I: pbuilder: network access will be disabled during build I: Current time: Tue Feb 11 18:39:49 -12 2025 I: pbuilder-time-stamp: 1739342389 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [stringtie_2.2.1+ds-2.dsc] I: copying [./stringtie_2.2.1+ds.orig-debian-tests-data.tar.xz] I: copying [./stringtie_2.2.1+ds.orig.tar.xz] I: copying [./stringtie_2.2.1+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Feb 19 17:34:50 2022 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./stringtie_2.2.1+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting stringtie in stringtie-2.2.1+ds dpkg-source: info: unpacking stringtie_2.2.1+ds.orig.tar.xz dpkg-source: info: unpacking stringtie_2.2.1+ds.orig-debian-tests-data.tar.xz dpkg-source: info: unpacking stringtie_2.2.1+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile.patch dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1060812/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='29e0f2633fb14364931d8557f04f8e1c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1060812' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Sz88ZCuX/pbuilderrc_ZvTA --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Sz88ZCuX/b1 --logfile b1/build.log stringtie_2.2.1+ds-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 23 2023 more -rwsr-xr-x 1 root root 59704 Mar 23 2023 mount -rwxr-xr-x 1 root root 18744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 23 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/1060812/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), libbam-dev, libhts-dev, libbz2-dev, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18148 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 libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 24.3 MB of archives. After unpacking 89.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u4 [385 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-10+deb12u4 [485 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Fetched 24.3 MB in 0s (84.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 18148 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-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 .../15-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-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 .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../23-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../25-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3~deb12u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package gettext. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/stringtie-2.2.1+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../stringtie_2.2.1+ds-2_source.changes dpkg-buildpackage: info: source package stringtie dpkg-buildpackage: info: source version 2.2.1+ds-2 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 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_auto_clean make -j16 clean make[2]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' rm -f stringtie stringtie.o* ./gclib/GBase.o ./gclib/GArgs.o ./gclib/GStr.o ./gclib/GSam.o ./gclib/gdna.o ./gclib/codons.o ./gclib/GFastaIndex.o ./gclib/GFaSeqGet.o ./gclib/gff.o ./gclib/GThreads.o rlink.o tablemaker.o tmerge.o rm -f core.* make[2]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+ds' rm -fr test_data rm -f SuperReads_RNA/global-1/SuperReadsR/all_tests make[1]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/stringtie.substvars debian/files rm -fr -- debian/stringtie/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) 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/stringtie-2.2.1+ds' dh_auto_build -- 'LINKER=$(CXX)' make -j16 "INSTALL=install --strip-program=true" LINKER=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GBase.cpp -o gclib/GBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GArgs.cpp -o gclib/GArgs.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GStr.cpp -o gclib/GStr.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GSam.cpp -o gclib/GSam.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gdna.cpp -o gclib/gdna.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/codons.cpp -o gclib/codons.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gff.cpp -o gclib/gff.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GThreads.cpp -o gclib/GThreads.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c rlink.cpp -o rlink.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tablemaker.cpp -o tablemaker.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tmerge.cpp -o tmerge.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c stringtie.cpp -o stringtie.o In file included from gclib/GSam.cpp:1: gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ In file included from gclib/GStr.h:5, from gclib/GStr.cpp:2: gclib/GBase.h: In static member function 'static GStr::Data* GStr::new_data(const char*, uint)': gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:38:15: note: 'data' was declared here 38 | Data* data; | ^~~~ In file included from gclib/gff.cpp:1: gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ gclib/gff.cpp: In constructor 'GffLine::GffLine(GffReader*, const char*)': gclib/gff.cpp:426:19: warning: unknown escape sequence: '\%' 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gclib/GBase.h: In constructor 'GStr::GStr(const char*, uint)': gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:38:15: note: 'data' was declared here 38 | Data* data; | ^~~~ In file included from rlink.h:5, from rlink.cpp:1: ./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ ./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ ./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ ./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ In file included from rlink.h:5, from tablemaker.cpp:2: ./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ ./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ ./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ In file included from rlink.h:5, from tmerge.h:5, from tmerge.cpp:1: ./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ ./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ ./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ ./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ ./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ ./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ ./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ ./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ In file included from rlink.h:6: ./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ In file included from rlink.h:6: ./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ In file included from rlink.h:6: ./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ In file included from rlink.h:5, from stringtie.cpp:2: ./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ ./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ ./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ ./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ ./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ In file included from rlink.h:6: ./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ tablemaker.cpp: In function 'void rc_update_exons(RC_BundleData&)': tablemaker.cpp:205:29: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 205 | bind2nd( minus(), avg)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_function.h:1438, from /usr/include/c++/12/functional:49, from ./gclib/khashl.hh:25, from ./gclib/GHashMap.hh:8, from ./gclib/GFastaIndex.h:11, from ./gclib/GFaSeqGet.h:3, from ./gclib/gff.h:9: /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ tablemaker.cpp:212:29: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 212 | bind2nd( minus(), mavg)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ stringtie.cpp: In function 'int main(int, char**)': stringtie.cpp:468:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 468 | if (tstackSize::setCapacity(int) [with OBJ = bool]', inlined from 'void GVec::setCapacity(int) [with OBJ = bool]' at ./gclib/GVec.hh:95:17, inlined from 'GVec::GVec(int, OBJ) [with OBJ = bool]' at ./gclib/GVec.hh:248:14, inlined from 'int printMergeResults(BundleData*, int, GStr&)' at rlink.cpp:17262:34: ./gclib/GVec.hh:107:24: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 107 | fArray=new OBJ[NewCapacity]; | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/functional:53, from ./gclib/khashl.hh:25, from ./gclib/GHashMap.hh:8, from ./gclib/GFastaIndex.h:11: /usr/include/c++/12/new: In function 'int printMergeResults(BundleData*, int, GStr&)': /usr/include/c++/12/new:128:26: note: in a call to allocation function 'void* operator new [](std::size_t)' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ In file included from /usr/include/string.h:535, from ./gclib/GBase.h:64, from ./gclib/GStr.h:5, from rlink.h:4: In function 'void* memset(void*, int, size_t)', inlined from 'void GBitVec::init_words(BitWord*, uint, bool)' at ./gclib/GBitVec.h:496:11, inlined from 'GBitVec::GBitVec(uint, bool)' at ./gclib/GBitVec.h:127:15, inlined from 'GBitVec::GBitVec(uint, bool)' at ./gclib/GBitVec.h:118:12, inlined from 'void process_transfrags(int, int, int, GPVec&, GPVec&, CTreePat*, GIntHash&, GVec&, GList&, GVec&)' at rlink.cpp:5826:29: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: '*(void**)((char*)&trpat + offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 60 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ rlink.cpp: In function 'void process_transfrags(int, int, int, GPVec&, GPVec&, CTreePat*, GIntHash&, GVec&, GList&, GVec&)': rlink.cpp:5826:41: note: '*(void**)((char*)&trpat + offsetof(GBitVec, GBitVec::fBits))' was declared here 5826 | GBitVec trpat(gno+edgeno); | ^~~~~ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:159:11, inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:150:3, inlined from 'void process_refguides(int, int, GIntHash&, int&, GPVec&, GPVec&, int, GVec&, BundleData*)' at rlink.cpp:11677:44: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: '*(void**)((char*)&trpattern + offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ rlink.cpp: In function 'void process_refguides(int, int, GIntHash&, int&, GPVec&, GPVec&, int, GVec&, BundleData*)': rlink.cpp:11677:41: note: '*(void**)((char*)&trpattern + offsetof(GBitVec, GBitVec::fBits))' was declared here 11677 | GBitVec trpattern(transfrag[t]->pattern); | ^~~~~~~~~ In function 'bool GMalloc(void**, long unsigned int)', inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:158:5, inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:150:3, inlined from 'GBitVec traverse_dfs(int, int, CGraphnode*, CGraphnode*, GBitVec, int, GVec&, GPVec**, GPVec**, int&, GIntHash**, int&)' at rlink.cpp:2461:28: ./gclib/GBase.h:254:12: warning: '*(void**)((char*)&childparents + offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ rlink.cpp: In function 'GBitVec traverse_dfs(int, int, CGraphnode*, CGraphnode*, GBitVec, int, GVec&, GPVec**, GPVec**, int&, GIntHash**, int&)': rlink.cpp:2461:25: note: 'childparents' declared here 2461 | GBitVec childparents=parents; | ^~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o stringtie gclib/GBase.o gclib/GArgs.o gclib/GStr.o gclib/GSam.o gclib/gdna.o gclib/codons.o gclib/GFastaIndex.o gclib/GFaSeqGet.o gclib/gff.o gclib/GThreads.o rlink.o tablemaker.o tmerge.o stringtie.o -pthread -lhts -lbz2 -lz -lm WARNING: built DEBUG version [much slower], use "make clean release" for a faster, optimized version of the program. make[2]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+ds' make[1]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+ds' rm -f debian/stringtie.