I: pbuilder: network access will be disabled during build
I: Current time: Fri Apr 3 19:09:38 -12 2026
I: pbuilder-time-stamp: 1775286578
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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 [snpomatic_1.0-7.dsc]
I: copying [./snpomatic_1.0.orig.tar.gz]
I: copying [./snpomatic_1.0-7.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./snpomatic_1.0-7.dsc: unsupported subcommand
dpkg-source: info: extracting snpomatic in snpomatic-1.0
dpkg-source: info: unpacking snpomatic_1.0.orig.tar.gz
dpkg-source: info: unpacking snpomatic_1.0-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_ungap
dpkg-source: info: applying hardening
dpkg-source: info: applying build_all_binaries
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1222299/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=42 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='6a8f32b8e16d4774903156db68c8cf50'
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='1222299'
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.6EUWbLPz/pbuilderrc_LgTY --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6EUWbLPz/b1 --logfile b1/build.log snpomatic_1.0-7.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://213.165.73.152:3128'
I: uname -a
Linux ionos15-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) 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/1222299/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), asciidoctor, antiword
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19780 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 asciidoctor; however:
Package asciidoctor is not installed.
pbuilder-satisfydepends-dummy depends on antiword; however:
Package antiword 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:
antiword{a} asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{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} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libruby{a} libruby3.3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.3{a} rubygems-integration{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl fonts-lato libarchive-cpio-perl libjs-jquery libltdl-dev libmail-sendmail-perl lynx ruby-sdbm wget zip
0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded.
Need to get 30.5 MB of archives. After unpacking 117 MB will be used.
Writing extended state information...
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Get: 9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 antiword amd64 0.37-16 [123 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.19 [5488 B]
Get: 15 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 ruby-minitest all 5.25.4-2 [66.2 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 ruby-power-assert all 2.0.3-1 [11.8 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 ruby-test-unit all 3.6.2-1 [79.1 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libruby3.3 amd64 3.3.7-1 [6274 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 ruby3.3 amd64 3.3.7-1 [827 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.3+b1 [5440 B]
Get: 28 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.6.3-1 [406 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.3+b1 [6560 B]
Get: 30 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.23-1 [88.7 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Fetched 30.5 MB in 1s (49.6 MB/s)
Preconfiguring packages ...
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(Reading database ... 19780 files and directories currently installed.)
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Setting up libmagic-mgc (1:5.45-3+b1) ...
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Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up antiword (0.37-16) ...
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Setting up ruby-xmlrpc (0.3.3-2) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
152 added, 0 removed; done.
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 rubygems-integration (1.19) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Setting up rake (13.2.1-1) ...
Setting up libruby3.3:amd64 (3.3.7-1) ...
Setting up ruby-rubygems (3.6.3-1) ...
Setting up ruby3.3 (3.3.7-1) ...
Setting up libruby:amd64 (1:3.3+b1) ...
Setting up ruby (1:3.3+b1) ...
Setting up ruby-asciidoctor (2.0.23-1) ...
Setting up asciidoctor (2.0.23-1) ...
Processing triggers for libc-bin (2.41-3) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
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/snpomatic-1.0/ && 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 > ../snpomatic_1.0-7_source.changes
dpkg-buildpackage: info: source package snpomatic
dpkg-buildpackage: info: source version 1.0-7
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Sascha Steinbiss <satta@debian.org>
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/snpomatic-1.0'
/usr/bin/make clean
make[2]: Entering directory '/build/reproducible-path/snpomatic-1.0'
