Sat Feb 22 09:19:46 UTC 2025 I: starting to build lagan/trixie/amd64 on jenkins on '2025-02-22 09:19'
Sat Feb 22 09:19:46 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/47685/console.log
Sat Feb 22 09:19:46 UTC 2025 I: Downloading source for trixie/lagan=2.0-10
--2025-02-22 09:19:46-- http://deb.debian.org/debian/pool/main/l/lagan/lagan_2.0-10.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 1354 (1.3K) [text/prs.lines.tag]
Saving to: ‘lagan_2.0-10.dsc’
0K . 100% 245M=0s
2025-02-22 09:19:46 (245 MB/s) - ‘lagan_2.0-10.dsc’ saved [1354/1354]
Sat Feb 22 09:19:46 UTC 2025 I: lagan_2.0-10.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: lagan
Binary: lagan
Architecture: any
Version: 2.0-10
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Steffen Moeller <moeller@debian.org>
Homepage: http://lagan.stanford.edu/lagan_web/index.shtml
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/lagan
Vcs-Git: https://salsa.debian.org/med-team/lagan.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libboost-dev
Package-List:
lagan deb science optional arch=any
Checksums-Sha1:
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54fa9631bdac105245aaf917f96951ddd7396770 10268 lagan_2.0-10.debian.tar.xz
Checksums-Sha256:
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ccec357e8c330b4f546dcfbd1608d58e1488e8e361bd444d70c020d4ff3d45bc 10268 lagan_2.0-10.debian.tar.xz
Files:
7027ba63a2a5115871b85e205aa36bb7 192945 lagan_2.0.orig.tar.gz
981c1cb44dce36fbdb1f6f444885e419 10268 lagan_2.0-10.debian.tar.xz
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Sat Feb 22 09:19:46 UTC 2025 I: Checking whether the package is not for us
Sat Feb 22 09:19:46 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net.
Sat Feb 22 09:19:46 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net.
Sat Feb 22 09:23:12 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Feb 21 21:19:49 -12 2025
I: pbuilder-time-stamp: 1740215989
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 [lagan_2.0-10.dsc]
I: copying [./lagan_2.0.orig.tar.gz]
I: copying [./lagan_2.0-10.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: unsupported subcommand
dpkg-source: info: extracting lagan in lagan-2.0
dpkg-source: info: unpacking lagan_2.0.orig.tar.gz
dpkg-source: info: unpacking lagan_2.0-10.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying do_not_define_conflicting_getline.patch
dpkg-source: info: applying gcc-4.8.patch
dpkg-source: info: applying ambiuousEnd.patch
dpkg-source: info: applying addTest.patch
dpkg-source: info: applying adjustPerlPaths.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying cross.patch
dpkg-source: info: applying gcc9.patch
dpkg-source: info: applying gcc10.patch
dpkg-source: info: applying gcc-lto.patch
dpkg-source: info: applying fixup-implicit-function-declaration.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2287016/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='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='b237b2d291d94d3aa10437958520eca9'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
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='2287016'
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.07q5SM2R/pbuilderrc_6cQ0 --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.07q5SM2R/b1 --logfile b1/build.log lagan_2.0-10.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://46.16.76.132:3128'
I: uname -a
Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2287016/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <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), libboost-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19858 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.
pbuilder-satisfydepends-dummy depends on libboost-dev; however:
Package libboost-dev 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} libboost-dev{a} libboost1.83-dev{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, 32 newly installed, 0 to remove and 0 not upgraded.
Need to get 31.2 MB of archives. After unpacking 239 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1 [10.6 MB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B]
Fetched 31.2 MB in 8s (4040 kB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 19858 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_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ...
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Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ...
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Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ...
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Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ...
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Setting up libboost1.83-dev:amd64 (1.83.0-4.1) ...
Setting up libicu72:amd64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-3) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
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Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
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Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libboost-dev:amd64 (1.83.0.2+b2) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
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...
