I: pbuilder: network access will be disabled during build
I: Current time: Wed Apr 8 14:51:37 +14 2026
I: pbuilder-time-stamp: 1775609497
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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_1.20-6.dsc]
I: copying [./lucy_1.20.orig.tar.gz]
I: copying [./lucy_1.20-6.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./lucy_1.20-6.dsc: unsupported subcommand
dpkg-source: info: extracting lucy in lucy-1.20
dpkg-source: info: unpacking lucy_1.20.orig.tar.gz
dpkg-source: info: unpacking lucy_1.20-6.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
dpkg-source: info: applying declare-function-prototypes-in-header.patch
dpkg-source: info: applying fixup-manpage.patch
dpkg-source: info: applying gcc-14.patch
dpkg-source: info: applying gcc-15.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3123384/tmp/hooks/D01_modify_environment starting
debug: Running on codethink03-arm64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Apr 8 00:51 /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/3123384/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/3123384/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=arm64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DIRSTACK=()
DISTRIBUTION=trixie
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=aarch64
HOST_ARCH=arm64
IFS='
'
INVOCATION_ID=b21c2b35cb104bd58bebbf3542a69fd1
LANG=C
LANGUAGE=nl_BE:nl
LC_ALL=C
MACHTYPE=aarch64-unknown-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=3123384
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.4mbcqJ8T/pbuilderrc_ZfyG --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4mbcqJ8T/b2 --logfile b2/build.log lucy_1.20-6.dsc'
SUDO_GID=109
SUDO_UID=104
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://192.168.101.4:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/3123384/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: arm64
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 (= 13)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19914 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
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} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{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 20.1 MB of archives. After unpacking 80.2 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB]
Fetched 20.1 MB in 0s (91.1 MB/s)
Preconfiguring packages ...
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 ... 100%
(Reading database ... 19914 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:arm64.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.4-5_arm64.deb ...
Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-5_arm64.deb ...
Unpacking m4 (1.4.19-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
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%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ...
Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.5.4-3_all.deb ...
Unpacking libtool (2.5.4-3) ...
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 libfile-stripnondeterminism-perl.
Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.1-2) ...
Selecting previously unselected package libelf1t64:arm64.
Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ...
Unpacking libelf1t64:arm64 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:arm64.
Preparing to unpack .../23-libunistring5_1.3-1_arm64.deb ...
Unpacking libunistring5:arm64 (1.3-1) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../24-libicu72_72.1-6_arm64.deb ...
Unpacking libicu72:arm64 (72.1-6) ...
Selecting previously unselected package libxml2:arm64.
Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_arm64.deb ...
Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ...
Unpacking gettext (0.23.1-1) ...
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_13.24.1_all.deb ...
Unpacking debhelper (13.24.1) ...
Setting up libpipeline1:arm64 (1.5.8-1) ...
Setting up libicu72:arm64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:arm64 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:arm64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:arm64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:arm64 (0.0.8-1+b2) ...
Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/3123384/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/3123384/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/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_1.20-6_source.changes
dpkg-buildpackage: info: source package lucy
dpkg-buildpackage: info: source version 1.20-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
dh_auto_clean
make -j12 clean
make[1]: Entering directory '/build/reproducible-path/lucy-1.20'
rm -f lucy.o qual_trim.o abi.o vector.o splice.o poly.o lucy
make[1]: Leaving directory '/build/reproducible-path/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 \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j12 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/lucy-1.20'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lucy-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lucy.o lucy.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lucy-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qual_trim.o qual_trim.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lucy-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abi.o abi.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lucy-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vector.o vector.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lucy-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c -o splice.o splice.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lucy-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 | /**************************************************************************/
lucy.c: In function 'hashstring':
abi.c: In function 'abi_align':
abi.c:196:18: warning: array subscript has type 'char' [-Wchar-subscripts]
196 | if (badness[a[i]][b[j]]) {
| ~^~~
abi.c:196:24: warning: array subscript has type 'char' [-Wchar-subscripts]
196 | if (badness[a[i]][b[j]]) {
| ~^~~
abi.c:222:18: warning: array subscript has type 'char' [-Wchar-subscripts]
222 | if (badness[a[i]][b[j]]) {
| ~^~~
abi.c:222:24: warning: array subscript has type 'char' [-Wchar-subscripts]
222 | if (badness[a[i]][b[j]]) {
| ~^~~
abi.c:227:46: warning: array subscript has type 'char' [-Wchar-subscripts]
227 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
abi.c:227:52: warning: array subscript has type 'char' [-Wchar-subscripts]
227 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
abi.c:234:30: warning: array subscript has type 'char' [-Wchar-subscripts]
234 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:234:36: warning: array subscript has type 'char' [-Wchar-subscripts]
234 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:246:46: warning: array subscript has type 'char' [-Wchar-subscripts]
246 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
lucy.c:112:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
112 | if (g = value&0xF0000000) {
| ^
abi.c:246:52: warning: array subscript has type 'char' [-Wchar-subscripts]
246 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
abi.c:253:30: warning: array subscript has type 'char' [-Wchar-subscripts]
253 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:253:36: warning: array subscript has type 'char' [-Wchar-subscripts]
253 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
lucy.c: In function 'worker':
lucy.c:173:10: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
173 | int id=(int)arg;
| ^
abi.c:267:46: warning: array subscript has type 'char' [-Wchar-subscripts]
267 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
done!
