Diff of the two buildlogs: -- --- b1/build.log 2024-04-28 04:28:41.489467135 +0000 +++ b2/build.log 2024-04-28 04:31:05.039343497 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 30 22:49:33 -12 2025 -I: pbuilder-time-stamp: 1748688573 +I: Current time: Sun Apr 28 18:28:44 +14 2024 +I: pbuilder-time-stamp: 1714278524 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,54 +32,86 @@ dpkg-source: info: applying 0001-src-Makefile.Linux-Do-not-set-CFLAGS-and-CXXFLAGS-to.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14003/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/49680/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 28 04:28 /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/49680/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/49680/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='1e3ec00294df4c7a884cba7c3b097476' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='14003' - PS1='# ' - PS2='> ' + INVOCATION_ID=ad5c541408c04acabcf8f346c143f23e + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=49680 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.mGVSuYUs/pbuilderrc_ZoyZ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mGVSuYUs/b1 --logfile b1/build.log subread_2.0.6+dfsg-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.mGVSuYUs/pbuilderrc_owfm --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mGVSuYUs/b2 --logfile b2/build.log subread_2.0.6+dfsg-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + 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 ionos16-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + 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 May 27 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/14003/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 21 07:13 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/49680/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -92,7 +124,7 @@ Depends: bc, debhelper-compat (= 13), architecture-is-little-endian, python3, 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 ... 19708 files and directories currently installed.) +(Reading database ... 19884 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: @@ -117,11 +149,11 @@ pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: - architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1{a} libnsl2{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsub-override-perl{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} + architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{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} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: - ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget -0 packages upgraded, 55 newly installed, 0 to remove and 0 not upgraded. -Need to get 27.1 MB of archives. After unpacking 102 MB will be used. + ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget +0 packages upgraded, 46 newly installed, 0 to remove and 0 not upgraded. +Need to get 26.3 MB of archives. After unpacking 99.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.2-1 [107 kB] @@ -130,58 +162,49 @@ Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-3 [255 kB] -Get: 8 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.20.1-5+b1 [35.9 kB] -Get: 9 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.0-2.4 [20.6 kB] -Get: 10 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.20.1-5+b1 [83.2 kB] -Get: 11 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] -Get: 12 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.20.1-5+b1 [359 kB] -Get: 13 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.20.1-5+b1 [145 kB] -Get: 14 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] -Get: 15 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3 [90.2 kB] -Get: 16 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b2 [42.4 kB] -Get: 17 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-4 [69.3 kB] -Get: 18 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-4 [171 kB] -Get: 19 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] -Get: 20 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] -Get: 21 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] -Get: 22 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] -Get: 23 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] -Get: 24 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] -Get: 25 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] -Get: 26 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] -Get: 27 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] -Get: 28 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] -Get: 29 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] -Get: 30 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] -Get: 31 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] -Get: 32 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] -Get: 33 http://deb.debian.org/debian trixie/main i386 architecture-properties i386 0.1.1+b1 [1900 B] -Get: 34 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] -Get: 35 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] -Get: 36 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] -Get: 37 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] -Get: 38 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] -Get: 39 http://deb.debian.org/debian trixie/main i386 bc i386 1.07.1-3 [111 kB] -Get: 40 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] -Get: 41 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] -Get: 42 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] -Get: 43 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] -Get: 44 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] -Get: 45 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] -Get: 46 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] -Get: 47 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] -Get: 48 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] -Get: 49 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] -Get: 50 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] -Get: 51 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] -Get: 52 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] -Get: 