | FREEMEMORY(space, s->strings[i].str); | ^~~~~~~~~~ libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause 273 | if(s->strings[i].str != NULL) | ^~ Building... library for source build/kdseed.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdseed.o libs/kdseed.c Building... library for source build/manopt.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manopt.o libs/manopt.c Building... library for source build/bedfiles.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bedfiles.o libs/bedfiles.c libs/fileio.c: In function 'bl_rm': libs/fileio.c:220:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 220 | system(cmd); | ^~~~~~~~~~~ Building... library for source build/kdchain.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdchain.o libs/kdchain.c Building... library for source build/intervaltree.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/intervaltree.o libs/intervaltree.c Building... library for source build/queryalign.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/queryalign.o libs/queryalign.c In file included from include/mathematics.h:117, from libs/intervaltree.c:27: libs/intervaltree.c: In function 'bl_intervaltreeDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/intervaltree.c:443:19: note: in expansion of macro 'FREEMEMORY' 443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions); | ^~~~~~~~~~ libs/intervaltree.c:443:3: note: some parts of macro expansion are not guarded by this 'if' clause 443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions); | ^~ Linking segemehl Linking haarz cc build/nw.o build/bgzip.o build/pigeon.o build/biofiles.o build/gzip.o build/fileBins.o build/locus.o build/vstack.o build/aluruSort.o build/splitalign.o build/mathematics.o build/mappingqual.o build/segemehl_helper.o build/sw.o build/bamio.o build/charsequence.o build/samio.o build/mapfrag.o build/md5.o build/filebuffer.o build/junctions.o build/sufarray.o build/iupac.o build/stack.o build/vtprogressbar.o build/bitArray.o build/annotation.o build/memory.o build/debug.o build/merge.o build/seqclip.o build/container.o build/manout.o build/radixsort.o build/bitvectoralg.o build/match.o build/vqueue.o build/portable_endian.o build/samheader.o build/alignment.o build/matealign.o build/info.o build/bitVector.o build/karlin.o build/gzidx.o build/multicharseq.o build/brendel.o build/sort.o build/stringutils.o build/fileio.o build/kdseed.o build/manopt.o build/bedfiles.o build/kdchain.o build/intervaltree.o build/queryalign.o build/segemehl.o -o ./segemehl.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now cc build/nw.o build/bgzip.o build/pigeon.o build/biofiles.o build/gzip.o build/fileBins.o build/locus.o build/vstack.o build/aluruSort.o build/splitalign.o build/mathematics.o build/mappingqual.o build/segemehl_helper.o build/sw.o build/bamio.o build/charsequence.o build/samio.o build/mapfrag.o build/md5.o build/filebuffer.o build/junctions.o build/sufarray.o build/iupac.o build/stack.o build/vtprogressbar.o build/bitArray.o build/annotation.o build/memory.o build/debug.o build/merge.o build/seqclip.o build/container.o build/manout.o build/radixsort.o build/bitvectoralg.o build/match.o build/vqueue.o build/portable_endian.o build/samheader.o build/alignment.o build/matealign.o build/info.o build/bitVector.o build/karlin.o build/gzidx.o build/multicharseq.o build/brendel.o build/sort.o build/stringutils.o build/fileio.o build/kdseed.o build/manopt.o build/bedfiles.o build/kdchain.o build/intervaltree.o build/queryalign.o build/haarz.o -o ./haarz.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/segemehl-0.3.4' make[1]: Leaving directory '/build/reproducible-path/segemehl-0.3.4' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/segemehl/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/segemehl-0.3.4' mv segemehl.x segemehl mv haarz.x haarz find . -name "*.x" dh_install make[1]: Leaving directory '/build/reproducible-path/segemehl-0.3.4' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'segemehl' in '../segemehl_0.3.4-5_amd64.deb'. dpkg-deb: building package 'segemehl-dbgsym' in '../segemehl-dbgsym_0.3.4-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../segemehl_0.3.4-5_amd64.buildinfo dpkg-genchanges --build=binary -O../segemehl_0.3.4-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/73462/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/73462/tmp/hooks/B01_cleanup finished 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/73462 and its subdirectories I: Current time: Sun Apr 28 03:47:30 +14 2024 I: pbuilder-time-stamp: 1714225650