Sun Jan 26 20:13:46 UTC 2025 I: starting to build daligner/trixie/i386 on jenkins on '2025-01-26 20:13'
Sun Jan 26 20:13:46 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_11/43222/console.log
Sun Jan 26 20:13:46 UTC 2025 I: Downloading source for trixie/daligner=1.0+git20240119.335105d-3
--2025-01-26 20:13:46-- http://deb.debian.org/debian/pool/main/d/daligner/daligner_1.0%2bgit20240119.335105d-3.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2287 (2.2K) [text/prs.lines.tag]
Saving to: ‘daligner_1.0+git20240119.335105d-3.dsc’
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2025-01-26 20:13:46 (294 MB/s) - ‘daligner_1.0+git20240119.335105d-3.dsc’ saved [2287/2287]
Sun Jan 26 20:13:46 UTC 2025 I: daligner_1.0+git20240119.335105d-3.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: daligner
Binary: daligner
Architecture: any
Version: 1.0+git20240119.335105d-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://dazzlerblog.wordpress.com
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/daligner
Vcs-Git: https://salsa.debian.org/med-team/daligner.git
Testsuite: autopkgtest
Testsuite-Triggers: dazzdb
Build-Depends: debhelper-compat (= 13)
Package-List:
daligner deb science optional arch=any
Checksums-Sha1:
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Files:
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4ceab3dd0c1fe15c0124ebbcaead4e0e 6660 daligner_1.0+git20240119.335105d-3.debian.tar.xz
Dgit: e54816c7eec1edc38760e9b623bcf67634916e8b debian archive/debian/1.0+git20240119.335105d-3 https://git.dgit.debian.org/daligner
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Sun Jan 26 20:13:46 UTC 2025 I: Checking whether the package is not for us
Sun Jan 26 20:13:46 UTC 2025 I: Starting 1st build on remote node ionos6-i386.debian.net.
Sun Jan 26 20:13:46 UTC 2025 I: Preparing to do remote build '1' on ionos6-i386.debian.net.
Sun Jan 26 20:15:55 UTC 2025 I: Deleting $TMPDIR on ionos6-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Feb 28 14:36:51 -12 2026
I: pbuilder-time-stamp: 1772332611
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: using eatmydata during job
I: Copying source file
I: copying [daligner_1.0+git20240119.335105d-3.dsc]
I: copying [./daligner_1.0+git20240119.335105d.orig.tar.xz]
I: copying [./daligner_1.0+git20240119.335105d-3.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./daligner_1.0+git20240119.335105d-3.dsc: unsupported subcommand
dpkg-source: info: extracting daligner in daligner-1.0+git20240119.335105d
dpkg-source: info: unpacking daligner_1.0+git20240119.335105d.orig.tar.xz
dpkg-source: info: unpacking daligner_1.0+git20240119.335105d-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying cflags.patch
dpkg-source: info: applying lddflags.patch
dpkg-source: info: applying destdir-install.patch
dpkg-source: info: applying cross.patch
dpkg-source: info: applying cppflags.patch
dpkg-source: info: applying fix-missing-include.patch
dpkg-source: info: applying gcc-14.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/56645/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='a2c8563043c54623867a75f9503b8005'
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='56645'
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.s4nq91O8/pbuilderrc_TKH2 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.s4nq91O8/b1 --logfile b1/build.log daligner_1.0+git20240119.335105d-3.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos6-i386 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/56645/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 (= 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 ... 19842 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 20.6 MB of archives. After unpacking 77.9 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-4 [201 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-1 [96.1 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-4 [723 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.23 [90.6 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-2 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-1 [8584 B]
Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-4 [1632 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.23 [919 kB]
Fetched 20.6 MB in 1s (17.8 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 19842 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
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Unpacking libmagic-mgc (1:5.45-3+b1) ...
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Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
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Unpacking gettext-base (0.22.5-4) ...
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Preparing to unpack .../06-groff-base_1.23.0-7_i386.deb ...
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Setting up m4 (1.4.19-5) ...