rm -f *.o
rm -f src/*.o
rm -f findknownsnps
rm -f variety
make[2]: Leaving directory '/build/reproducible-path/snpomatic-1.0'
rm -rf debian/findknownsnps.1
rm -rf debian/findknownsnps.1.html
rm -f mapcontigs reassemble ungap
rm -f doc/Manual.txt
dh_auto_clean --
make -j42 clean
make[2]: Entering directory '/build/reproducible-path/snpomatic-1.0'
rm -f *.o
rm -f src/*.o
rm -f findknownsnps
rm -f variety
make[2]: Leaving directory '/build/reproducible-path/snpomatic-1.0'
make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/snpomatic.substvars debian/files
rm -fr -- debian/snpomatic/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j42 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/snpomatic-1.0'
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/findknownsnps.cpp -o src/findknownsnps.o
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/global_functions.cpp -o src/global_functions.o
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosome.cpp -o src/TChromosome.o
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.o
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/reassemble.cpp -o src/reassemble.o
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.o
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/mapcontigs.cpp -o src/mapcontigs.o
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/ungap.cpp -o src/ungap.o
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++
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++
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++
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
src/TChromosome.cpp: In member function 'void TChromosome::read_chromosome(std::string, std::string)':
src/TChromosome.cpp:41:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
41 | if ( DEBUGGING ) { fprintf ( stdout , "read %d nucleotides.\n" , sequence.length() ) ; fflush(stdout); }
| ~^ ~~~~~~~~~~~~~~~~~
| | |
| int std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
| %ld
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::init()':
src/TChromosomeAlign.cpp:83:58: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
83 | fprintf ( sam , "@SQ\tSN:%s\tLN:%d\n" , (*chrs)[i].name.c_str() , (*chrs)[i].sequence.length() ) ;
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
| %ld
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run(chrvec*)':
src/TChromosomalIndices.cpp:262:87: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<TChromosome>::size_type' {aka 'long unsigned int'} [-Wformat=]
262 | if ( index_from == 0 && index_to == 0 ) fprintf ( stdout , "Indexing %d chromosomes ... " , chrs->size() ) ;
| ~^ ~~~~~~~~~~~~
| | |
| int std::vector<TChromosome>::size_type {aka long unsigned int}
| %ld
src/TChromosomalIndices.cpp:263:52: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<TChromosome>::size_type' {aka 'long unsigned int'} [-Wformat=]
263 | else fprintf ( stdout , "Indexing %d chromosomes (%d-%d) ... " , chrs->size() , index_from , index_to ) ;
| ~^ ~~~~~~~~~~~~
| | |
| int std::vector<TChromosome>::size_type {aka long unsigned int}
| %ld
src/global_functions.cpp: In function 'void load_all_chromosomes(std::string, std::vector<TChromosome>&, bool)':
src/global_functions.cpp:146:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<TChromosome>::size_type' {aka 'long unsigned int'} [-Wformat=]
146 | if ( DEBUGGING ) { fprintf ( stdout , "read %d chromosomes.\n" , chrs.size() ) ; fflush(stdout); }
| ~^ ~~~~~~~~~~~
| | |
| int std::vector<TChromosome>::size_type {aka long unsigned int}
| %ld
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)':
src/TChromosomeAlign.cpp:956:98: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
956 | fprintf ( sqlite , "INSERT INTO chromosomes ( name , size ) VALUES ( \"%s\" , \"%d\") ;\n" , (*chrs)[a].name.c_str() , (*chrs)[a].sequence.length() ) ;
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
| %ld
src/TChromosome.cpp:13:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
13 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::string)':
src/TChromosome.cpp:54:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
54 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::string)':
src/TChromosome.cpp:95:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
95 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_cigar_sqlite(const std::string&, const std::string&, uint, uint, char)':
src/TChromosomeAlign.cpp:1583:43: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
1583 | fprintf ( cigar , "%s %d %d %c %s %d %d + %d %s\n" ,
| ~^
| |
| int
| %ld
......
1586 | sequence.length() , // Read end
| ~~~~~~~~~~~~~~~~~
| |
| std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
src/TChromosomeAlign.cpp:1583:55: warning: format '%d' expects argument of type 'int', but argument 9 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
1583 | fprintf ( cigar , "%s %d %d %c %s %d %d + %d %s\n" ,
| ~^
| |
| int
| %ld
......