abi.c:267:52: warning: array subscript has type 'char' [-Wchar-subscripts]
267 | l<width && r<height && badness[a[l]][b[r]]==0
| ~^~~
abi.c:274:30: warning: array subscript has type 'char' [-Wchar-subscripts]
274 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:274:36: warning: array subscript has type 'char' [-Wchar-subscripts]
274 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:290:18: warning: array subscript has type 'char' [-Wchar-subscripts]
290 | if (badness[a[i]][b[j]]) {
| ~^~~
abi.c:290:24: warning: array subscript has type 'char' [-Wchar-subscripts]
290 | if (badness[a[i]][b[j]]) {
| ~^~~
abi.c:295:39: warning: array subscript has type 'char' [-Wchar-subscripts]
295 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:295:45: warning: array subscript has type 'char' [-Wchar-subscripts]
295 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:302:30: warning: array subscript has type 'char' [-Wchar-subscripts]
302 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:302:36: warning: array subscript has type 'char' [-Wchar-subscripts]
302 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:314:39: warning: array subscript has type 'char' [-Wchar-subscripts]
314 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:314:45: warning: array subscript has type 'char' [-Wchar-subscripts]
314 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:321:30: warning: array subscript has type 'char' [-Wchar-subscripts]
321 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:321:36: warning: array subscript has type 'char' [-Wchar-subscripts]
321 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:335:39: warning: array subscript has type 'char' [-Wchar-subscripts]
335 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:335:45: warning: array subscript has type 'char' [-Wchar-subscripts]
335 | l>=0 && r>=0 && badness[a[l]][b[r]]==0
| ~^~~
abi.c:342:30: warning: array subscript has type 'char' [-Wchar-subscripts]
342 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
abi.c:342:36: warning: array subscript has type 'char' [-Wchar-subscripts]
342 | if ((count+=badness[a[l]][b[r]])<VERYBAD) {
| ~^~~
splice.c: In function 'splice_align_left':
lucy.c: In function 'main':
lucy.c:532:51: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
532 | if (pthread_create(&threads[i], NULL, worker, (void*)i))
| ^
splice.c:69:32: warning: array subscript has type 'char' [-Wchar-subscripts]
69 | Score(0,0)=max_score=match[*a][*b];
| ^~
splice.c:69:36: warning: array subscript has type 'char' [-Wchar-subscripts]
69 | Score(0,0)=max_score=match[*a][*b];
| ^~
splice.c:76:20: warning: array subscript has type 'char' [-Wchar-subscripts]
76 | score=match[a[i]][*b];
| ~^~~
splice.c:76:25: warning: array subscript has type 'char' [-Wchar-subscripts]
76 | score=match[a[i]][*b];
| ^~
splice.c:17:38: warning: array subscript has type 'char' [-Wchar-subscripts]
17 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
splice.c:77:38: note: in expansion of macro 'Direc'
77 | left=Score(i-1,0)+left_penalty[Direc(i-1,0)];
| ^~~~~
splice.c:91:19: warning: array subscript has type 'char' [-Wchar-subscripts]
91 | score=match[*a][b[j]];
| ^~
splice.c:91:24: warning: array subscript has type 'char' [-Wchar-subscripts]
91 | score=match[*a][b[j]];
| ~^~~
splice.c:17:38: warning: array subscript has type 'char' [-Wchar-subscripts]
17 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
splice.c:92:36: note: in expansion of macro 'Direc'
92 | top=Score(0,j-1)+top_penalty[Direc(0,j-1)];
| ^~~~~
splice.c:108:25: warning: array subscript has type 'char' [-Wchar-subscripts]
108 | score+=match[a[i]][b[j]];
| ~^~~
lucy.c:793:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
793 | (i=(int)fgets(buf, BUFFER_LENGTH, spl_file)) && buf[0]!='>'; ) {
| ^
vector.c: In function 'construct_vector_tags':
vector.c:86:34: warning: array subscript has type 'char' [-Wchar-subscripts]
86 | accr|=tag_code(rev_code[seq[len-k%len-1]]);
| ~~~^~~~~~~~~~~~~