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' echo "Disabling tests, as they require network access." Disabling tests, as they require network access. make[1]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+ds' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/stringtie.substvars rm -fr -- debian/.debhelper/generated/stringtie/ debian/stringtie/ debian/tmp/ dh_auto_install --destdir=debian/stringtie/ install -m0755 -d /build/reproducible-path/stringtie-2.2.1\+ds/debian/stringtie dh_install install -m0755 -d debian/stringtie/usr/bin cp --reflink=auto -a ./stringtie debian/stringtie/usr/bin/ dh_installdocs install -m0755 -d debian/stringtie/usr/share/doc/stringtie install -p -m0644 debian/copyright debian/stringtie/usr/share/doc/stringtie/copyright dh_installchangelogs install -m0755 -d debian/stringtie/usr/share/doc/stringtie install -p -m0644 debian/.debhelper/generated/stringtie/dh_installchangelogs.dch.trimmed debian/stringtie/usr/share/doc/stringtie/changelog.Debian dh_installman install -m0755 -d debian/stringtie/usr/share/man/man1/ install -p -m0644 ./debian/stringtie.1 debian/stringtie/usr/share/man/man1/stringtie.1 man-recode --to-code UTF-8 --suffix .dh-new debian/stringtie/usr/share/man/man1/stringtie.1 mv debian/stringtie/usr/share/man/man1/stringtie.1.dh-new debian/stringtie/usr/share/man/man1/stringtie.1 chmod 0644 -- debian/stringtie/usr/share/man/man1/stringtie.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/stringtie chmod a-x usr/share/doc/stringtie/changelog.Debian usr/share/man/man1/stringtie.1 gzip -9nf usr/share/doc/stringtie/changelog.Debian usr/share/man/man1/stringtie.1 cd '/build/reproducible-path/stringtie-2.2.1+ds' dh_fixperms find debian/stringtie ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/stringtie/usr/share/doc -type f -a -true -a ! -regex 'debian/stringtie/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/stringtie/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/stringtie/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/stringtie -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/stringtie/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/stringtie/usr/bin/stringtie dh_strip -a install -m0755 -d debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/8c objcopy --only-keep-debug --compress-debug-sections debian/stringtie/usr/bin/stringtie debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/8c/20b69ba20a687b39f07b7f8e5de4a07e186247.debug chmod 0644 -- debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/8c/20b69ba20a687b39f07b7f8e5de4a07e186247.debug strip --remove-section=.comment --remove-section=.note debian/stringtie/usr/bin/stringtie objcopy --add-gnu-debuglink debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/8c/20b69ba20a687b39f07b7f8e5de4a07e186247.debug debian/stringtie/usr/bin/stringtie install -m0755 -d debian/.debhelper/stringtie/dbgsym-root/usr/share/doc ln -s stringtie debian/.debhelper/stringtie/dbgsym-root/usr/share/doc/stringtie-dbgsym install -m0755 -d debian/.debhelper/stringtie dh_makeshlibs -a rm -f debian/stringtie/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/stringtie/DEBIAN dpkg-shlibdeps -Tdebian/stringtie.substvars debian/stringtie/usr/bin/stringtie dh_installdeb install -m0755 -d debian/stringtie/DEBIAN dh_gencontrol install -m0755 -d debian/stringtie/DEBIAN echo misc:Depends= >> debian/stringtie.substvars echo misc:Pre-Depends= >> debian/stringtie.substvars install -m0755 -d debian/.debhelper/stringtie/dbgsym-root/DEBIAN dpkg-gencontrol -pstringtie -ldebian/changelog -Tdebian/stringtie.substvars -Pdebian/.debhelper/stringtie/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=stringtie-dbgsym "-DDepends=stringtie (= \${binary:Version})" "-DDescription=debug symbols for stringtie" -DBuild-Ids=8c20b69ba20a687b39f07b7f8e5de4a07e186247 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/stringtie/dbgsym-root/DEBIAN/control dpkg-gencontrol -pstringtie -ldebian/changelog -Tdebian/stringtie.substvars -Pdebian/stringtie chmod 0644 -- debian/stringtie/DEBIAN/control dh_md5sums install -m0755 -d debian/stringtie/DEBIAN cd debian/stringtie >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/stringtie/DEBIAN/md5sums install -m0755 -d debian/.debhelper/stringtie/dbgsym-root/DEBIAN cd debian/.debhelper/stringtie/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/stringtie/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/stringtie .. dpkg-deb --root-owner-group --build debian/.debhelper/stringtie/dbgsym-root .. dpkg-deb: building package 'stringtie' in '../stringtie_2.2.1+ds-2_amd64.deb'. dpkg-deb: building package 'stringtie-dbgsym' in '../stringtie-dbgsym_2.2.1+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../stringtie_2.2.1+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../stringtie_2.2.1+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1060812 and its subdirectories I: Current time: Tue Feb 11 18:41:20 -12 2025 I: pbuilder-time-stamp: 1739342480