1590 | position + sequence.length() , // End on chromosome
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
src/global_functions.cpp:116:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
116 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/global_functions.cpp: In function 'void incorporate_all_gff(std::string, std::vector<TChromosome>&)':
src/global_functions.cpp:165:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
165 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/global_functions.cpp: In function 'void incorporate_simple_snps(std::string, std::vector<TChromosome>&)':
src/global_functions.cpp:220:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
220 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_reads(std::string)':
src/TChromosomalIndices.cpp:33:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
33 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:37:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
37 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::reassemble_reads(FILE*, uint, index2type, index2type)':
src/TChromosomalIndices.cpp:126:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
126 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:127:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
127 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_regions(chrvec*, std::string)':
src/TChromosomalIndices.cpp:167:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
167 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::load_index(std::string)':
src/TChromosomalIndices.cpp:409:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
409 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Version
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:410:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
410 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // position size
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:415:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
415 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Sub-index size
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:419:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
419 | fread ( &i.index2 , sizeof ( i.index2 ) , 1 , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:420:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
420 | fread ( &i.position , sizeof ( i.position ) , 1 , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:421:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
421 | fread ( &i.chromosome , sizeof ( i.chromosome ) , 1 , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:422:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
422 | fread ( &i.reverse_complement , sizeof ( i.reverse_complement ) , 1 , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_nono_list(std::string)':
src/TChromosomeAlign.cpp:93:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
93 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/reassemble.cpp: In function 'void read_fastq(std::string, std::vector<TRead>&, int)':
src/reassemble.cpp:319:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
319 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)':
src/TChromosomeAlign.cpp:972:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
972 | fgets ( dummy , READ_CHAR_BUFFER , sqlite_cache ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_paired(std::string, std::string, uint, uint, uint)':
src/TChromosomeAlign.cpp:1070:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1070 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1075:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1075 | fgets ( c1 , READ_CHAR_BUFFER , file2 ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq(std::string)':
src/TChromosomeAlign.cpp:1296:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1296 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1306:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1306 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1316:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1316 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1325:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1325 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fasta(std::string)':
src/TChromosomeAlign.cpp:1374:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1374 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq_variety(std::string)':
src/TChromosomeAlign.cpp:1628:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1628 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1637:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1637 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1647:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1647 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1655:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1655 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:51,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from src/snpomatic.h:13,
from src/TChromosomeAlign.cpp:1:
In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const TPositionWithIndex; _Up = TPositionWithIndex; bool _IsMove = false]',
inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const TPositionWithIndex*; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30,
inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const TPositionWithIndex*; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42,
inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const TPositionWithIndex*, vector<TPositionWithIndex> >; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31,
inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const TPositionWithIndex*, vector<TPositionWithIndex> >; _OI = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7,
inlined from 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const TPositionWithIndex*, std::vector<TPositionWithIndex> >; _ForwardIterator = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27,
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const TPositionWithIndex*, vector<TPositionWithIndex> >; _ForwardIterator = TPositionWithIndex*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const TPositionWithIndex*, vector<TPositionWithIndex> >; _ForwardIterator = TPositionWithIndex*; _Tp = TPositionWithIndex]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator<TPositionWithIndex>]' at /usr/include/c++/14/bits/stl_vector.h:606:31,
inlined from 'void TChromosomeAlign::run_wobble(const std::string&, const std::string&, const std::string&, const std::string&, const pwi_vector&, const pwi_vector&, uint)' at src/TChromosomeAlign.cpp:337:50:
/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 17 and 9223372036854775807 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=]
452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/string:43:
In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = TPositionWithIndex]',
inlined from 'static _Tp* std::allocator_traits<std::allocator<_CharT> >::allocate(allocator_type&, size_type) [with _Tp = TPositionWithIndex]' at /usr/include/c++/14/bits/alloc_traits.h:515:28,
inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = TPositionWithIndex; _Alloc = std::allocator<TPositionWithIndex>]' at /usr/include/c++/14/bits/stl_vector.h:380:33,
inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = TPositionWithIndex; _Alloc = std::allocator<TPositionWithIndex>]' at /usr/include/c++/14/bits/stl_vector.h:398:44,
inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator<TPositionWithIndex>]' at /usr/include/c++/14/bits/stl_vector.h:334:26,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = TPositionWithIndex; _Alloc = std::allocator<TPositionWithIndex>]' at /usr/include/c++/14/bits/stl_vector.h:603:61,
inlined from 'void TChromosomeAlign::run_wobble(const std::string&, const std::string&, const std::string&, const std::string&, const pwi_vector&, const pwi_vector&, uint)' at src/TChromosomeAlign.cpp:337:50:
/usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 16 allocated by 'operator new'
151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o findknownsnps
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o reassemble
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/variety.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o variety
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/mapcontigs.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o mapcontigs
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o ungap
make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-i4iSTK45
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/snpomatic.substvars
rm -fr -- debian/.debhelper/generated/snpomatic/ debian/snpomatic/ debian/tmp/
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/snpomatic-1.0'
mkdir -p /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin
install -p findknownsnps /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin
# -- we don't install the others as they seem unmaintained/undocumented
#cp reassemble /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin
#cp variety /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin
#cp mapcontigs /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin
#cp ungap /build/reproducible-path/snpomatic-1.0/debian/snpomatic/usr/bin
make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0'
debian/rules override_dh_installdocs
make[1]: Entering directory '/build/reproducible-path/snpomatic-1.0'
antiword doc/Manual.doc > doc/Manual.txt
mkdir -p debian/snpomatic/usr/share/doc/snpomatic
cp doc/Manual.txt debian/snpomatic/usr/share/doc/snpomatic
dh_installdocs --
install -p -m0644 debian/copyright debian/snpomatic/usr/share/doc/snpomatic/copyright
install -m0755 -d debian/snpomatic/usr/share/doc-base/
install -p -m0644 debian/doc-base debian/snpomatic/usr/share/doc-base/snpomatic.snpomatic
make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0'
dh_installchangelogs
install -m0755 -d debian/snpomatic/usr/share/doc/snpomatic
install -p -m0644 debian/.debhelper/generated/snpomatic/dh_installchangelogs.dch.trimmed debian/snpomatic/usr/share/doc/snpomatic/changelog.Debian
rm -f debian/snpomatic.debhelper.log
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/snpomatic-1.0'
asciidoctor -a docdate='' -b manpage debian/findknownsnps.1.adoc
dh_installman --
install -m0755 -d debian/snpomatic/usr/share/man/man1/
install -p -m0644 ./debian/findknownsnps.1 debian/snpomatic/usr/share/man/man1/findknownsnps.1
man-recode --to-code UTF-8 --suffix .dh-new debian/snpomatic/usr/share/man/man1/findknownsnps.1
mv debian/snpomatic/usr/share/man/man1/findknownsnps.1.dh-new debian/snpomatic/usr/share/man/man1/findknownsnps.1
chmod 0644 -- debian/snpomatic/usr/share/man/man1/findknownsnps.1
make[1]: Leaving directory '/build/reproducible-path/snpomatic-1.0'
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
cd debian/snpomatic
chmod a-x usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1
gzip -9nf usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1
cd '/build/reproducible-path/snpomatic-1.0'
dh_fixperms
find debian/snpomatic ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/snpomatic/usr/share/doc -type f -a -true -a ! -regex 'debian/snpomatic/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/snpomatic/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/snpomatic/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/snpomatic -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/snpomatic/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing
dh_dwz -a
dwz -- debian/snpomatic/usr/bin/findknownsnps
dh_strip -a
install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/cf
objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/cf/ad7ea37d00184508c18c4556e6f22808dc19ce.debug
chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/cf/ad7ea37d00184508c18c4556e6f22808dc19ce.debug
strip --remove-section=.comment --remove-section=.note debian/snpomatic/usr/bin/findknownsnps
objcopy --add-gnu-debuglink debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/cf/ad7ea37d00184508c18c4556e6f22808dc19ce.debug debian/snpomatic/usr/bin/findknownsnps
install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc
ln -s snpomatic debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc/snpomatic-dbgsym
install -m0755 -d debian/.debhelper/snpomatic
dh_makeshlibs -a
rm -f debian/snpomatic/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/snpomatic/DEBIAN
dpkg-shlibdeps -Tdebian/snpomatic.substvars debian/snpomatic/usr/bin/findknownsnps
dh_installdeb
install -m0755 -d debian/snpomatic/DEBIAN
dh_gencontrol
install -m0755 -d debian/snpomatic/DEBIAN
echo misc:Depends= >> debian/snpomatic.substvars
echo misc:Pre-Depends= >> debian/snpomatic.substvars
install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/DEBIAN
dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -cdebian/control -Pdebian/.debhelper/snpomatic/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=snpomatic-dbgsym "-DDepends=snpomatic (= \${binary:Version})" "-DDescription=debug symbols for snpomatic" -DBuild-Ids=cfad7ea37d00184508c18c4556e6f22808dc19ce -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -cdebian/control -Pdebian/snpomatic
chmod 0644 -- debian/snpomatic/DEBIAN/control
dh_md5sums
install -m0755 -d debian/snpomatic/DEBIAN
cd debian/snpomatic >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/snpomatic/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/DEBIAN
cd debian/.debhelper/snpomatic/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/snpomatic ..
dpkg-deb --root-owner-group --build debian/.debhelper/snpomatic/dbgsym-root ..
dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-7_amd64.deb'.
dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-7_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-7_amd64.buildinfo
dpkg-genchanges --build=binary -O../snpomatic_1.0-7_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/1222299 and its subdirectories
I: Current time: Fri Apr 3 19:10:34 -12 2026
I: pbuilder-time-stamp: 1775286634