I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 12 07:48:52 +14 2023 I: pbuilder-time-stamp: 1686505732 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [lucy_1.20-3.dsc] I: copying [./lucy_1.20.orig.tar.gz] I: copying [./lucy_1.20-3.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Apr 20 06:58:04 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lucy_1.20-3.dsc: no acceptable signature found dpkg-source: info: extracting lucy in lucy-1.20 dpkg-source: info: unpacking lucy_1.20.orig.tar.gz dpkg-source: info: unpacking lucy_1.20-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying helpingMakefile.patch dpkg-source: info: applying spellings.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1792570/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 12 07:49 /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/1792570/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1792570/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=16ed08289acf421d8ee9dd20db9ae0ad LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1792570 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bVjonQ1M/pbuilderrc_w2EA --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bVjonQ1M/b2 --logfile b2/build.log --extrapackages usrmerge lucy_1.20-3.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Jun 12 07:49 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/1792570/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19591 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After unpacking 72.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Fetched 18.7 MB in 1s (31.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19591 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../22-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/1792570/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/1792570/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/lucy-1.20/ && 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 > ../lucy_1.20-3_source.changes dpkg-buildpackage: info: source package lucy dpkg-buildpackage: info: source version 1.20-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j15 clean make[1]: Entering directory '/build/lucy-1.20' rm -f lucy.o qual_trim.o abi.o vector.o splice.o poly.o lucy make[1]: Leaving directory '/build/lucy-1.20' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/lucy.substvars debian/files rm -fr -- debian/lucy/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/lucy-1.20' cc -g -O2 -ffile-prefix-map=/build/lucy-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lucy.o lucy.c cc -g -O2 -ffile-prefix-map=/build/lucy-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qual_trim.o qual_trim.c cc -g -O2 -ffile-prefix-map=/build/lucy-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abi.o abi.c cc -g -O2 -ffile-prefix-map=/build/lucy-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vector.o vector.c cc -g -O2 -ffile-prefix-map=/build/lucy-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o splice.o splice.c cc -g -O2 -ffile-prefix-map=/build/lucy-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o poly.o poly.c qual_trim.c:10:1: warning: "/*" within comment [-Wcomment] 10 | /* qual_trim.c - Quality trimming algorithm which determines a "clean" | qual_trim.c:11:1: warning: "/*" within comment [-Wcomment] 11 | /* range for a sequence based on its phred quality values. | qual_trim.c:12:1: warning: "/*" within comment [-Wcomment] 12 | /* | qual_trim.c:13:1: warning: "/*" within comment [-Wcomment] 13 | /* Written by Michael Holmes, 4/13/99. | qual_trim.c:14:1: warning: "/*" within comment [-Wcomment] 14 | /* | qual_trim.c:15:1: warning: "/*" within comment [-Wcomment] 15 | /* 1/31/2000, Michael Holmes -- Added default_windows(). | qual_trim.c:16:1: warning: "/*" within comment [-Wcomment] 16 | /* 2/15/2000, Michael Holmes -- Added bracket_clean_range() and | qual_trim.c:17:1: warning: "/*" within comment [-Wcomment] 17 | /* set_bracket(). | qual_trim.c:18:1: warning: "/*" within comment [-Wcomment] 18 | /* 2/18/2000, Michael