splice.c:108:31: warning: array subscript has type 'char' [-Wchar-subscripts]
108 | score+=match[a[i]][b[j]];
| ~^~~
splice.c:111:24: warning: array subscript has type 'char' [-Wchar-subscripts]
111 | score=match[a[i]][b[j]];
| ~^~~
splice.c:111:30: warning: array subscript has type 'char' [-Wchar-subscripts]
111 | score=match[a[i]][b[j]];
| ~^~~
splice.c:17:38: warning: array subscript has type 'char' [-Wchar-subscripts]
17 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
splice.c:114:38: note: in expansion of macro 'Direc'
114 | top=Score(i,j-1)+top_penalty[Direc(i,j-1)];
| ^~~~~
splice.c:17:38: warning: array subscript has type 'char' [-Wchar-subscripts]
17 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
splice.c:115:40: note: in expansion of macro 'Direc'
115 | left=Score(i-1,j)+left_penalty[Direc(i-1,j)];
| ^~~~~
splice.c:140:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
140 | while (direc=Direc(i,j))
| ^~~~~
splice.c: In function 'splice_align_right':
splice.c:190:30: warning: array subscript has type 'char' [-Wchar-subscripts]
190 | Score(0,0)=max_score=match[*a][*b];
| ^~
splice.c:190:34: warning: array subscript has type 'char' [-Wchar-subscripts]
190 | Score(0,0)=max_score=match[*a][*b];
| ^~
splice.c:197:18: warning: array subscript has type 'char' [-Wchar-subscripts]
197 | score=match[a[i]][*b];
| ~^~~
splice.c:197:23: warning: array subscript has type 'char' [-Wchar-subscripts]
197 | score=match[a[i]][*b];
| ^~
splice.c:17:38: warning: array subscript has type 'char' [-Wchar-subscripts]
17 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
splice.c:198:36: note: in expansion of macro 'Direc'
198 | left=Score(i-1,0)+left_penalty[Direc(i-1,0)];
| ^~~~~
splice.c:212:17: warning: array subscript has type 'char' [-Wchar-subscripts]
212 | score=match[*a][b[j]];
| ^~
splice.c:212:22: warning: array subscript has type 'char' [-Wchar-subscripts]
212 | score=match[*a][b[j]];
| ~^~~
splice.c:17:38: warning: array subscript has type 'char' [-Wchar-subscripts]
17 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
splice.c:213:34: note: in expansion of macro 'Direc'
213 | top=Score(0,j-1)+top_penalty[Direc(0,j-1)];
| ^~~~~
splice.c:229:23: warning: array subscript has type 'char' [-Wchar-subscripts]
229 | score+=match[a[i]][b[j]];
| ~^~~
splice.c:229:29: warning: array subscript has type 'char' [-Wchar-subscripts]
229 | score+=match[a[i]][b[j]];
| ~^~~
splice.c:232:22: warning: array subscript has type 'char' [-Wchar-subscripts]
232 | score=match[a[i]][b[j]];
| ~^~~
splice.c:232:28: warning: array subscript has type 'char' [-Wchar-subscripts]
232 | score=match[a[i]][b[j]];
| ~^~~
splice.c:17:38: warning: array subscript has type 'char' [-Wchar-subscripts]
17 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
splice.c:235:36: note: in expansion of macro 'Direc'
235 | top=Score(i,j-1)+top_penalty[Direc(i,j-1)];
| ^~~~~
splice.c:17:38: warning: array subscript has type 'char' [-Wchar-subscripts]
17 | #define Direc(x, y) splice_direc_base[(y)*width+(x)]
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
splice.c:236:38: note: in expansion of macro 'Direc'
236 | left=Score(i-1,j)+left_penalty[Direc(i-1,j)];
| ^~~~~
splice.c:261:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
261 | while (direc=Direc(i,j))
| ^~~~~
splice.c:277:15: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
277 | if (j>=span && j>=width-max_i || j>height/2)
| ~~~~~~~~^~~~~~~~~~~~~~~~~
lucy.c:632:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
632 | fgets(buf, BUFFER_LENGTH, qul_file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vector.c: In function 'tag_code':
vector.c:45:10: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized]
45 | return tmp;
| ^~~
vector.c:23:16: note: 'tmp' was declared here
23 | register int tmp;
| ^~~
qual_trim.c:215:1: warning: "/*" within comment [-Wcomment]
215 | /* Determines some number of candidate clean ranges using a particular
qual_trim.c:216:1: warning: "/*" within comment [-Wcomment]
216 | /* window size.