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Setting up libelf1t64:i386 (0.192-4) ...
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Setting up autopoint (0.22.5-4) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
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 (1.14.1-1) ...
Setting up gettext (0.22.5-4) ...
Setting up libtool (2.5.4-2) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-1) ...
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 (13.23) ...
Processing triggers for libc-bin (2.40-5) ...
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/reproducible-path/daligner-1.0+git20240119.335105d/ && 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 > ../daligner_1.0+git20240119.335105d-3_source.changes
dpkg-buildpackage: info: source package daligner
dpkg-buildpackage: info: source version 1.0+git20240119.335105d-3
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 i386
debian/rules clean
dh clean
dh_auto_clean
make -j22 clean
make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d'
rm -f daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA
rm -fr *.dSYM
rm -f daligner.tar.gz
make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j22 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm -Wl,-z,relro -Wl,-z,now
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o HPC.daligner HPC.daligner.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAsort LAsort.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAmerge LAmerge.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAsplit LAsplit.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAcat LAcat.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAshow LAshow.c align.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm -Wl,-z,relro -Wl,-z,now
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAcheck LAcheck.c align.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm -Wl,-z,relro -Wl,-z,now
ONE2LA.c: In function 'main':
ONE2LA.c:30:20: warning: variable 'small' set but not used [-Wunused-but-set-variable]
30 | int tspace, small, tbytes;
| ^~~~~
LAshow.c: In function 'main':
LAshow.c:415:36: warning: variable 'lhalf' set but not used [-Wunused-but-set-variable]
415 | int blast, match, seen, lhalf, rhalf;
| ^~~~~
LAshow.c:415:30: warning: variable 'seen' set but not used [-Wunused-but-set-variable]
415 | int blast, match, seen, lhalf, rhalf;
| ^~~~
LAshow.c:415:23: warning: variable 'match' set but not used [-Wunused-but-set-variable]
415 | int blast, match, seen, lhalf, rhalf;
| ^~~~~
LAshow.c:415:16: warning: variable 'blast' set but not used [-Wunused-but-set-variable]
415 | int blast, match, seen, lhalf, rhalf;
| ^~~~~
LAshow.c:743:5: warning: 'bmap' may be used uninitialized [-Wmaybe-uninitialized]
743 | free(bmap);
| ^~~~~~~~~~
LAshow.c:55:11: note: 'bmap' was declared here
55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax;
| ^~~~
LAshow.c:549:25: warning: 'blen' may be used uninitialized [-Wmaybe-uninitialized]
549 | blens = blen[bread];
| ^
LAshow.c:55:18: note: 'blen' was declared here
55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax;
| ^~~~
LAshow.c:588:40: warning: 'bctg' may be used uninitialized [-Wmaybe-uninitialized]
588 | printf(".%0*d",bc_wide,bctg[bread]+1);
| ^
LAshow.c:55:25: note: 'bctg' was declared here
55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax;
| ^~~~
LAshow.c:448:19: warning: 'nbscaff' may be used uninitialized [-Wmaybe-uninitialized]
448 | { br_wide = Number_Digits((int64) nbscaff);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LAshow.c:55:31: note: 'nbscaff' was declared here
55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax;
| ^~~~~~~
LAshow.c:449:19: warning: 'bmaxlen' may be used uninitialized [-Wmaybe-uninitialized]
449 | bi_wide = Number_Digits((int64) bmaxlen);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LAshow.c:55:40: note: 'bmaxlen' was declared here
55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax;
| ^~~~~~~
LAshow.c:450:19: warning: 'bctgmax' may be used uninitialized [-Wmaybe-uninitialized]
450 | bc_wide = Number_Digits((int64) bctgmax);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LAshow.c:55:49: note: 'bctgmax' was declared here
55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax;
| ^~~~~~~
LAshow.c:744:3: warning: 'amap' may be used uninitialized [-Wmaybe-uninitialized]
744 | free(amap);
| ^~~~~~~~~~
LAshow.c:54:11: note: 'amap' was declared here