Holmes -- Minor change to test-mode output only. | qual_trim.c:19:1: warning: "/*" within comment [-Wcomment] 19 | /* | qual_trim.c:20:1: warning: "/*" within comment [-Wcomment] 20 | /* Copyright (C) 1999, 2000, The Institute for Genomic Research. All rights | qual_trim.c:21:1: warning: "/*" within comment [-Wcomment] 21 | /* reserved. | qual_trim.c:22:1: warning: "/*" within comment [-Wcomment] 22 | /* | qual_trim.c:23:1: warning: "/*" within comment [-Wcomment] 23 | /* Note: phred quality values are based on the log (base 10) of the | qual_trim.c:24:1: warning: "/*" within comment [-Wcomment] 24 | /* probability that the corresponding base call is in error: | qual_trim.c:25:1: warning: "/*" within comment [-Wcomment] 25 | /* | qual_trim.c:26:1: warning: "/*" within comment [-Wcomment] 26 | /* Q = -10 log(P_error) | qual_trim.c:27:1: warning: "/*" within comment [-Wcomment] 27 | /* | qual_trim.c:28:1: warning: "/*" within comment [-Wcomment] 28 | /* Thanks to Granger Sutton for valuable suggestions. | qual_trim.c:29:1: warning: "/*" within comment [-Wcomment] 29 | /* | qual_trim.c:30:1: warning: "/*" within comment [-Wcomment] 30 | /* The main functions of interest to external code (such as lucy) are | qual_trim.c:31:1: warning: "/*" within comment [-Wcomment] 31 | /* default_windows() and quality_trim(). The grim() function emulates the | qual_trim.c:32:1: warning: "/*" within comment [-Wcomment] 32 | /* interface that was used by the old quality trimmimg algorithm (grim), | qual_trim.c:33:1: warning: "/*" within comment [-Wcomment] 33 | /* but it is not called by lucy. The main() function is compiled only if | qual_trim.c:34:1: warning: "/*" within comment [-Wcomment] 34 | /* TEST_THIS_CODE is #defined. | qual_trim.c:35:1: warning: "/*" within comment [-Wcomment] 35 | /* | qual_trim.c:36:1: warning: "/*" within comment [-Wcomment] 36 | /* The calling hierarchy is: | qual_trim.c:37:1: warning: "/*" within comment [-Wcomment] 37 | /* | qual_trim.c:38:1: warning: "/*" within comment [-Wcomment] 38 | /* main() | qual_trim.c:39:1: warning: "/*" within comment [-Wcomment] 39 | /* grim() | qual_trim.c:40:1: warning: "/*" within comment [-Wcomment] 40 | /* default_windows() | qual_trim.c:41:1: warning: "/*" within comment [-Wcomment] 41 | /* quality_trim() | qual_trim.c:42:1: warning: "/*" within comment [-Wcomment] 42 | /* bracket_clean_range() | qual_trim.c:43:1: warning: "/*" within comment [-Wcomment] 43 | /* multi_window_trim() | qual_trim.c:44:1: warning: "/*" within comment [-Wcomment] 44 | /* window_trim() | qual_trim.c:45:1: warning: "/*" within comment [-Wcomment] 45 | /* multi_window_trim() [recursive call] | qual_trim.c:46:1: warning: "/*" within comment [-Wcomment] 46 | /* average_error_trim() | qual_trim.c:47:1: warning: "/*" within comment [-Wcomment] 47 | /* | qual_trim.c:48:1: warning: "/*" within comment [-Wcomment] 48 | /**************************************************************************/ | abi.c:24:8: warning: type defaults to 'int' in declaration of 'condition' [-Wimplicit-int] 24 | static condition[]={ | ^~~~~~~~~ abi.c: In function 'abi_code': abi.c:70:15: warning: implicit declaration of function 'random' [-Wimplicit-function-declaration] 70 | case 5: tmp=random()%2 ? 2 : 0; break; | ^~~~~~ abi.c:82:5: warning: implicit declaration of function 'giveup' [-Wimplicit-function-declaration] 82 | giveup("how can other cases happen in tag_code?"); | ^~~~~~ abi.c: In function 'abi_align': abi.c:195:18: warning: array subscript has type 'char' [-Wchar-subscripts] 195 | if (badness[a[i]][b[j]]) { | ~^~~ abi.c:195:24: warning: array subscript has type 'char' [-Wchar-subscripts] 195 | if (badness[a[i]][b[j]]) { | ~^~~ abi.c:221:18: warning: array subscript has type 'char' [-Wchar-subscripts] 221 | if (badness[a[i]][b[j]]) { | ~^~~ abi.c:221:24: warning: array subscript has type 'char' [-Wchar-subscripts] 221 | if (badness[a[i]][b[j]]) { | ~^~~ abi.c:226:46: warning: array subscript has type 'char' [-Wchar-subscripts] 226 | l=0 && r>=0 && badness[a[l]][b[r]]==0 | ~^~~ splice.c: In function 'splice_align_left': splice.c:53:12: warning: type defaults to 'int' in declaration of 'left' [-Wimplicit-int] 53 | register left, top, direc, score, i, j; | ^~~~ splice.c:53:18: warning: type defaults to 'int' in declaration of 'top' [-Wimplicit-int] 53 | register left, top, direc, score, i, j; | ^~~ splice.c:53:23: warning: type defaults to 'int' in declaration of 'direc' [-Wimplicit-int] 53 | register left, top, direc, score, i, j; | ^~~~~ splice.c:53:30: warning: type defaults to 'int' in declaration of 'score' [-Wimplicit-int] 53 | register left, top, direc, score, i, j; | ^~~~~ splice.c:53:37: warning: type defaults to 'int' in declaration of 'i' [-Wimplicit-int] 53 | register left, top, direc, score, i, j; | ^ splice.c:53:40: warning: type defaults to 'int' in declaration of 'j' [-Wimplicit-int] 53 | register left, top, direc, score, i, j; | ^ splice.c:68:32: warning: array subscript has type 'char' [-Wchar-subscripts] 68 | Score(0,0)=max_score=match[*a][*b]; | ^~ splice.c:68:36: warning: array subscript has type 'char' [-Wchar-subscripts] 68 | Score(0,0)=max_score=match[*a][*b]; | ^~ splice.c:75:20: warning: array subscript has type 'char' [-Wchar-subscripts] 75 | score=match[a[i]][*b]; | ~^~~ splice.c:75:25: warning: array subscript has type 'char' [-Wchar-subscripts] 75 | score=match[a[i]][*b]; | ^~ splice.c:16:38: warning: array subscript has type 'char' [-Wchar-subscripts] 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)] | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ splice.c:76:38: note: in expansion of macro 'Direc' 76 | left=Score(i-1,0)+left_penalty[Direc(i-1,0)]; | ^~~~~ splice.c:90:19: warning: array subscript has type 'char' [-Wchar-subscripts] 90 | score=match[*a][b[j]]; | ^~ splice.c:90:24: warning: array subscript has type 'char' [-Wchar-subscripts] 90 | score=match[*a][b[j]]; | ~^~~ splice.c:16:38: warning: array subscript has type 'char' [-Wchar-subscripts] 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)] | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ splice.c:91:36: note: in expansion of macro 'Direc' 91 | top=Score(0,j-1)+top_penalty[Direc(0,j-1)]; | ^~~~~ splice.c:107:25: warning: array subscript has type 'char' [-Wchar-subscripts] 107 | score+=match[a[i]][b[j]]; | ~^~~ splice.c:107:31: warning: array subscript has type 'char' [-Wchar-subscripts] 107 | score+=match[a[i]][b[j]]; | ~^~~ splice.c:110:24: warning: array subscript has type 'char' [-Wchar-subscripts] 110 | score=match[a[i]][b[j]]; | ~^~~ splice.c:110:30: warning: array subscript has type 'char' [-Wchar-subscripts] 110 | score=match[a[i]][b[j]]; | ~^~~ abi.c:294:45: warning: array subscript has type 'char' [-Wchar-subscripts] 294 | l>=0 && r>=0 && badness[a[l]][b[r]]==0 | ~^~~ splice.c:16:38: warning: array subscript has type 'char' [-Wchar-subscripts] 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)] | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ splice.c:113:38: note: in expansion of macro 'Direc' 113 | top=Score(i,j-1)+top_penalty[Direc(i,j-1)]; | ^~~~~ splice.c:16:38: warning: array subscript has type 'char' [-Wchar-subscripts] 16 | #define Direc(x, y) splice_direc_base[(y)*width+(x)] | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ splice.c:114:40: note: in expansion of macro 'Direc' 114 | left=Score(i-1,j)+left_penalty[Direc(i-1,j)]; | ^~~~~ abi.c:301:30: warning: array subscript has type 'char' [-Wchar-subscripts] 301 | if ((count+=badness[a[l]][b[r]])=0 && r>=0 && badness[a[l]][b[r]]==0 | ~^~~ splice.c: In function 'splice_align_right': splice.c:176:12: warning: type defaults to 'int' in declaration of 'left' [-Wimplicit-int] 176 | register left, top, direc, score, i, j; | ^~~~ abi.c:313:45: warning: array subscript has type 'char' [-Wchar-subscripts] 313 | l>=0 && r>=0 && badness[a[l]][b[r]]==0 | ~^~~ splice.c:176:18: warning: type defaults to 'int' in declaration of 'top' [-Wimplicit-int] 176 | register left, top, direc, score, i, j; | ^~~ splice.c:176:23: warning: type defaults to 'int' in declaration of 'direc' [-Wimplicit-int] 176 | register left, top, direc, score, i, j; | ^~~~~ splice.c:176:30: warning: type defaults to 'int' in declaration of 'score' [-Wimplicit-int] 176 | register left, top, direc, score, i, j; | ^~~~~ splice.c:176:37: warning: type defaults to 'int' in declaration of 'i' [-Wimplicit-int] 176 | register left, top, direc, score, i, j; | ^ abi.c:320:30: warning: array subscript has type 'char' [-Wchar-subscripts] 320 | if ((count+=badness[a[l]][b[r]])=0 && r>=0 && badness[a[l]][b[r]]==0 | ~^~~ splice.c:189:34: warning: array subscript has type 'char' [-Wchar-subscripts] 189 | Score(0,0)=max_score=match[*a][*b]; | ^~ abi.c:334:45: warning: array subscript has type 'char' [-Wchar-subscripts] 334 | l>=0 && r>=0 && badness[a[l]][b[r]]==0 | ~^~~ splice.c:196:18: warning: array subscript has type 'char' [-Wchar-subscripts] 196 | score=match[a[i]][*b]; | ~^~~ splice.c:196:23: warning: array subscript has type 'char' [-Wchar-subscripts] 196 | score=match[a[i]][*b]; | ^~ abi.c:341:30: warning: array subscript has type 'char' [-Wchar-subscripts] 341 | if ((count+=badness[a[l]][b[r]])=span && j>=width-max_i || j>height/2) | ~~~~~~~~^~~~~~~~~~~~~~~~~ poly.c: In function 'poly_at_left': poly.c:22:9: warning: implicit declaration of function 'abi_code' [-Wimplicit-function-declaration] 22 | if (abi_code(*seq)==T) { | ^~~~~~~~ lucy.c: In function 'hashstring': lucy.c:111:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 111 | if (g = value&0xF0000000) { | ^ lucy.c: In function 'worker': lucy.c:172:10: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 172 | int id=(int)arg; | ^ lucy.c: In function 'work_splice': lucy.c:206:5: warning: implicit declaration of function 'splice_align_left' [-Wimplicit-function-declaration] 206 | splice_align_left(id, target_seq[id], | ^~~~~~~~~~~~~~~~~ lucy.c:247:7: warning: implicit declaration of function 'splice_align_right' [-Wimplicit-function-declaration] 247 | splice_align_right(id, target_seq[id]+seqs[i].left, | ^~~~~~~~~~~~~~~~~~ vector.c: In function 'construct_vector_tags': vector.c:85:34: warning: array subscript has type 'char' [-Wchar-subscripts] 85 | accr|=tag_code(rev_code[seq[len-k%len-1]]); | ~~~^~~~~~~~~~~~~ lucy.c: At top level: lucy.c:284:1: warning: return type defaults to 'int' [-Wimplicit-int] 284 | main (argc, argv) | ^~~~ lucy.c: In function 'main': lucy.c:361:9: warning: implicit declaration of function 'set_bracket' [-Wimplicit-function-declaration] 361 | set_bracket(bracket_size, bracket_err); | ^~~~~~~~~~~ lucy.c:469:5: warning: implicit declaration of function 'default_windows' [-Wimplicit-function-declaration] 469 | default_windows(); | ^~~~~~~~~~~~~~~ lucy.c:531:51: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 531 | if (pthread_create(&threads[i], NULL, worker, (void*)i)) | ^ lucy.c:639:7: warning: implicit declaration of function 'quality_trim' [-Wimplicit-function-declaration] 639 | quality_trim(conf_val_raw, j, minimum, &(ptr->left), &(ptr->right)); | ^~~~~~~~~~~~ lucy.c:669:5: warning: implicit declaration of function 'prepare_abi_mask' [-Wimplicit-function-declaration] 669 | prepare_abi_mask(); | ^~~~~~~~~~~~~~~~ lucy.c:713:9: warning: implicit declaration of function 'abi_align' [-Wimplicit-function-declaration] 713 | abi_align(phred_seq, ptr->len, abi_seq, bases, &left, &right); | ^~~~~~~~~ lucy.c:792:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 792 | (i=(int)fgets(buf, BUFFER_LENGTH, spl_file)) && buf[0]!='>'; ) { | ^ lucy.c:891:14: warning: implicit declaration of function 'poly_at_left' [-Wimplicit-function-declaration] 891 | left=poly_at_left(&phred_seq[seqs[i].left], | ^~~~~~~~~~~~ qual_trim.c:214:1: warning: "/*" within comment [-Wcomment] 214 | /* Determines some number of candidate clean ranges using a particular | qual_trim.c:215:1: warning: "/*" within comment [-Wcomment] 215 | /* window size. | qual_trim.c:216:1: warning: "/*" within comment [-Wcomment] 216 | /* | qual_trim.c:217:1: warning: "/*" within comment [-Wcomment] 217 | /* Globals used: | qual_trim.c:218:1: warning: "/*" within comment [-Wcomment] 218 | /* double