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Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/lagan-2.0/ && 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 > ../lagan_2.0-10_source.changes
dpkg-buildpackage: info: source package lagan
dpkg-buildpackage: info: source version 2.0-10
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@iki.fi>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/lagan-2.0'
dh_auto_clean
make -j20 clean
make[2]: Entering directory '/build/reproducible-path/lagan-2.0'
rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
make -C src clean
make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src'
rm -f *.o *~ utils/*~ mlagan.purify core
(cd glocal; make clean)
make[4]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal'
rm -f *.o ./*~ *~ core
make[4]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal'
make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src'
make[2]: Leaving directory '/build/reproducible-path/lagan-2.0'
rm -f prolagan
make[1]: Leaving directory '/build/reproducible-path/lagan-2.0'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/lagan-2.0'
dh_auto_build --sourcedirectory=src
cd src && make -j20 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../anchors anchors.c skiplist.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../order order.c diagmatrix.c filebuffer.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2mf utils/bin2mf.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2bl utils/bin2bl.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro
anchors.c: In function 'anchors_getline':
anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
232 | fgets(temp, 1024, infile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.c -Wl,-z,relro
order.c: In function 'readfile':
order.c:63:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
63 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
order.c: In function 'readSubstMatrix':
order.c:147:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
147 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
order.c:151:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
151 | fscanf (file, "%d", &gapstart);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
order.c:152:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
152 | fscanf (file, "%d", &gapcont);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro
utils/contigorder.c: In function 'getFileInfo':
utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=]
15 | fprintf (stderr, "contigorder: Error opening file: %s\n");
| ~^
| |
| char *
utils/contigorder.c:26:25: warning: unknown conversion type character '&' in format [-Wformat=]
26 | fscanf (file, "%&d", &dummy);
| ^
utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args]
26 | fscanf (file, "%&d", &dummy);
| ^~~~~
utils/contigorder.c: In function 'getScores':
utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=]
52 | fprintf (stderr, "contigorder: Error opening file: %s\n");
| ~^
| |
| char *
utils/contigorder.c: In function 'getFileInfo':
utils/contigorder.c:19:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
19 | fscanf (file, "numContigs = %d\n", numContigs);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:20:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
20 | fscanf (file, "seqLen = %d\n", seqLen);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:26:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | fscanf (file, "%&d", &dummy);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c: In function 'getScores':
utils/contigorder.c:56:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
56 | fscanf (file, "numContigs = %*d\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:57:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
57 | fscanf (file, "seqLen = %*d\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:63:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
63 | fscanf (file, "%d", &((*score)[i][j]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro
prolagan.c: In function 'readfile':
prolagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args]
95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c: In function 'readfile':
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -Wl,-z,relro
utils/cextract.c: In function 'getLength':
utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/cextract.c: In function 'readfile':
utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
41 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args]
357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mlagan.c: In function 'readfile':
mlagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args]
95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
81 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
utils/seqmerge.c: In function 'main':
utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
19 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getlength.c: In function 'main':
utils/getlength.c:20:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
20 | fgets (buffer, BUF_SIZE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
81 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
344 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
fchaos.c: In function 'readSubstMatrix':
fchaos.c:622:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:627:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
627 | fscanf (file, "%d", &gappenstart);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
628 | fscanf (file, "%d", &gappenext);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/rc.c: In function 'main':
utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
39 | fgets(temp, 255, stdin);
| ^~~~~~~~~~~~~~~~~~~~~~~
utils/getcontigpos.c: In function 'getLength':
utils/getcontigpos.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getcontigpos.c: In function 'readfile':
utils/getcontigpos.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
41 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getbounds.c: In function 'getLength':
utils/getbounds.c:18:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
18 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c: In function 'getSequence':
utils/scorealign.c:266:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
266 | fgets (line, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c: In function 'readScoreMatrix':
utils/scorealign.c:415:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
415 | fgets (line, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c:423:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
423 | fscanf (file, "%1s", &(line[0]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c:425:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
425 | fscanf (file, "%d", &k);
| ^~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c:430:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
430 | fscanf (file, "%d%d", &gapopen, &gapcont);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/fa2xfa.c: In function 'getLength':
utils/fa2xfa.c:30:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
30 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/cstat.c: In function 'cntlets':
utils/cstat.c:45:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
utils/fa2xfa.c: In function 'readfile':
utils/fa2xfa.c:55:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