qual_trim.c:217:1: warning: "/*" within comment [-Wcomment]
217 | /*
qual_trim.c:218:1: warning: "/*" within comment [-Wcomment]
218 | /* Globals used:
qual_trim.c:219:1: warning: "/*" within comment [-Wcomment]
219 | /* double end_limit, (maximum allowed probability of error for bases)
qual_trim.c:220:1: warning: "/*" within comment [-Wcomment]
220 | /* ( at each end of clean range)
qual_trim.c:221:1: warning: "/*" within comment [-Wcomment]
221 | /*
qual_trim.c:333:1: warning: "/*" within comment [-Wcomment]
333 | /* Finds the largest subsequence of a sequence whose average probability
qual_trim.c:334:1: warning: "/*" within comment [-Wcomment]
334 | /* of error does not exceed a specified maximum.
qual_trim.c:335:1: warning: "/*" within comment [-Wcomment]
335 | /*
qual_trim.c:336:1: warning: "/*" within comment [-Wcomment]
336 | /* Globals used:
qual_trim.c:337:1: warning: "/*" within comment [-Wcomment]
337 | /* double max_avg_error, (maximum allowed average probability of error)
qual_trim.c:338:1: warning: "/*" within comment [-Wcomment]
338 | /* double end_limit, (maximum allowed probability of error for bases)
qual_trim.c:339:1: warning: "/*" within comment [-Wcomment]
339 | /* ( at each end of clean range)
qual_trim.c:340:1: warning: "/*" within comment [-Wcomment]
340 | /*
qual_trim.c:435:1: warning: "/*" within comment [-Wcomment]
435 | /* Determines a single clean range, after recursively considering all of
qual_trim.c:436:1: warning: "/*" within comment [-Wcomment]
436 | /* the specified window sizes. Calls average_error_trim to trim the
qual_trim.c:437:1: warning: "/*" within comment [-Wcomment]
437 | /* results of the final window based on overall average probability of
qual_trim.c:438:1: warning: "/*" within comment [-Wcomment]
438 | /* error.
qual_trim.c:439:1: warning: "/*" within comment [-Wcomment]
439 | /*
qual_trim.c:440:1: warning: "/*" within comment [-Wcomment]
440 | /* Globals used:
qual_trim.c:441:1: warning: "/*" within comment [-Wcomment]
441 | /* double max_avg_error, (maximum allowed average probability of error)
qual_trim.c:442:1: warning: "/*" within comment [-Wcomment]
442 | /* double end_limit, (maximum allowed probability of error for bases)
qual_trim.c:443:1: warning: "/*" within comment [-Wcomment]
443 | /* ( at each end of clean range)
qual_trim.c:444:1: warning: "/*" within comment [-Wcomment]
444 | /*
qual_trim.c:570:1: warning: "/*" within comment [-Wcomment]
570 | /* Sets the window size and average probability of error allowed for the
qual_trim.c:571:1: warning: "/*" within comment [-Wcomment]
571 | /* terminal windows that "bracket" the candidate clean range.