54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax;
| ^~~~
LAshow.c:541:25: warning: 'alen' may be used uninitialized [-Wmaybe-uninitialized]
541 | alens = alen[aread];
| ^
LAshow.c:54:18: note: 'alen' was declared here
54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax;
| ^~~~
LAshow.c:581:40: warning: 'actg' may be used uninitialized [-Wmaybe-uninitialized]
581 | printf(".%0*d",ac_wide,actg[aread]+1);
| ^
LAshow.c:54:25: note: 'actg' was declared here
54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax;
| ^~~~
LAshow.c:439:19: warning: 'nascaff' may be used uninitialized [-Wmaybe-uninitialized]
439 | { ar_wide = Number_Digits((int64) nascaff);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LAshow.c:54:31: note: 'nascaff' was declared here
54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax;
| ^~~~~~~
LAshow.c:440:19: warning: 'amaxlen' may be used uninitialized [-Wmaybe-uninitialized]
440 | ai_wide = Number_Digits((int64) amaxlen);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LAshow.c:54:40: note: 'amaxlen' was declared here
54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax;
| ^~~~~~~
LAshow.c:441:19: warning: 'actgmax' may be used uninitialized [-Wmaybe-uninitialized]
441 | ac_wide = Number_Digits((int64) actgmax);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LAshow.c:54:49: note: 'actgmax' was declared here
54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax;
| ^~~~~~~
filter.c: In function 'MapToTPAbove':
filter.c:1130:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1130 | { uint16 *trace = tbuf->trace + (uint64) path->trace;
| ^
filter.c: In function 'MapToTPBelow':
filter.c:1164:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1164 | { uint16 *trace = tbuf->trace + (uint64) path->trace;
| ^
filter.c: In function 'Check_Bridge':
filter.c:1198:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1198 | { uint16 *trace = tbuf->trace + (uint64) path->trace;
| ^
filter.c: In function 'Compute_Bridge_Path':
filter.c:1336:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
1336 | apath->trace = (void *) (tbuf->top);
| ^
filter.c: In function 'Entwine':
filter.c:1349:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1349 | uint16 *ktrace = tbuf->trace + (uint64) (kpath->trace);
| ^
filter.c:1350:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1350 | uint16 *jtrace = tbuf->trace + (uint64) (jpath->trace);
| ^
filter.c: In function 'Fusion':
filter.c:1475:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1475 | { uint16 *t = tbuf->trace + (uint64) (path1->trace);
| ^
filter.c:1483:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1483 | { uint16 *t = tbuf->trace + (uint64) (path2->trace);
| ^
filter.c: In function 'Bridge':
filter.c:1528:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1528 | { uint16 *t = tbuf->trace + (uint64) (path1->trace);
| ^
filter.c:1536:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1536 | { uint16 *t = tbuf->trace + (uint64) (path2->trace);
| ^
filter.c:1544:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
1544 | { uint16 *t = tbuf->trace + (uint64) (path3->trace);
| ^
filter.c: In function 'report_thread':
filter.c:2112:46: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2112 | amatch[novl].trace = (void *) (tbuf->top);
| ^
filter.c:2117:46: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
2117 | bmatch[novl].trace = (void *) (tbuf->top);
| ^
filter.c:2155:23: warning: suggest braces around empty body in an 'else' statement [-Wempty-body]
2155 | ;
| ^
filter.c:2202:53: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
2202 | ovla->path.trace = tbuf->trace + (uint64) (ovla->path.trace);
| ^
filter.c:2215:53: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
2215 | ovlb->path.trace = tbuf->trace + (uint64) (ovlb->path.trace);
| ^
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
ONElib.c: In function 'oneSchemaCreateDynamic':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:392:3: note: in expansion of macro 'assert'
392 | assert (fileType && strlen(fileType) > 0) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:393:3: note: in expansion of macro 'assert'
393 | assert (!subType || strlen(subType) > 0) ;
| ^~~~~~
ONElib.c:395:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ;
| ~~^ ~~~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
ONElib.c:395:35: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ;
| ~~^ ~~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