55 | fgets (buffer, 1024, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/cstat.c: In function 'readseq':
utils/cstat.c:68:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
68 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
utils/scorecontigs.c: In function 'main':
utils/scorecontigs.c:385:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=]
385 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| char * char (*)[1024]
utils/scorecontigs.c: In function 'cntlets':
utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
56 | fgets(temp, 1024, input);
| ^~~~~~~~~~~~~~~~~~~~~~~~
utils/scorecontigs.c: In function 'readseq':
utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
82 | fgets (temp, 1024, input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
utils/dotplot.cpp: In function 'int main(int, char**)':
utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
37 | fgets (buffer, 105, file);
| ~~~~~~^~~~~~~~~~~~~~~~~~~
utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
74 | fgets (buffer, 105, file);
| ~~~~~~^~~~~~~~~~~~~~~~~~~
utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
97 | fgets (buffer, 105, file);
| ~~~~~~^~~~~~~~~~~~~~~~~~~
skiplist.c: In function 'printSLE':
skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
utils/overlay.c: In function 'read_align':
utils/overlay.c:110:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
110 | fgets(temp, 255, input);
| ^~~~~~~~~~~~~~~~~~~~~~~
utils/Glue.cpp: In function 'void calculateScoreMatrix(int)':
utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
64 | char *alpha = "ATCG";
| ^~~~~~
utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
| ^~~~~~~~~~~~~~~
utils/Glue.cpp:72:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE'
72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE);
| ^~~~~~~~~~~~~~~~~~~~~~
utils/Glue.cpp: In function 'void readScoreMatrix(char*)':
utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
44 | fgets (line, 1024, file);
| ~~~~~~^~~~~~~~~~~~~~~~~~
utils/Glue.cpp:52:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
52 | fscanf (file, "%1s", &(line[0]));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
utils/Glue.cpp:54:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
54 | fscanf (file, "%d", &k);
| ~~~~~~~^~~~~~~~~~~~~~~~
utils/Glue.cpp:59:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
59 | fscanf (file, "%d%d", &gapopen, &gapcont);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static
603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) |
| ^~~~~~~~
multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static
586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) |
| ^~~~~~~~
multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static
581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) |
| ^~~~~~~~
multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static
576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) |
| ^~~~~~~~
multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static
570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) |
| ^~~~~~~~
multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static
563 | return matchcache[v(other->cnts[0][ow]) |
| ^~~~~~~~~~
multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static
556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) |
| ^~~~~~~~
multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static
552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) |
| ^~~~~~~~~~
multial.c: In function 'readSubstMatrix':
multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
478 | fscanf (file, "%d", &k);
| ^~~~~~~~~~~~~~~~~~~~~~~
multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
486 | fscanf (file, "%d", &gapstart);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
487 | fscanf (file, "%d", &gapcont);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static
603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) |
| ^~~~~~~~
multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static
586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) |
| ^~~~~~~~
multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static
581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) |
| ^~~~~~~~
multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static
576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) |
| ^~~~~~~~
multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static
570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) |
| ^~~~~~~~
multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static
563 | return matchcache[v(other->cnts[0][ow]) |
| ^~~~~~~~~~
multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static
556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) |
| ^~~~~~~~
multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static
552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) |
| ^~~~~~~~~~
multial.c: In function 'readSubstMatrix':
multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
478 | fscanf (file, "%d", &k);
| ^~~~~~~~~~~~~~~~~~~~~~~
multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
486 | fscanf (file, "%d", &gapstart);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
487 | fscanf (file, "%d", &gapcont);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
skiplist.c: In function 'printSLE':
skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
skiplist.c: In function 'printSLE':
skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
skiplist.c: In function 'printSLE':
skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=]
12 | printf(" %d %x\n", tbp->index, tbp->myelem);
| ~^ ~~~~~~~~~~~
| | |
| unsigned int void *
| %p
(cd glocal; make LDFLAGS="-Wl,-z,relro")
make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal'
g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c glocal.cpp -Wl,-z,relro
g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c rightinfluence.cpp -Wl,-z,relro
g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c score.cpp -Wl,-z,relro
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
io.cpp: In function 'long long int getline(FILE*, hll*)':
io.cpp:60:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | fgets(temp, 1024, infile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro
make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal'
make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src'
make[1]: Leaving directory '/build/reproducible-path/lagan-2.0'
dh_auto_test
make -j20 test
make[1]: Entering directory '/build/reproducible-path/lagan-2.0'
make -C src
make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src'
(cd glocal; make LDFLAGS="-Wl,-z,relro")
make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal'
g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro
make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal'
make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src'
(LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]"
[ok]
make[1]: Leaving directory '/build/reproducible-path/lagan-2.0'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/lagan/
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/reproducible-path/lagan-2.0'
dh_fixperms
find debian -name flipchaos.pl -exec chmod +x \{\} \;
make[1]: Leaving directory '/build/reproducible-path/lagan-2.0'
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_amd64.deb'.