end_limit, (maximum allowed probability of error for bases) | qual_trim.c:219:1: warning: "/*" within comment [-Wcomment] 219 | /* ( at each end of clean range) | qual_trim.c:220:1: warning: "/*" within comment [-Wcomment] 220 | /* | qual_trim.c:332:1: warning: "/*" within comment [-Wcomment] 332 | /* Finds the largest subsequence of a sequence whose average probability | qual_trim.c:333:1: warning: "/*" within comment [-Wcomment] 333 | /* of error does not exceed a specified maximum. | qual_trim.c:334:1: warning: "/*" within comment [-Wcomment] 334 | /* | qual_trim.c:335:1: warning: "/*" within comment [-Wcomment] 335 | /* Globals used: | qual_trim.c:336:1: warning: "/*" within comment [-Wcomment] 336 | /* double max_avg_error, (maximum allowed average probability of error) | qual_trim.c:337:1: warning: "/*" within comment [-Wcomment] 337 | /* double end_limit, (maximum allowed probability of error for bases) | lucy.c:894:15: warning: implicit declaration of function 'poly_at_right' [-Wimplicit-function-declaration] 894 | right=poly_at_right(&phred_seq[seqs[i].right], | ^~~~~~~~~~~~~ qual_trim.c:338:1: warning: "/*" within comment [-Wcomment] 338 | /* ( at each end of clean range) | qual_trim.c:339:1: warning: "/*" within comment [-Wcomment] 339 | /* | vector.c: In function 'tag_code': vector.c:44:10: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 44 | return tmp; | ^~~ vector.c:22:16: note: 'tmp' was declared here 22 | register int tmp; | ^~~ lucy.c:934:5: warning: implicit declaration of function 'construct_vector_tags' [-Wimplicit-function-declaration] 934 | construct_vector_tags(vec_seq, bases); | ^~~~~~~~~~~~~~~~~~~~~ qual_trim.c:434:1: warning: "/*" within comment [-Wcomment] 434 | /* Determines a single clean range, after recursively considering all of | qual_trim.c:435:1: warning: "/*" within comment [-Wcomment] 435 | /* the specified window sizes. Calls average_error_trim to trim the | qual_trim.c:436:1: warning: "/*" within comment [-Wcomment] 436 | /* results of the final window based on overall average probability of | qual_trim.c:437:1: warning: "/*" within comment [-Wcomment] 437 | /* error. | qual_trim.c:438:1: warning: "/*" within comment [-Wcomment] 438 | /* | qual_trim.c:439:1: warning: "/*" within comment [-Wcomment] 439 | /* Globals used: | qual_trim.c:440:1: warning: "/*" within comment [-Wcomment] 440 | /* double max_avg_error, (maximum allowed average probability of error) | qual_trim.c:441:1: warning: "/*" within comment [-Wcomment] 441 | /* double end_limit, (maximum allowed probability of error for bases) | qual_trim.c:442:1: warning: "/*" within comment [-Wcomment] 442 | /* ( at each end of clean range) | qual_trim.c:443:1: warning: "/*" within comment [-Wcomment] 443 | /* | qual_trim.c:569:1: warning: "/*" within comment [-Wcomment] 569 | /* Sets the window size and average probability of error allowed for the | qual_trim.c:570:1: warning: "/*" within comment [-Wcomment] 570 | /* terminal windows that "bracket" the candidate clean range. | qual_trim.c:571:1: warning: "/*" within comment [-Wcomment] 571 | /* | qual_trim.c:572:1: warning: "/*" within comment [-Wcomment] 572 | /* Globals used: | qual_trim.c:573:1: warning: "/*" within comment [-Wcomment] 573 | /* int bracket_window, (size of terminal window) | qual_trim.c:574:1: warning: "/*" within comment [-Wcomment] 574 | /* double bracket_error (allowable average prob. error in window) | qual_trim.c:575:1: warning: "/*" within comment [-Wcomment] 575 | /* | qual_trim.c:587:1: warning: "/*" within comment [-Wcomment] 587 | /* Finds the leftmost window, and the rightmost window, which meet the | qual_trim.c:588:1: warning: "/*" within comment [-Wcomment] 588 | /* specified error criterion. The purpose of this function is to bracket | qual_trim.c:589:1: warning: "/*" within comment [-Wcomment] 589 | /* the portion of the sequence that is of decent quality -- i.e. to | qual_trim.c:590:1: warning: "/*" within comment [-Wcomment] 590 | /* eliminate the really bad quality stuff that is often found on either | qual_trim.c:591:1: warning: "/*" within comment [-Wcomment] 591 | /* end. The beginning of the first matching window, and the end of the | qual_trim.c:592:1: warning: "/*" within comment [-Wcomment] 592 | /* last, bracket the sequence range that will be looked at to find the | qual_trim.c:593:1: warning: "/*" within comment [-Wcomment] 593 | /* final clean range. | qual_trim.c:594:1: warning: "/*" within comment [-Wcomment] 594 | /* | qual_trim.c:595:1: warning: "/*" within comment [-Wcomment] 595 | /* This function is called before the multi_window_trim function, and | qual_trim.c:596:1: warning: "/*" within comment [-Wcomment] 596 | /* its results are used to limit the range of sequence that will be | qual_trim.c:597:1: warning: "/*" within comment [-Wcomment] 597 | /* considered by that function. | qual_trim.c:598:1: warning: "/*" within comment [-Wcomment] 598 | /* | qual_trim.c:678:1: warning: "/*" within comment [-Wcomment] 678 | /* Determines the clean range. Calls multi_window_trim, which calls both | qual_trim.c:679:1: warning: "/*" within comment [-Wcomment] 679 | /* window_trim and average_error_trim. | qual_trim.c:680:1: warning: "/*" within comment [-Wcomment] 680 | /* | qual_trim.c:681:1: warning: "/*" within comment [-Wcomment] 681 | /* Globals used: | qual_trim.c:682:1: warning: "/*" within comment [-Wcomment] 682 | /* int num_windows, (number of windows) | qual_trim.c:683:1: warning: "/*" within comment [-Wcomment] 683 | /* int *windows, (array of window sizes (largest to smallest)) | qual_trim.c:684:1: warning: "/*" within comment [-Wcomment] 684 | /* double *err_limits, (array of maximum allowed average probability) | lucy.c:947:11: warning: implicit declaration of function 'match_vector_tags' [-Wimplicit-function-declaration] 947 | j=match_vector_tags(phred_seq+seqs[i].left, bases); | ^~~~~~~~~~~~~~~~~ qual_trim.c:685:1: warning: "/*" within comment [-Wcomment] 685 | /* ( for each window size) | qual_trim.c:686:1: warning: "/*" within comment [-Wcomment] 686 | /* double max_avg_error, (maximum allowed average probability of error) | qual_trim.c:687:1: warning: "/*" within comment [-Wcomment] 687 | /* double end_limit, (maximum allowed probability of error for bases) | qual_trim.c:688:1: warning: "/*" within comment [-Wcomment] 688 | /* ( at each end of clean range) | qual_trim.c:689:1: warning: "/*" within comment [-Wcomment] 689 | /* int bracket_window, (size of terminal window) | qual_trim.c:690:1: warning: "/*" within comment [-Wcomment] 690 | /* double bracket_error (allowable average prob. error in window) | qual_trim.c:691:1: warning: "/*" within comment [-Wcomment] 691 | /* | qual_trim.c: In function 'quality_trim': qual_trim.c:705:21: warning: unused variable 'sum' [-Wunused-variable] 705 | double err, sum; | ^~~ qual_trim.c:705:16: warning: unused variable 'err' [-Wunused-variable] 705 | double err, sum; | ^~~ qual_trim.c: At top level: qual_trim.c:792:1: warning: "/*" within comment [-Wcomment] 792 | /* Sets up 3 windows for quality trimming, with the average error allowed | qual_trim.c:793:1: warning: "/*" within comment [-Wcomment] 793 | /* in each window calculated from max_avg_error. | qual_trim.c:794:1: warning: "/*" within comment [-Wcomment] 794 | /* | qual_trim.c:795:1: warning: "/*" within comment [-Wcomment] 795 | /* Globals used: | qual_trim.c:796:1: warning: "/*" within comment [-Wcomment] 796 | /* int num_windows, (number of windows) | qual_trim.c:797:1: warning: "/*" within comment [-Wcomment] 797 | /* int *windows, (array of window sizes (largest to smallest)) | qual_trim.c:798:1: warning: "/*" within comment [-Wcomment] 798 | /* double *err_limits, (array of maximum allowed average probability) | qual_trim.c:799:1: warning: "/*" within comment [-Wcomment] 799 | /* (for each window size) | qual_trim.c:800:1: warning: "/*" within comment [-Wcomment] 800 | /* double max_avg_error, (maximum allowed average probability of error) | qual_trim.c:801:1: warning: "/*" within comment [-Wcomment] 801 | /* | qual_trim.c:826:1: warning: "/*" within comment [-Wcomment] 