53 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] -Get: 54 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] -Get: 55 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] -Fetched 27.1 MB in 0s (91.3 MB/s) +Get: 8 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-4 [69.3 kB] +Get: 9 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-4 [171 kB] +Get: 10 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] +Get: 11 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] +Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] +Get: 13 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] +Get: 14 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] +Get: 15 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] +Get: 16 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] +Get: 17 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] +Get: 18 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] +Get: 19 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] +Get: 20 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] +Get: 21 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] +Get: 22 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] +Get: 23 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] +Get: 24 http://deb.debian.org/debian trixie/main i386 architecture-properties i386 0.1.1+b1 [1900 B] +Get: 25 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] +Get: 26 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] +Get: 27 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] +Get: 28 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] +Get: 29 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] +Get: 30 http://deb.debian.org/debian trixie/main i386 bc i386 1.07.1-3 [111 kB] +Get: 31 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] +Get: 32 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] +Get: 33 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] +Get: 34 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] +Get: 35 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] +Get: 36 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] +Get: 37 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] +Get: 38 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] +Get: 39 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] +Get: 40 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] +Get: 41 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] +Get: 42 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] +Get: 43 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] +Get: 44 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] +Get: 45 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] +Get: 46 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] +Fetched 26.3 MB in 0s (62.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. -(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 ... 19708 files and directories currently installed.) +(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 ... 19884 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. @@ -194,69 +217,40 @@ Setting up libexpat1:i386 (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... Selecting previously unselected package python3-minimal. -(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 ... 20024 files and directories currently installed.) -Preparing to unpack .../00-python3-minimal_3.11.6-1_i386.deb ... +(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 ... 20200 files and directories currently installed.) +Preparing to unpack .../0-python3-minimal_3.11.6-1_i386.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. -Preparing to unpack .../01-media-types_10.1.0_all.deb ... +Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... 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(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 ... 21194 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.6-1_i386.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sensible-utils. @@ -360,31 +354,26 @@ Unpacking zlib1g-dev:i386 (1:1.3.dfsg-3.1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:i386 (1.5.7-2) ... -Setting up libkeyutils1:i386 (1.6.3-3) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:i386 (0.1.1+b1) ... -Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... -Setting up libcom-err2:i386 (1.47.0-2.4) ... Setting up file (1:5.45-2+b1) ... Setting up libelf1t64:i386 (0.191-1+b1) ... -Setting up libkrb5support0:i386 (1.20.1-5+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat May 31 10:49:53 UTC 2025. -Universal Time is now: Sat May 31 10:49:53 UTC 2025. +Local time is now: Sun Apr 28 04:29:12 UTC 2024. +Universal Time is now: Sun Apr 28 04:29:12 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... -Setting up libk5crypto3:i386 (1.20.1-5+b1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... @@ -392,7 +381,6 @@ Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... -Setting up libkrb5-3:i386 (1.20.1-5+b1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... @@ -402,20 +390,17 @@ Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... -Setting up libgssapi-krb5-2:i386 (1.20.1-5+b1) ... Setting up libreadline8t64:i386 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... -Setting up libtirpc3t64:i386 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... +Setting up libpython3.11-stdlib:i386 (3.11.8-1) ... Setting up bc (1.07.1-3) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. -Setting up libnsl2:i386 (1.3.0-3+b2) ... -Setting up libpython3.11-stdlib:i386 (3.11.8-1) ... -Setting up debhelper (13.15.3) ... Setting up libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... +Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Processing triggers for libc-bin (2.37-18) ... Reading package lists... @@ -427,7 +412,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/subread-2.0.6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../subread_2.0.6+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/49680/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/49680/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/subread-2.0.6+dfsg/ && 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 > ../subread_2.0.6+dfsg-3_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.6+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -443,7 +432,7 @@ rm -rf bin src/longread-one/make.version find . -name "*.o" -delete dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux - cd src && make -j22 clean -f Makefile.Linux + cd src && make -j10 clean -f Makefile.Linux make[2]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src' rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o make[2]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg/src' @@ -471,7 +460,7 @@ make[1]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg' dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=i686-linux-gnu-gcc ; \ - cd src && make -j22 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=i686-linux-gnu-gcc + cd src && make -j10 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=i686-linux-gnu-gcc make[2]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c @@ -483,21 +472,6 @@ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c -gene-algorithms.c: In function 'miltime': -gene-algorithms.c:1395:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] - 1395 | ftime(&trp); - | ^~~~~ -In file included from gene-algorithms.c:33: -/usr/include/i386-linux-gnu/sys/timeb.h:29:12: note: declared here - 29 | extern int ftime (struct timeb *__timebuf) - | ^~~~~ gene-value-index.c: In function 'is_offset_in_chro': gene-value-index.c:85:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding )) @@ -510,14 +484,36 @@ gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ -input-blc.c: In function 'iCache_continuous_read_lanes': -input-blc.c:579:59: warning: unused variable 'npos' [-Wunused-variable] - 579 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); - | ^~~~ +core-junction.c: In function 'find_donor_receptor': +core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) + | ^~ +core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ + | ^~ +gene-algorithms.c: In function 'miltime': +gene-algorithms.c:1395:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] + 1395 | ftime(&trp); + | ^~~~~ +In file included from gene-algorithms.c:33: +/usr/include/i386-linux-gnu/sys/timeb.h:29:12: note: declared here + 29 | extern int ftime (struct timeb *__timebuf) + | ^~~~~ +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c long-hashtable.c: In function 'lnhash_create': long-hashtable.c:46:60: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '8589934592' to '0' [-Woverflow] 46 | the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c +input-blc.c: In function 'iCache_continuous_read_lanes': +input-blc.c:579:59: warning: unused variable 'npos' [-Wunused-variable] + 579 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); + | ^~~~ input-blc.c: In function 'iCache_write_supIdx_result': input-blc.c:1123:24: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=] 1123 | fprintf(ofp, "%s\t%lld\n", ky, va-NULL); @@ -547,13 +543,6 @@ | | | long int | %d -core-junction.c: In function 'find_donor_receptor': -core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) - | ^~ -core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ - | ^~ input-blc.c: In function 'iCache_continuous_read_lanes': input-blc.c:489:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 489 | read(tfp -> cbcl_bin_fd,&btmp,1);// bits per call. @@ -601,27 +590,15 @@ echo " " > longread-one/make.version i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -rm -f longread-one/*.o i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +rm -f longread-one/*.o i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm cd longread-one && make +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm make[3]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src/longread-one' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c -i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c detection-calls.c: In function 'DTCwrite_annotations': detection-calls.c:155:9: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); @@ -724,10 +701,22 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm readSummary.c: In function 'scRNA_find_gene_to_umi_mark_deletee': readSummary.c:5691:71: warning: right shift count >= width of type [-Wshift-count-overflow] 5691 | int cellno = ( key_bc_umi_p1-NULL-1 ) >> 32; | ^~ +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c +i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE longread-mapping.c: In function 'LRMmiltime': longread-mapping.c:234:9: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] @@ -799,15 +788,11 @@ || Repeat threshold : 100 repeats || || Gapped index : no || || || -|| Free / total memory : 2.1GB / 0.0GB || +|| Free / total memory : 3.8GB / 0.0GB || || || || Input files : 1 file in total || || o chr901.fa || || || -|| || -|| WARNING: the free memory is lower than 3.0GB. || -|| the program may run very slow or crash. || -|| || \\============================================================================// //================================= Running ==================================\\ @@ -817,7 +802,7 @@ || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || subread-buildindex: hashtable.c:470: HashTablePutReplaceEx: Assertion `key != NULL' failed. -Aborted +subread-align-test.sh: line 7: 56401 Aborted $SUBREAD_HOME/subread-buildindex -B -F -o ../small1 -M100 ../chr901.fa md5sum: ../small1.00.b.array: No such file or directory md5sum: ../small1.00.b.tab: No such file or directory @@ -848,7 +833,7 @@ || || \\============================================================================// -//================ Running (30-May-2025 22:50:34, pid=22786) =================\\ +//================ Running (28-Apr-2024 18:29:52, pid=56820) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -894,7 +879,7 @@ || || \\============================================================================// -//================ Running (30-May-2025 22:50:34, pid=22795) =================\\ +//================ Running (28-Apr-2024 18:29:52, pid=56823) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -945,7 +930,7 @@ || || \\============================================================================// -//================ Running (30-May-2025 22:50:34, pid=22803) =================\\ +//================ Running (28-Apr-2024 18:29:52, pid=56826) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -996,7 +981,7 @@ || || \\============================================================================// -//================ Running (30-May-2025 22:50:34, pid=22811) =================\\ +//================ Running (28-Apr-2024 18:29:52, pid=56833) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1047,7 +1032,7 @@ || || \\============================================================================// -//================ Running (30-May-2025 22:50:34, pid=22820) =================\\ +//================ Running (28-Apr-2024 18:29:52, pid=56836) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1099,7 +1084,7 @@ || || \\============================================================================// -//================ Running (30-May-2025 22:50:34, pid=22828) =================\\ +//================ Running (28-Apr-2024 18:29:52, pid=56846) =================\\ || || ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. @@ -1162,15 +1147,11 @@ || Repeat threshold : 100 repeats || || Gapped index : yes || || || -|| Free / total memory : 1.9GB / 0.0GB || +|| Free / total memory : 3.2GB / 0.0GB || || || || Input files : 1 file in total || || o chr901.fa || || || -|| || -|| WARNING: the free memory is lower than 3.0GB. || -|| the program may run very slow or crash. || -|| || \\============================================================================// //================================= Running ==================================\\ @@ -1180,7 +1161,7 @@ || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || subread-buildindex: hashtable.c:470: HashTablePutReplaceEx: Assertion `key != NULL' failed. -Aborted +subjunc-test.sh: line 3: 56852 Aborted ../../bin/subread-buildindex -o ../small1 ../chr901.fa ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ @@ -1214,7 +1195,7 @@ || || \\============================================================================// -//================ Running (30-May-2025 22:50:45, pid=24057) =================\\ +//================ Running (28-Apr-2024 18:29:54, pid=56881) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1258,7 +1239,7 @@ || || \\============================================================================// -//================ Running (30-May-2025 22:50:45, pid=24058) =================\\ +//================ Running (28-Apr-2024 18:29:54, pid=56892) =================\\ || || || Check the input reads. || || The input file contains base space reads. || @@ -1372,9 +1353,7 @@ Testing Allowing multi-mapped reads ... [PASS] Testing not sorting input file ... [PASS] Testing minimum overlapping length ... [PASS] -Testing minimum overlapping fraction ... [data/compare.sh: line 12: 24237 Aborted nohup ../../bin/featureCounts $PARAMETERS -o $TMPF.FC -a $ANNO_FILE $SAM_FILE > /dev/null 2>&1 -cat: data/DEL4-1748688645.FC: No such file or directory -FAILED] +Testing minimum overlapping fraction ... [PASS] Testing Largest Overlapping ... [PASS] Testing paired-end distance ... [PASS] Testing Read to position (5' end) ... [PASS] @@ -1385,9 +1364,7 @@ Testing minimum mapping quality ... [PASS] Testing Ignoring duplicated reads ... [PASS] Testing Fraction counting ... [PASS] -Testing Advanced fractions ... [data/compare.sh: line 12: 24346 Aborted nohup ../../bin/featureCounts $PARAMETERS -o $TMPF.FC -a $ANNO_FILE $SAM_FILE > /dev/null 2>&1 -cat: data/DEL4-1748688646.FC: No such file or directory -FAILED] +Testing Advanced fractions ... [PASS] Testing Junction counting ... [PASS,PASS] Skipping Junction counting (with genome). Testing GTF format annotations ... [PASS] @@ -1442,9 +1419,9 @@ || || \\============================================================================// -//====================== Running (30-May-2025 22:50:46) ======================\\ +//====================== Running (28-Apr-2024 18:29:56) ======================\\ || || -|| Split BAM file into result/temp-snps-024598-9A075E69ECE2-* ... || +|| Split BAM file into result/temp-snps-057465-0E441F44608B-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || @@ -1508,10 +1485,10 @@ install -m0755 -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright dh_installchangelogs -O--buildsystem=makefile - install -m0755 -d debian/subread-data/usr/share/doc/subread-data - install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian install -m0755 -d debian/subread/usr/share/doc/subread install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian + install -m0755 -d debian/subread-data/usr/share/doc/subread-data + install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg' @@ -1550,48 +1527,34 @@ install -p -m0644 ./debian/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-buildindex.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/subread-fullscan.1 debian/subread/usr/share/man/man1/subread-fullscan.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/featureCounts.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/genRandomReads.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/qualityScores.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/repair.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subjunc.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-align.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 - chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 - mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 - chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 - mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 - chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1 mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 - chmod 0644 -- debian/subread/usr/share/man/man1/repair.1 + chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 + mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 - chmod 0644 -- debian/subread/usr/share/man/man1/genRandomReads.1 + chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 - chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 - mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-fullscan.1 - mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 - chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 + mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 + chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 + mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 + mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 + chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 + mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 - mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 + mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 + chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 - chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 - mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 - chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 - chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 + chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile @@ -1599,12 +1562,12 @@ Using 1714041519 as canonical time Normalizing debian/subread-data/usr/share/doc/subread/examples/annotation/mm39_RefSeq_exon.txt.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--buildsystem=makefile - cd debian/subread cd debian/subread-data + cd debian/subread chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 - gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt + gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 cd '/build/reproducible-path/subread-2.0.6+dfsg' cd '/build/reproducible-path/subread-2.0.6+dfsg' dh_fixperms -O--buildsystem=makefile @@ -1626,26 +1589,16 @@ objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/i386-linux-gnu/subread.debug chmod 0644 -- debian/subread/usr/lib/debug/.dwz/i386-linux-gnu/subread.debug dh_strip -a -O--buildsystem=makefile - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a5 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a5/1fc5aef8565575b2b38b0501ed1007ae98c649.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a5/1fc5aef8565575b2b38b0501ed1007ae98c649.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a5/1fc5aef8565575b2b38b0501ed1007ae98c649.debug debian/subread/usr/bin/subindel - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/46 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/46/a8894cb7d9beba0e27619796a5ea049495b496.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/46/a8894cb7d9beba0e27619796a5ea049495b496.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/46/a8894cb7d9beba0e27619796a5ea049495b496.debug debian/subread/usr/bin/subjunc + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/62 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/62/df315a8a68d2bae3944ddedcf015544c2e19d3.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/62/df315a8a68d2bae3944ddedcf015544c2e19d3.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/62/df315a8a68d2bae3944ddedcf015544c2e19d3.debug debian/subread/usr/bin/exactSNP install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/73 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/73/66e43e9996105b52be82eb2c7dfde64b969979.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/73/66e43e9996105b52be82eb2c7dfde64b969979.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/73/66e43e9996105b52be82eb2c7dfde64b969979.debug debian/subread/usr/bin/sublong - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/359a27fd0ab9514da6b309d503403f815cb3e2.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/359a27fd0ab9514da6b309d503403f815cb3e2.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/359a27fd0ab9514da6b309d503403f815cb3e2.debug debian/subread/usr/bin/featureCounts install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/aa objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/aa/17ec094e15f60e96a99db4a4c18b179e43ab19.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/aa/17ec094e15f60e96a99db4a4c18b179e43ab19.debug @@ -1656,51 +1609,61 @@ chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/960585187f9381596f5285263f8e0490ecb6ac.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/54/960585187f9381596f5285263f8e0490ecb6ac.debug debian/subread/usr/bin/subread-buildindex - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/62 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/62/df315a8a68d2bae3944ddedcf015544c2e19d3.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/62/df315a8a68d2bae3944ddedcf015544c2e19d3.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/62/df315a8a68d2bae3944ddedcf015544c2e19d3.debug debian/subread/usr/bin/exactSNP - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/42400ac11ad410f8d84cbd70f83706d88b0218.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/42400ac11ad410f8d84cbd70f83706d88b0218.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/42400ac11ad410f8d84cbd70f83706d88b0218.debug debian/subread/usr/lib/subread/propmapped - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/fd4a0b03a6315e9a19fc8dd4cbb40fc18edf5e.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/fd4a0b03a6315e9a19fc8dd4cbb40fc18edf5e.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/fd4a0b03a6315e9a19fc8dd4cbb40fc18edf5e.debug debian/subread/usr/lib/subread/removeDup + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/359a27fd0ab9514da6b309d503403f815cb3e2.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/359a27fd0ab9514da6b309d503403f815cb3e2.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b3/359a27fd0ab9514da6b309d503403f815cb3e2.debug debian/subread/usr/bin/featureCounts + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a5 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a5/1fc5aef8565575b2b38b0501ed1007ae98c649.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a5/1fc5aef8565575b2b38b0501ed1007ae98c649.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a5/1fc5aef8565575b2b38b0501ed1007ae98c649.debug debian/subread/usr/bin/subindel + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/46 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/46/a8894cb7d9beba0e27619796a5ea049495b496.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/46/a8894cb7d9beba0e27619796a5ea049495b496.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/46/a8894cb7d9beba0e27619796a5ea049495b496.debug debian/subread/usr/bin/subjunc install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ab objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ab/a73e3b753b590d9a07fe8cfa6e233836a22869.