ONElib.c:397:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
397 | sprintf (text, "P %ld %s\n", strlen(fileType), fileType) ;
| ~~^ ~~~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
ONElib.c: In function 'oneReadLine':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:945:3: note: in expansion of macro 'assert'
945 | assert (!vf->isWrite) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:946:3: note: in expansion of macro 'assert'
946 | assert (!vf->isFinal) ;
| ^~~~~~
ONElib.c: In function 'oneFileOpenRead':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1158:3: note: in expansion of macro 'assert'
1158 | assert (fileType == NULL || strlen(fileType) > 0) ;
| ^~~~~~
ONElib.c: In function 'addProvenance':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1760:3: note: in expansion of macro 'assert'
1760 | assert (!vf->isHeaderOut) ;
| ^~~~~~
ONElib.c: In function 'addReference':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1811:3: note: in expansion of macro 'assert'
1811 | assert (!vf->isHeaderOut) ;
| ^~~~~~
ONElib.c: In function 'writeHeader':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1885:3: note: in expansion of macro 'assert'
1885 | assert (vf->isWrite) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1886:3: note: in expansion of macro 'assert'
1886 | assert (vf->line == 0) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1887:3: note: in expansion of macro 'assert'
1887 | assert (vf->share >= 0) ;
| ^~~~~~
ONElib.c:1891:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1891 | fprintf (vf->f, "1 %lu %s %d %d", strlen(vf->fileType), vf->fileType, MAJOR, MINOR);
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| | size_t {aka unsigned int}
| long unsigned int
| %u
ONElib.c:1894:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1894 | { fprintf (vf->f, "\n2 %lu %s", strlen(vf->subType), vf->subType);
| ~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| | size_t {aka unsigned int}
| long unsigned int
| %u
ONElib.c:1903:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1903 | { fprintf (vf->f, "\n! 4 %lu %s %lu %s %lu %s %lu %s",
| ~~^
| |
| long unsigned int
| %u
1904 | strlen(p->program), p->program, strlen(p->version), p->version,
| ~~~~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
ONElib.c:1903:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1903 | { fprintf (vf->f, "\n! 4 %lu %s %lu %s %lu %s %lu %s",
| ~~^
| |
| long unsigned int
| %u
1904 | strlen(p->program), p->program, strlen(p->version), p->version,
| ~~~~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
ONElib.c:1903:50: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1903 | { fprintf (vf->f, "\n! 4 %lu %s %lu %s %lu %s %lu %s",
| ~~^
| |
| long unsigned int
| %u
1904 | strlen(p->program), p->program, strlen(p->version), p->version,
1905 | strlen(p->command), p->command, strlen(p->date), p->date);
| ~~~~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
ONElib.c:1903:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1903 | { fprintf (vf->f, "\n! 4 %lu %s %lu %s %lu %s %lu %s",
| ~~^
| |
| long unsigned int
| %u
1904 | strlen(p->program), p->program, strlen(p->version), p->version,
1905 | strlen(p->command), p->command, strlen(p->date), p->date);
| ~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
ONElib.c:1917:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1917 | { fprintf (vf->f, "\n< %lu %s %" PRId64 "", strlen(r->filename), r->filename, r->count);
| ~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
ONElib.c:1924:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1924 | { fprintf (vf->f, "\n> %lu %s", strlen(r->filename), r->filename);
| ~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| | size_t {aka unsigned int}
| long unsigned int
| %u
ONElib.c: In function 'oneWriteLine':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2029:3: note: in expansion of macro 'assert'
2029 | assert (vf->isWrite) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2030:3: note: in expansion of macro 'assert'
2030 | assert (!vf->isFinal || !isalpha(t)) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2033:3: note: in expansion of macro 'assert'
2033 | assert (li) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2040:7: note: in expansion of macro 'assert'
2040 | { assert (listLen >= 0) ;
| ^~~~~~
ONElib.c: In function 'oneFileClose':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2488:3: note: in expansion of macro 'assert'
