I: pbuilder: network access will be disabled during build
I: Current time: Sat May 18 06:36:54 -12 2024
I: pbuilder-time-stamp: 1716057414
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: using eatmydata during job
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 Sun Apr 19 04:58:04 2020 -12
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/26139/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='eb307e5bccf24c45b4acd774e8d1e343'
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='26139'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2X2cBvsT/pbuilderrc_pxie --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2X2cBvsT/b1 --logfile b1/build.log lucy_1.20-3.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://85.184.249.68:3128'
I: uname -a
Linux ionos16-i386 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Feb 12 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 218680 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 22 2023 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 22 2023 more
-rwsr-xr-x 1 root root 58912 Mar 22 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 22 2023 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 2023 tar
-rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 22 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/26139/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19604 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 19.0 MB of archives. After unpacking 72.7 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Fetched 19.0 MB in 0s (56.7 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%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19604 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_i386.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ...
Unpacking libmagic1:i386 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ...
Unpacking libuchardet0:i386 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_i386.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_i386.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:i386.
Preparing to unpack .../22-libelf1_0.188-2.1_i386.deb ...
Unpacking libelf1:i386 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1_i386.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:i386.
Preparing to unpack .../24-libicu72_72.1-3_i386.deb ...
Unpacking libicu72:i386 (72.1-3) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.1+b3_i386.deb ...
Unpacking libxml2:i386 (2.9.14+dfsg-1.1+b3) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.21-12_i386.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:i386 (1.5.7-1) ...
Setting up libicu72:i386 (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:i386 (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:i386 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:i386 (0.188-2.1) ...
Setting up libxml2:i386 (2.9.14+dfsg-1.1+b3) ...
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 (2.36-8) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/lucy-1.20/ && 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 > ../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 <npatra974@gmail.com>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
dh_auto_clean
make -j16 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 -j16 "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
done!
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.
|
abi.c:24:8: warning: type defaults to 'int' in declaration of 'condition' [-Wimplicit-int]
24 | static condition[]={
| ^~~~~~~~~
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: 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?");
| ^~~~~~
poly.c: In function 'poly_at_left':
splice.c: In function 'splice_align_left':
poly.c:22:9: warning: implicit declaration of function 'abi_code' [-Wimplicit-function-declaration]
22 | if (abi_code(*seq)==T) {
| ^~~~~~~~
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]];
| ~^~~
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]]) {
| ~^~~
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)];
| ^~~~~
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]]) {
| ~^~~
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]];
| ~^~~
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)];
| ^~~~~
abi.c:226:46: warning: array subscript has type 'char' [-Wchar-subscripts]
226 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
abi.c:226:52: warning: array subscript has type 'char' [-Wchar-subscripts]
226 | l<width && r<height && 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:114:40: note: in expansion of macro 'Direc'
114 | left=Score(i-1,j)+left_penalty[Direc(i-1,j)];
| ^~~~~
abi.c:233:30: warning: array subscript has type 'char' [-Wchar-subscripts]
233 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:233:36: warning: array subscript has type 'char' [-Wchar-subscripts]
233 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
splice.c:139:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
139 | while (direc=Direc(i,j))
| ^~~~~
abi.c:245:46: warning: array subscript has type 'char' [-Wchar-subscripts]
245 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
abi.c:245:52: warning: array subscript has type 'char' [-Wchar-subscripts]
245 | l<width && r<height && 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:252:30: warning: array subscript has type 'char' [-Wchar-subscripts]
252 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
splice.c:176:18: warning: type defaults to 'int' in declaration of 'top' [-Wimplicit-int]
176 | register left, top, direc, score, i, j;
| ^~~
abi.c:252:36: warning: array subscript has type 'char' [-Wchar-subscripts]
252 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
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:266:46: warning: array subscript has type 'char' [-Wchar-subscripts]
266 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
splice.c:176:40: warning: type defaults to 'int' in declaration of 'j' [-Wimplicit-int]
176 | register left, top, direc, score, i, j;
| ^
abi.c:266:52: warning: array subscript has type 'char' [-Wchar-subscripts]
266 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
abi.c:273:30: warning: array subscript has type 'char' [-Wchar-subscripts]
273 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
splice.c:189:30: warning: array subscript has type 'char' [-Wchar-subscripts]
189 | Score(0,0)=max_score=match[*a][*b];
| ^~