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ab/a73e3b753b590d9a07fe8cfa6e233836a22869.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ab/a73e3b753b590d9a07fe8cfa6e233836a22869.debug debian/subread/usr/lib/subread/qualityScores - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/7edb6f5712bb8440aeff45afe6071b15bf81ce.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/7edb6f5712bb8440aeff45afe6071b15bf81ce.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/7edb6f5712bb8440aeff45afe6071b15bf81ce.debug debian/subread/usr/lib/subread/txUnique - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78 - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/2980d53f358f47bb0c8f0ddf6424f597837ec6.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/2980d53f358f47bb0c8f0ddf6424f597837ec6.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/2980d53f358f47bb0c8f0ddf6424f597837ec6.debug debian/subread/usr/lib/subread/subread-fullscan - install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2b - objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2b/c93722e89d38c17f3083277e52c86707badc18.debug - chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2b/c93722e89d38c17f3083277e52c86707badc18.debug - strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair - objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2b/c93722e89d38c17f3083277e52c86707badc18.debug debian/subread/usr/lib/subread/repair install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/c6d9f4071d2ab0f997c6e51c7a5ef66a01a2fc.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/c6d9f4071d2ab0f997c6e51c7a5ef66a01a2fc.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/c6d9f4071d2ab0f997c6e51c7a5ef66a01a2fc.debug debian/subread/usr/lib/subread/genRandomReads + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2b + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2b/c93722e89d38c17f3083277e52c86707badc18.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2b/c93722e89d38c17f3083277e52c86707badc18.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2b/c93722e89d38c17f3083277e52c86707badc18.debug debian/subread/usr/lib/subread/repair + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/fd4a0b03a6315e9a19fc8dd4cbb40fc18edf5e.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/fd4a0b03a6315e9a19fc8dd4cbb40fc18edf5e.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/16/fd4a0b03a6315e9a19fc8dd4cbb40fc18edf5e.debug debian/subread/usr/lib/subread/removeDup install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d2 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d2/8a1ba9db02d7f8844143a47c28751805a5db33.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d2/8a1ba9db02d7f8844143a47c28751805a5db33.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d2/8a1ba9db02d7f8844143a47c28751805a5db33.debug debian/subread/usr/lib/subread/flattenGTF + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/42400ac11ad410f8d84cbd70f83706d88b0218.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/42400ac11ad410f8d84cbd70f83706d88b0218.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/42400ac11ad410f8d84cbd70f83706d88b0218.debug debian/subread/usr/lib/subread/propmapped + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/7edb6f5712bb8440aeff45afe6071b15bf81ce.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/7edb6f5712bb8440aeff45afe6071b15bf81ce.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/7edb6f5712bb8440aeff45afe6071b15bf81ce.debug debian/subread/usr/lib/subread/txUnique + install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78 + objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/2980d53f358f47bb0c8f0ddf6424f597837ec6.debug + chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/2980d53f358f47bb0c8f0ddf6424f597837ec6.debug + strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan + objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/78/2980d53f358f47bb0c8f0ddf6424f597837ec6.debug debian/subread/usr/lib/subread/subread-fullscan install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/subread/usr/lib/debug/.dwz @@ -1712,7 +1675,7 @@ rm -f debian/subread/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN - dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/flattenGTF + dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/exactSNP debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/subread-fullscan dh_installdeb -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN @@ -1726,10 +1689,10 @@ echo misc:Depends= >> debian/subread-data.substvars echo misc:Pre-Depends= >> debian/subread-data.substvars dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -cdebian/control -Pdebian/subread-data -dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined - chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/subread +dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined + chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums -O--buildsystem=makefile install -m0755 -d debian/subread-data/DEBIAN @@ -1745,9 +1708,9 @@ dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. dpkg-deb --root-owner-group --build debian/subread-data .. -dpkg-deb: building package 'subread-data' in '../subread-data_2.0.6+dfsg-3_all.deb'. -dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.6+dfsg-3_i386.deb'. dpkg-deb: building package 'subread' in '../subread_2.0.6+dfsg-3_i386.deb'. +dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.6+dfsg-3_i386.deb'. +dpkg-deb: building package 'subread-data' in '../subread-data_2.0.6+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.6+dfsg-3_i386.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.6+dfsg-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1755,12 +1718,14 @@ 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/49680/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/49680/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/14003 and its subdirectories -I: Current time: Fri May 30 22:51:39 -12 2025 -I: pbuilder-time-stamp: 1748688699 +I: removing directory /srv/workspace/pbuilder/49680 and its subdirectories +I: Current time: Sun Apr 28 18:31:04 +14 2024 +I: pbuilder-time-stamp: 1714278664