dpkg-deb: building package 'lagan' in '../lagan_2.0-10_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_amd64.buildinfo
dpkg-genchanges --build=binary -O../lagan_2.0-10_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: 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/2287016 and its subdirectories
I: Current time: Fri Feb 21 21:23:11 -12 2025
I: pbuilder-time-stamp: 1740216191
Sat Feb 22 09:23:13 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net.
Sat Feb 22 09:23:13 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net.
Sat Feb 22 09:25:34 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
Sat Feb 22 09:25:34 UTC 2025 I: lagan_2.0-10_amd64.changes:
Format: 1.8
Date: Mon, 25 Mar 2024 12:32:30 +0530
Source: lagan
Binary: lagan lagan-dbgsym
Architecture: amd64
Version: 2.0-10
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@iki.fi>
Description:
lagan - highly parametrizable pairwise global genome sequence aligner
Closes: 1066580
Changes:
lagan (2.0-10) unstable; urgency=medium
.
* Team Upload.
* Add patch to fix FTBFS with
implicit-function-declaration (Closes: #1066580)
Checksums-Sha1:
5cb4f1dab75fd678496e84d4bc78bc878420790e 854744 lagan-dbgsym_2.0-10_amd64.deb
54ecc78ccfa627a8b6bfce701e787f731638c528 4897 lagan_2.0-10_amd64.buildinfo
7aa8f79a12ca7638411024d252c71324dcfe8507 184860 lagan_2.0-10_amd64.deb
Checksums-Sha256:
579e83cf01e8e28af53f6822877bc9917c8df9cf53099a9d335ce172440484fb 854744 lagan-dbgsym_2.0-10_amd64.deb
2e15bfc1c3edabc9253a6d108044de1cf87abdd5f1f849bd8473ba99f15b3955 4897 lagan_2.0-10_amd64.buildinfo
51e6a782bd89e0435d3bdd34cab51f25cb8ed2da8fef44eef06fd9e3375f5bb5 184860 lagan_2.0-10_amd64.deb
Files:
35723c9a7f0dbed08440477dceb3ede2 854744 debug optional lagan-dbgsym_2.0-10_amd64.deb
11fa191e2e5d43da1a90f1045ec39681 4897 science optional lagan_2.0-10_amd64.buildinfo
4c34e2a1b0287d59c07885bc2fa929a1 184860 science optional lagan_2.0-10_amd64.deb
Sat Feb 22 09:25:35 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_23-47685.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/lagan_2.0-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/lagan_2.0-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/lagan_2.0-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b1/lagan_2.0-10_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b2/lagan_2.0-10_amd64.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: 258ms
CPU time consumed: 253ms
Sat Feb 22 09:25:36 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Sat Feb 22 09:25:36 UTC 2025 I: lagan from trixie built successfully and reproducibly on amd64.
Sat Feb 22 09:25:37 UTC 2025 I: Submitting .buildinfo files to external archives:
Sat Feb 22 09:25:37 UTC 2025 I: Submitting 8.0K b1/lagan_2.0-10_amd64.buildinfo.asc
Sat Feb 22 09:25:38 UTC 2025 I: Submitting 8.0K b2/lagan_2.0-10_amd64.buildinfo.asc
Sat Feb 22 09:25:38 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Feb 22 09:25:38 UTC 2025 I: Done submitting .buildinfo files.
Sat Feb 22 09:25:38 UTC 2025 I: Removing signed lagan_2.0-10_amd64.buildinfo.asc files:
removed './b1/lagan_2.0-10_amd64.buildinfo.asc'
removed './b2/lagan_2.0-10_amd64.buildinfo.asc'