2488 | assert (vf->share >= 0) ;
| ^~~~~~
ONElib.c: In function 'intGet':
ONElib.c:3490:17: warning: this statement may fall through [-Wimplicit-fallthrough=]
3490 | case 0: die ("int packing error") ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
ONElib.c:3491:9: note: here
3491 | case 1: *pval = *(I64*)(u+1) & 0x0000000000ffff ; return 3 ;
| ^~~~
ONElib.c:3502:17: warning: this statement may fall through [-Wimplicit-fallthrough=]
3502 | case 0: die ("int packing error") ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
ONElib.c:3503:9: note: here
3503 | case 1: *pval = *(I64*)(u+1) | 0xffffffffffff0000 ; return 3 ;
| ^~~~
ONElib.c:3488:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
3488 | switch (u[0] & 0x07)
| ^~~~~~
ONElib.c:3499:5: note: here
3499 | case 4:
| ^~~~
ONElib.c: In function 'oneSchemaCreateDynamic':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:392:3: note: in expansion of macro 'assert'
392 | assert (fileType && strlen(fileType) > 0) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:393:3: note: in expansion of macro 'assert'
393 | assert (!subType || strlen(subType) > 0) ;
| ^~~~~~
ONElib.c:395:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ;
| ~~^ ~~~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
ONElib.c:395:35: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ;
| ~~^ ~~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
ONElib.c:397:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
397 | sprintf (text, "P %ld %s\n", strlen(fileType), fileType) ;
| ~~^ ~~~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
ONElib.c: In function 'oneReadLine':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:945:3: note: in expansion of macro 'assert'
945 | assert (!vf->isWrite) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:946:3: note: in expansion of macro 'assert'
946 | assert (!vf->isFinal) ;
| ^~~~~~
ONElib.c: In function 'oneFileOpenRead':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1158:3: note: in expansion of macro 'assert'
1158 | assert (fileType == NULL || strlen(fileType) > 0) ;
| ^~~~~~
ONElib.c: In function 'addProvenance':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1760:3: note: in expansion of macro 'assert'
1760 | assert (!vf->isHeaderOut) ;
| ^~~~~~
ONElib.c: In function 'addReference':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1811:3: note: in expansion of macro 'assert'
1811 | assert (!vf->isHeaderOut) ;
| ^~~~~~
ONElib.c: In function 'writeHeader':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1885:3: note: in expansion of macro 'assert'
1885 | assert (vf->isWrite) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1886:3: note: in expansion of macro 'assert'
1886 | assert (vf->line == 0) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:1887:3: note: in expansion of macro 'assert'
1887 | assert (vf->share >= 0) ;
| ^~~~~~
ONElib.c:1891:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1891 | fprintf (vf->f, "1 %lu %s %d %d", strlen(vf->fileType), vf->fileType, MAJOR, MINOR);
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| | size_t {aka unsigned int}
| long unsigned int
| %u
ONElib.c:1894:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1894 | { fprintf (vf->f, "\n2 %lu %s", strlen(vf->subType), vf->subType);
| ~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| | size_t {aka unsigned int}
| long unsigned int
| %u
ONElib.c:1903:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1903 | { fprintf (vf->f, "\n! 4 %lu %s %lu %s %lu %s %lu %s",
| ~~^
| |
| long unsigned int
| %u
1904 | strlen(p->program), p->program, strlen(p->version), p->version,
| ~~~~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
ONElib.c:1903:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1903 | { fprintf (vf->f, "\n! 4 %lu %s %lu %s %lu %s %lu %s",
| ~~^
| |
| long unsigned int
| %u
1904 | strlen(p->program), p->program, strlen(p->version), p->version,
| ~~~~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
ONElib.c:1903:50: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1903 | { fprintf (vf->f, "\n! 4 %lu %s %lu %s %lu %s %lu %s",
| ~~^
| |
| long unsigned int
| %u
1904 | strlen(p->program), p->program, strlen(p->version), p->version,
1905 | strlen(p->command), p->command, strlen(p->date), p->date);
| ~~~~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
ONElib.c:1903:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1903 | { fprintf (vf->f, "\n! 4 %lu %s %lu %s %lu %s %lu %s",