qual_trim.c:572:1: warning: "/*" within comment [-Wcomment]
572 | /*
qual_trim.c:573:1: warning: "/*" within comment [-Wcomment]
573 | /* Globals used:
qual_trim.c:574:1: warning: "/*" within comment [-Wcomment]
574 | /* int bracket_window, (size of terminal window)
qual_trim.c:575:1: warning: "/*" within comment [-Wcomment]
575 | /* double bracket_error (allowable average prob. error in window)
qual_trim.c:576:1: warning: "/*" within comment [-Wcomment]
576 | /*
qual_trim.c:588:1: warning: "/*" within comment [-Wcomment]
588 | /* Finds the leftmost window, and the rightmost window, which meet the
qual_trim.c:589:1: warning: "/*" within comment [-Wcomment]
589 | /* specified error criterion. The purpose of this function is to bracket
qual_trim.c:590:1: warning: "/*" within comment [-Wcomment]
590 | /* the portion of the sequence that is of decent quality -- i.e. to
qual_trim.c:591:1: warning: "/*" within comment [-Wcomment]
591 | /* eliminate the really bad quality stuff that is often found on either
qual_trim.c:592:1: warning: "/*" within comment [-Wcomment]
592 | /* end. The beginning of the first matching window, and the end of the
qual_trim.c:593:1: warning: "/*" within comment [-Wcomment]
593 | /* last, bracket the sequence range that will be looked at to find the
qual_trim.c:594:1: warning: "/*" within comment [-Wcomment]
594 | /* final clean range.
qual_trim.c:595:1: warning: "/*" within comment [-Wcomment]
595 | /*
qual_trim.c:596:1: warning: "/*" within comment [-Wcomment]
596 | /* This function is called before the multi_window_trim function, and
qual_trim.c:597:1: warning: "/*" within comment [-Wcomment]
597 | /* its results are used to limit the range of sequence that will be
qual_trim.c:598:1: warning: "/*" within comment [-Wcomment]
598 | /* considered by that function.
qual_trim.c:599:1: warning: "/*" within comment [-Wcomment]
599 | /*
abi.c: In function 'abi_code':
qual_trim.c:679:1: warning: "/*" within comment [-Wcomment]
679 | /* Determines the clean range. Calls multi_window_trim, which calls both
qual_trim.c:680:1: warning: "/*" within comment [-Wcomment]
680 | /* window_trim and average_error_trim.
qual_trim.c:681:1: warning: "/*" within comment [-Wcomment]
681 | /*
qual_trim.c:682:1: warning: "/*" within comment [-Wcomment]
682 | /* Globals used:
qual_trim.c:683:1: warning: "/*" within comment [-Wcomment]
683 | /* int num_windows, (number of windows)
qual_trim.c:684:1: warning: "/*" within comment [-Wcomment]
684 | /* int *windows, (array of window sizes (largest to smallest))
abi.c:85:10: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized]
85 | return tmp;
| ^~~
qual_trim.c:685:1: warning: "/*" within comment [-Wcomment]
685 | /* double *err_limits, (array of maximum allowed average probability)
abi.c:63:16: note: 'tmp' was declared here
63 | register int tmp;
| ^~~
qual_trim.c:686:1: warning: "/*" within comment [-Wcomment]
686 | /* ( for each window size)
qual_trim.c:687:1: warning: "/*" within comment [-Wcomment]
687 | /* double max_avg_error, (maximum allowed average probability of error)
qual_trim.c:688:1: warning: "/*" within comment [-Wcomment]
688 | /* double end_limit, (maximum allowed probability of error for bases)
qual_trim.c:689:1: warning: "/*" within comment [-Wcomment]
689 | /* ( at each end of clean range)
qual_trim.c:690:1: warning: "/*" within comment [-Wcomment]
690 | /* int bracket_window, (size of terminal window)
qual_trim.c:691:1: warning: "/*" within comment [-Wcomment]
691 | /* double bracket_error (allowable average prob. error in window)
qual_trim.c:692:1: warning: "/*" within comment [-Wcomment]
692 | /*
qual_trim.c: In function 'quality_trim':
qual_trim.c:706:21: warning: unused variable 'sum' [-Wunused-variable]
706 | double err, sum;
| ^~~
qual_trim.c:706:16: warning: unused variable 'err' [-Wunused-variable]
706 | double err, sum;
| ^~~
qual_trim.c: At top level:
qual_trim.c:793:1: warning: "/*" within comment [-Wcomment]
793 | /* Sets up 3 windows for quality trimming, with the average error allowed
qual_trim.c:794:1: warning: "/*" within comment [-Wcomment]
794 | /* in each window calculated from max_avg_error.