splice.c:189:34: warning: array subscript has type 'char' [-Wchar-subscripts]
189 | Score(0,0)=max_score=match[*a][*b];
| ^~
abi.c:273:36: warning: array subscript has type 'char' [-Wchar-subscripts]
273 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
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];
| ^~
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:197:36: note: in expansion of macro 'Direc'
197 | left=Score(i-1,0)+left_penalty[Direc(i-1,0)];
| ^~~~~
splice.c:211:17: warning: array subscript has type 'char' [-Wchar-subscripts]
211 | score=match[*a][b[j]];
| ^~
abi.c:289:18: warning: array subscript has type 'char' [-Wchar-subscripts]
289 | if (badness[a[i]][b[j]]) {
| ~^~~
splice.c:211:22: warning: array subscript has type 'char' [-Wchar-subscripts]
211 | score=match[*a][b[j]];
| ~^~~
abi.c:289:24: warning: array subscript has type 'char' [-Wchar-subscripts]
289 | if (badness[a[i]][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:212:34: note: in expansion of macro 'Direc'
212 | top=Score(0,j-1)+top_penalty[Direc(0,j-1)];
| ^~~~~
abi.c:294:39: warning: array subscript has type 'char' [-Wchar-subscripts]
294 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:294:45: warning: array subscript has type 'char' [-Wchar-subscripts]
294 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:301:30: warning: array subscript has type 'char' [-Wchar-subscripts]
301 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
splice.c:228:23: warning: array subscript has type 'char' [-Wchar-subscripts]
228 | score+=match[a[i]][b[j]];
| ~^~~
splice.c:228:29: warning: array subscript has type 'char' [-Wchar-subscripts]
228 | score+=match[a[i]][b[j]];
| ~^~~
abi.c:301:36: warning: array subscript has type 'char' [-Wchar-subscripts]
301 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
splice.c:231:22: warning: array subscript has type 'char' [-Wchar-subscripts]
231 | score=match[a[i]][b[j]];
| ~^~~
splice.c:231:28: warning: array subscript has type 'char' [-Wchar-subscripts]
231 | score=match[a[i]][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:234:36: note: in expansion of macro 'Direc'
234 | 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:235:38: note: in expansion of macro 'Direc'
235 | left=Score(i-1,j)+left_penalty[Direc(i-1,j)];
| ^~~~~
abi.c:313:39: warning: array subscript has type 'char' [-Wchar-subscripts]
313 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
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:260:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
260 | while (direc=Direc(i,j))
| ^~~~~
splice.c:276:15: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
276 | if (j>=span && j>=width-max_i || j>height/2)
| ~~~~~~~~^~~~~~~~~~~~~~~~~
abi.c:320:30: warning: array subscript has type 'char' [-Wchar-subscripts]
320 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:320:36: warning: array subscript has type 'char' [-Wchar-subscripts]
320 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:334:39: warning: array subscript has type 'char' [-Wchar-subscripts]
334 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:334:45: warning: array subscript has type 'char' [-Wchar-subscripts]
334 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:341:30: warning: array subscript has type 'char' [-Wchar-subscripts]
341 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:341:36: warning: array subscript has type 'char' [-Wchar-subscripts]
341 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
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: 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 '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,
| ^~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~
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)
|
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 | /*
|
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 | /*
|
lucy.c:469:5: warning: implicit declaration of function 'default_windows' [-Wimplicit-function-declaration]
469 | default_windows();
| ^~~~~~~~~~~~~~~
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:
|
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;
| ^~~
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)
|
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)
|
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));
| ^~~~~~~~~~~~
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)
|
lucy.c:669:5: warning: implicit declaration of function 'prepare_abi_mask' [-Wimplicit-function-declaration]
669 | prepare_abi_mask();
| ^~~~~~~~~~~~~~~~
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
|
qual_trim.c:827:1: warning: "/*" within comment [-Wcomment]
827 | /* quality_trim().
|
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)
|
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);
| ^~~~~~~~~
qual_trim.c:837:1: warning: "/*" within comment [-Wcomment]
837 | /*
|
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],
| ^~~~~~~~~~~~
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],
| ^~~~~~~~~~~~~
abi.c: In function 'abi_code':
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;
| ^~~
lucy.c:934:5: warning: implicit declaration of function 'construct_vector_tags' [-Wimplicit-function-declaration]
934 | construct_vector_tags(vec_seq, bases);
| ^~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~
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/f4
objcopy --only-keep-debug --compress-debug-sections debian/lucy/usr/bin/lucy debian/.debhelper/lucy/dbgsym-root/usr/lib/debug/.build-id/f4/ddc1245bbadbe15b4d92e45ed9d40606068336.debug
chmod 0644 -- debian/.debhelper/lucy/dbgsym-root/usr/lib/debug/.build-id/f4/ddc1245bbadbe15b4d92e45ed9d40606068336.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/f4/ddc1245bbadbe15b4d92e45ed9d40606068336.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=f4ddc1245bbadbe15b4d92e45ed9d40606068336 -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/lucy ..
dpkg-deb --root-owner-group --build debian/.debhelper/lucy/dbgsym-root ..
dpkg-deb: building package 'lucy' in '../lucy_1.20-3_i386.deb'.
dpkg-deb: building package 'lucy-dbgsym' in '../lucy-dbgsym_1.20-3_i386.deb'.
dpkg-genbuildinfo --build=binary -O../lucy_1.20-3_i386.buildinfo
dpkg-genchanges --build=binary -O../lucy_1.20-3_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/26139 and its subdirectories
I: Current time: Sat May 18 06:37:16 -12 2024
I: pbuilder-time-stamp: 1716057436