| ~~^
| |
| long unsigned int
| %u
1904 | strlen(p->program), p->program, strlen(p->version), p->version,
1905 | strlen(p->command), p->command, strlen(p->date), p->date);
| ~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
ONElib.c:1917:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1917 | { fprintf (vf->f, "\n< %lu %s %" PRId64 "", strlen(r->filename), r->filename, r->count);
| ~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
ONElib.c:1924:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1924 | { fprintf (vf->f, "\n> %lu %s", strlen(r->filename), r->filename);
| ~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| | size_t {aka unsigned int}
| long unsigned int
| %u
ONElib.c: In function 'oneWriteLine':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2029:3: note: in expansion of macro 'assert'
2029 | assert (vf->isWrite) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2030:3: note: in expansion of macro 'assert'
2030 | assert (!vf->isFinal || !isalpha(t)) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2033:3: note: in expansion of macro 'assert'
2033 | assert (li) ;
| ^~~~~~
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2040:7: note: in expansion of macro 'assert'
2040 | { assert (listLen >= 0) ;
| ^~~~~~
ONElib.c: In function 'oneFileClose':
ONElib.c:37:19: warning: statement with no effect [-Wunused-value]
37 | #define assert(x) 0
| ^
ONElib.c:2488:3: note: in expansion of macro 'assert'
2488 | assert (vf->share >= 0) ;
| ^~~~~~
ONElib.c: In function 'intGet':
ONElib.c:3490:17: warning: this statement may fall through [-Wimplicit-fallthrough=]
3490 | case 0: die ("int packing error") ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
ONElib.c:3491:9: note: here
3491 | case 1: *pval = *(I64*)(u+1) & 0x0000000000ffff ; return 3 ;
| ^~~~
ONElib.c:3502:17: warning: this statement may fall through [-Wimplicit-fallthrough=]
3502 | case 0: die ("int packing error") ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
ONElib.c:3503:9: note: here
3503 | case 1: *pval = *(I64*)(u+1) | 0xffffffffffff0000 ; return 3 ;
| ^~~~
ONElib.c:3488:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
3488 | switch (u[0] & 0x07)
| ^~~~~~
ONElib.c:3499:5: note: here
3499 | case 4:
| ^~~~
ONElib.c: In function 'ltfRead':
ONElib.c:3564:10: warning: 'val' may be used uninitialized [-Wmaybe-uninitialized]
3564 | return val ;
| ^~~
ONElib.c:3544:7: note: 'val' was declared here
3544 | I64 val ;
| ^~~
ONElib.c: In function 'ltfRead':
ONElib.c:3564:10: warning: 'val' may be used uninitialized [-Wmaybe-uninitialized]
3564 | return val ;
| ^~~
ONElib.c:3544:7: note: 'val' was declared here
3544 | I64 val ;
| ^~~
QV.c: In function 'Build_Table':
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
127 | { uint64 symbol = (uint64) (node->lft);
| ^
QV.c: In function 'Huffman':
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
174 | node[value].lft = (HTree *) (uint64) i;
| ^
make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d'
dh_auto_install
make -j22 install DESTDIR=/build/reproducible-path/daligner-1.0\+git20240119.335105d/debian/daligner AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d'
install -d /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin
install daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin
make[2]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d'
mkdir -p /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/share/man/man1
for command in /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin/*; \
do \
if [ $(basename $command) != daligner ] ; \
then \
ln -s daligner.1 \
/build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/share/man/man1/$(basename $command).1 ; \
fi; \
done
make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d'
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'daligner' in '../daligner_1.0+git20240119.335105d-3_i386.deb'.
dpkg-deb: building package 'daligner-dbgsym' in '../daligner-dbgsym_1.0+git20240119.335105d-3_i386.deb'.
dpkg-genbuildinfo --build=binary -O../daligner_1.0+git20240119.335105d-3_i386.buildinfo
dpkg-genchanges --build=binary -O../daligner_1.0+git20240119.335105d-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/56645 and its subdirectories
I: Current time: Sat Feb 28 14:38:49 -12 2026
I: pbuilder-time-stamp: 1772332729
Sun Jan 26 20:15:56 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net.