826 | /* Simulates the functionality of the old grim() function, by calling | abi.c: In function 'abi_code': qual_trim.c:827:1: warning: "/*" within comment [-Wcomment] 827 | /* quality_trim(). | abi.c:84:10: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 84 | return tmp; | ^~~ abi.c:62:16: note: 'tmp' was declared here 62 | register int tmp; | ^~~ qual_trim.c:828:1: warning: "/*" within comment [-Wcomment] 828 | /* | qual_trim.c:829:1: warning: "/*" within comment [-Wcomment] 829 | /* Globals used: | qual_trim.c:830:1: warning: "/*" within comment [-Wcomment] 830 | /* int num_windows, (number of windows) | qual_trim.c:831:1: warning: "/*" within comment [-Wcomment] 831 | /* int *windows, (array of window sizes (largest to smallest)) | qual_trim.c:832:1: warning: "/*" within comment [-Wcomment] 832 | /* double *err_limits, (array of maximum allowed average probability) | qual_trim.c:833:1: warning: "/*" within comment [-Wcomment] 833 | /* (for each window size) | qual_trim.c:834:1: warning: "/*" within comment [-Wcomment] 834 | /* double max_avg_error, (maximum allowed average probability of error) | qual_trim.c:835:1: warning: "/*" within comment [-Wcomment] 835 | /* double end_limit, (maximum allowed probability of error for bases) | qual_trim.c:836:1: warning: "/*" within comment [-Wcomment] 836 | /* ( at each end of clean range) | qual_trim.c:837:1: warning: "/*" within comment [-Wcomment] 837 | /* | lucy.c:959:5: warning: implicit declaration of function 'destroy_vector_tags' [-Wimplicit-function-declaration] 959 | destroy_vector_tags(); | ^~~~~~~~~~~~~~~~~~~ lucy.c:631:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 631 | fgets(buf, BUFFER_LENGTH, qul_file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f lucy cc -g -O2 -ffile-prefix-map=/build/lucy-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -o lucy lucy.o qual_trim.o abi.o vector.o splice.o poly.o -lpthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed make[1]: Leaving directory '/build/lucy-1.20' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/lucy.substvars rm -fr -- debian/.debhelper/generated/lucy/ debian/lucy/ debian/tmp/ dh_auto_install --destdir=debian/lucy/ install -m0755 -d /build/lucy-1.20/debian/lucy dh_install install -m0755 -d debian/lucy/usr/bin cp --reflink=auto -a ./lucy debian/lucy/usr/bin/ dh_installdocs install -m0755 -d debian/lucy/usr/share/doc/lucy install -m0755 -d debian/lucy/usr/share/doc/lucy cp --reflink=auto -a ./debian/README.Debian debian/lucy/usr/share/doc/lucy cp --reflink=auto -a ./debian/README.source debian/lucy/usr/share/doc/lucy cp --reflink=auto -a ./README.FIRST debian/lucy/usr/share/doc/lucy cp --reflink=auto -a ./HISTORY debian/lucy/usr/share/doc/lucy chmod -R u\+rw,go=rX debian/lucy/usr/share/doc install -p -m0644 debian/README.Debian debian/lucy/usr/share/doc/lucy/README.Debian install -p -m0644 debian/copyright debian/lucy/usr/share/doc/lucy/copyright dh_installchangelogs install -m0755 -d debian/lucy/usr/share/doc/lucy install -p -m0644 debian/.debhelper/generated/lucy/dh_installchangelogs.dch.trimmed debian/lucy/usr/share/doc/lucy/changelog.Debian mv debian/lucy/usr/share/doc/lucy/HISTORY debian/lucy/usr/share/doc/lucy/changelog chmod 0644 -- debian/lucy/usr/share/doc/lucy/changelog dh_installexamples install -m0755 -d debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./ARMTM40TR.qul debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./ARMTM40TR.seq debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./PUC19 debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./PUC19splice debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./PUC19splice.for debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./PUC19splice.rev debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./atie.2nd debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./atie.qul debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./atie.seq debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./pSPORT1splice debian/lucy/usr/share/doc/lucy/examples cp --reflink=auto -a ./pSPORT1vector debian/lucy/usr/share/doc/lucy/examples debian/rules override_dh_installman make[1]: Entering directory '/build/lucy-1.20' sed 1d -i lucy.1 dh_installman install -m0755 -d debian/lucy/usr/share/man/man1/ install -p -m0644 ./lucy.1 debian/lucy/usr/share/man/man1/lucy.1 man-recode --to-code UTF-8 --suffix .dh-new debian/lucy/usr/share/man/man1/lucy.1 mv debian/lucy/usr/share/man/man1/lucy.1.dh-new debian/lucy/usr/share/man/man1/lucy.1 chmod 0644 -- debian/lucy/usr/share/man/man1/lucy.1 make[1]: Leaving directory '/build/lucy-1.20' dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/lucy chmod a-x usr/share/doc/lucy/README.FIRST usr/share/doc/lucy/changelog usr/share/doc/lucy/changelog.Debian usr/share/man/man1/lucy.1 gzip -9nf usr/share/doc/lucy/README.FIRST usr/share/doc/lucy/changelog usr/share/doc/lucy/changelog.Debian usr/share/man/man1/lucy.1 cd '/build/lucy-1.20' dh_fixperms find debian/lucy ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/lucy/usr/share/doc -type f -a -true -a ! -regex 'debian/lucy/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/lucy/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/lucy/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/lucy -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/lucy/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz dwz -- debian/lucy/usr/bin/lucy dh_strip install -m0755 -d debian/.debhelper/lucy/dbgsym-root/usr/lib/debug/.build-id/96 objcopy --only-keep-debug --compress-debug-sections debian/lucy/usr/bin/lucy debian/.debhelper/lucy/dbgsym-root/usr/lib/debug/.build-id/96/a394700d8fa29e5e7f34bd505cc8714d75d3d1.debug chmod 0644 -- debian/.debhelper/lucy/dbgsym-root/usr/lib/debug/.build-id/96/a394700d8fa29e5e7f34bd505cc8714d75d3d1.debug strip --remove-section=.comment --remove-section=.note debian/lucy/usr/bin/lucy objcopy --add-gnu-debuglink debian/.debhelper/lucy/dbgsym-root/usr/lib/debug/.build-id/96/a394700d8fa29e5e7f34bd505cc8714d75d3d1.debug debian/lucy/usr/bin/lucy install -m0755 -d debian/.debhelper/lucy/dbgsym-root/usr/share/doc ln -s lucy debian/.debhelper/lucy/dbgsym-root/usr/share/doc/lucy-dbgsym install -m0755 -d debian/.debhelper/lucy dh_makeshlibs rm -f debian/lucy/DEBIAN/shlibs dh_shlibdeps install -m0755 -d debian/lucy/DEBIAN dpkg-shlibdeps -Tdebian/lucy.substvars debian/lucy/usr/bin/lucy dh_installdeb install -m0755 -d debian/lucy/DEBIAN dh_gencontrol install -m0755 -d debian/lucy/DEBIAN echo misc:Depends= >> debian/lucy.substvars echo misc:Pre-Depends= >> debian/lucy.substvars install -m0755 -d debian/.debhelper/lucy/dbgsym-root/DEBIAN dpkg-gencontrol -plucy -ldebian/changelog -Tdebian/lucy.substvars -Pdebian/.debhelper/lucy/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=lucy-dbgsym "-DDepends=lucy (= \${binary:Version})" "-DDescription=debug symbols for lucy" -DBuild-Ids=96a394700d8fa29e5e7f34bd505cc8714d75d3d1 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/lucy/dbgsym-root/DEBIAN/control dpkg-gencontrol -plucy -ldebian/changelog -Tdebian/lucy.substvars -Pdebian/lucy chmod 0644 -- debian/lucy/DEBIAN/control dh_md5sums install -m0755 -d debian/lucy/DEBIAN cd debian/lucy >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/lucy/DEBIAN/md5sums install -m0755 -d debian/.debhelper/lucy/dbgsym-root/DEBIAN cd debian/.debhelper/lucy/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/lucy/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/.debhelper/lucy/dbgsym-root .. dpkg-deb --root-owner-group --build debian/lucy .. dpkg-deb: building package 'lucy-dbgsym' in '../lucy-dbgsym_1.20-3_amd64.deb'. dpkg-deb: building package 'lucy' in '../lucy_1.20-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../lucy_1.20-3_amd64.buildinfo dpkg-genchanges --build=binary -O../lucy_1.20-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1792570/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1792570/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/1792570 and its subdirectories I: Current time: Mon Jun 12 07:50:30 +14 2023 I: pbuilder-time-stamp: 1686505830