qual_trim.c:795:1: warning: "/*" within comment [-Wcomment]
795 | /*
qual_trim.c:796:1: warning: "/*" within comment [-Wcomment]
796 | /* Globals used:
qual_trim.c:797:1: warning: "/*" within comment [-Wcomment]
797 | /* int num_windows, (number of windows)
qual_trim.c:798:1: warning: "/*" within comment [-Wcomment]
798 | /* int *windows, (array of window sizes (largest to smallest))
qual_trim.c:799:1: warning: "/*" within comment [-Wcomment]
799 | /* double *err_limits, (array of maximum allowed average probability)
qual_trim.c:800:1: warning: "/*" within comment [-Wcomment]
800 | /* (for each window size)
qual_trim.c:801:1: warning: "/*" within comment [-Wcomment]
801 | /* double max_avg_error, (maximum allowed average probability of error)
qual_trim.c:802:1: warning: "/*" within comment [-Wcomment]
802 | /*
qual_trim.c:827:1: warning: "/*" within comment [-Wcomment]
827 | /* Simulates the functionality of the old grim() function, by calling
qual_trim.c:828:1: warning: "/*" within comment [-Wcomment]
828 | /* quality_trim().
qual_trim.c:829:1: warning: "/*" within comment [-Wcomment]
829 | /*
qual_trim.c:830:1: warning: "/*" within comment [-Wcomment]
830 | /* Globals used:
qual_trim.c:831:1: warning: "/*" within comment [-Wcomment]
831 | /* int num_windows, (number of windows)
qual_trim.c:832:1: warning: "/*" within comment [-Wcomment]
832 | /* int *windows, (array of window sizes (largest to smallest))
qual_trim.c:833:1: warning: "/*" within comment [-Wcomment]
833 | /* double *err_limits, (array of maximum allowed average probability)
qual_trim.c:834:1: warning: "/*" within comment [-Wcomment]
834 | /* (for each window size)
qual_trim.c:835:1: warning: "/*" within comment [-Wcomment]
835 | /* double max_avg_error, (maximum allowed average probability of error)
qual_trim.c:836:1: warning: "/*" within comment [-Wcomment]
836 | /* double end_limit, (maximum allowed probability of error for bases)
qual_trim.c:837:1: warning: "/*" within comment [-Wcomment]
837 | /* ( at each end of clean range)
qual_trim.c:838:1: warning: "/*" within comment [-Wcomment]
838 | /*
rm -f lucy
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lucy-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/lucy-1.20'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-r5__Gnix
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/reproducible-path/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
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
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/reproducible-path/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 -a
dwz -- debian/lucy/usr/bin/lucy
dh_strip -a
install -m0755 -d debian/.debhelper/lucy/dbgsym-root/usr/lib/debug/.build-id/1e
objcopy --only-keep-debug --compress-debug-sections debian/lucy/usr/bin/lucy debian/.debhelper/lucy/dbgsym-root/usr/lib/debug/.build-id/1e/d7f5c05f09474e0b3e8b480b2690e3e95cb8ab.debug
chmod 0644 -- debian/.debhelper/lucy/dbgsym-root/usr/lib/debug/.build-id/1e/d7f5c05f09474e0b3e8b480b2690e3e95cb8ab.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/1e/d7f5c05f09474e0b3e8b480b2690e3e95cb8ab.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 -a
rm -f debian/lucy/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/lucy/DEBIAN
dpkg-shlibdeps -Tdebian/lucy.substvars debian/lucy/usr/bin/lucy
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
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 -cdebian/control -Pdebian/.debhelper/lucy/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=lucy-dbgsym "-DDepends=lucy (= \${binary:Version})" "-DDescription=debug symbols for lucy" -DBuild-Ids=1ed7f5c05f09474e0b3e8b480b2690e3e95cb8ab -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/lucy/dbgsym-root/DEBIAN/control
dpkg-gencontrol -plucy -ldebian/changelog -Tdebian/lucy.substvars -cdebian/control -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_1.20-6_arm64.deb'.
dpkg-deb: building package 'lucy-dbgsym' in '../lucy-dbgsym_1.20-6_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../lucy_1.20-6_arm64.buildinfo
dpkg-genchanges --build=binary -O../lucy_1.20-6_arm64.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/3123384/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/3123384/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/3123384 and its subdirectories
I: Current time: Wed Apr 8 14:52:27 +14 2026
I: pbuilder-time-stamp: 1775609547