Sun Jan 26 20:15:56 UTC 2025 I: Preparing to do remote build '2' on ionos12-i386.debian.net.
Sun Jan 26 20:17:05 UTC 2025 I: Deleting $TMPDIR on ionos12-i386.debian.net.
Sun Jan 26 20:17:05 UTC 2025 I: daligner_1.0+git20240119.335105d-3_i386.changes:
Format: 1.8
Date: Wed, 03 Jul 2024 22:45:58 +0200
Source: daligner
Binary: daligner daligner-dbgsym
Architecture: i386
Version: 1.0+git20240119.335105d-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
daligner - local alignment discovery between long nucleotide sequencing read
Closes: 1074900
Changes:
daligner (1.0+git20240119.335105d-3) unstable; urgency=medium
.
* d/control: declare compliance to standards version 4.7.0.
* gcc-14.patch: fix build failure with gcc-14. (Closes: #1074900)
Checksums-Sha1:
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bccea0c9929269cc5a17072b702032db13a0aedd 5089 daligner_1.0+git20240119.335105d-3_i386.buildinfo
03fbd0e6496069303e0fb34ab0323d32420af292 233068 daligner_1.0+git20240119.335105d-3_i386.deb
Checksums-Sha256:
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1857af92a0b621cc67fb19e893980fb452551507ff7241fefd8dd8a7921ccc78 5089 daligner_1.0+git20240119.335105d-3_i386.buildinfo
82bcf0967c936596526e46560efaf79fc8f2107178dfa19a336f871329d63b13 233068 daligner_1.0+git20240119.335105d-3_i386.deb
Files:
38c212b2af447952ab931af27b98da87 1589968 debug optional daligner-dbgsym_1.0+git20240119.335105d-3_i386.deb
608d3ce1f825ab9b0d180aeb7f794875 5089 science optional daligner_1.0+git20240119.335105d-3_i386.buildinfo
2a294eeca38b71e6c11c111d0053083d 233068 science optional daligner_1.0+git20240119.335105d-3_i386.deb
Sun Jan 26 20:17:06 UTC 2025 I: diffoscope 286 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_11-43222.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.s4nq91O8/daligner_1.0+git20240119.335105d-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.s4nq91O8/daligner_1.0+git20240119.335105d-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.s4nq91O8/daligner_1.0+git20240119.335105d-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.s4nq91O8/b1/daligner_1.0+git20240119.335105d-3_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.s4nq91O8/b2/daligner_1.0+git20240119.335105d-3_i386.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 223ms
CPU time consumed: 224ms
Sun Jan 26 20:17:07 UTC 2025 I: diffoscope 286 found no differences in the changes files, and a .buildinfo file also exists.
Sun Jan 26 20:17:07 UTC 2025 I: daligner from trixie built successfully and reproducibly on i386.
Sun Jan 26 20:17:08 UTC 2025 I: Submitting .buildinfo files to external archives:
Sun Jan 26 20:17:08 UTC 2025 I: Submitting 8.0K b1/daligner_1.0+git20240119.335105d-3_i386.buildinfo.asc
Sun Jan 26 20:17:24 UTC 2025 I: Submitting 8.0K b2/daligner_1.0+git20240119.335105d-3_i386.buildinfo.asc
Sun Jan 26 20:17:30 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Jan 26 20:17:30 UTC 2025 I: Done submitting .buildinfo files.
Sun Jan 26 20:17:30 UTC 2025 I: Removing signed daligner_1.0+git20240119.335105d-3_i386.buildinfo.asc files:
removed './b1/daligner_1.0+git20240119.335105d-3_i386.buildinfo.asc'
removed './b2/daligner_1.0+git20240119.335105d-3_i386.buildinfo.asc'