I: pbuilder: network access will be disabled during build
I: Current time: Sun Dec 15 02:35:02 -12 2024
I: pbuilder-time-stamp: 1734273302
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
gpgv: Signature made Sat Dec 23 08:22:17 2023
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./snpomatic_1.0-7.dsc: no acceptable signature found
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/18564/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='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='4a6793531a6f46c0a2423d3b8795c784'
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='18564'
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.ardb8Sln/pbuilderrc_lDnc --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.ardb8Sln/b1 --logfile b1/build.log snpomatic_1.0-7.dsc'
SUDO_GID='113'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux virt64b 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/18564/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: armhf
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 ... 19680 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} libedit2{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libpipeline1{a} libruby{a} libruby3.1t64{a} libtool{a} libuchardet0{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-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl fonts-lato libarchive-cpio-perl libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx wget zip
0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
Need to get 27.5 MB of archives. After unpacking 100 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
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Get: 3 http://deb.debian.org/debian unstable/main armhf ca-certificates all 20240203 [158 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-6 [1091 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf antiword armhf 0.37-16 [110 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf rubygems-integration all 1.18 [6704 B]
Get: 15 http://deb.debian.org/debian unstable/main armhf rake all 13.2.1-1 [65.2 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf ruby-webrick all 1.8.1-1 [51.4 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf ruby-xmlrpc all 0.3.3-2 [24.4 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf libruby armhf 1:3.1+nmu1 [4664 B]
Get: 20 http://deb.debian.org/debian unstable/main armhf ruby-sdbm armhf 1.0.0-5+b5 [13.3 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf libedit2 armhf 3.1-20240808-1 [77.9 kB]
Get: 22 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2+b1 [82.3 kB]
Get: 23 http://deb.debian.org/debian unstable/main armhf libyaml-0-2 armhf 0.2.5-1+b2 [45.4 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf libruby3.1t64 armhf 3.1.2-8.4 [5081 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf ruby3.1 armhf 3.1.2-8.4 [664 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf ruby-rubygems all 3.4.20-1 [309 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf ruby armhf 1:3.1+nmu1 [5584 B]
Get: 28 http://deb.debian.org/debian unstable/main armhf ruby-asciidoctor all 2.0.23-1 [214 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf asciidoctor all 2.0.23-1 [88.7 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 33 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 34 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB]
Get: 36 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB]
Get: 37 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 38 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 39 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 40 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 41 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 42 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 43 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 44 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 45 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB]
Get: 46 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 47 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 48 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB]
Fetched 27.5 MB in 1s (20.9 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
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(Reading database ... 19680 files and directories currently installed.)
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Unpacking debhelper (13.20) ...
Setting up libpipeline1:armhf (1.5.8-1) ...
Setting up libicu72:armhf (72.1-5+b1) ...
Setting up bsdextrautils (2.40.2-12) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:armhf (0.2.5-1+b2) ...
Setting up libdebhelper-perl (13.20) ...
Setting up libedit2:armhf (3.1-20240808-1) ...
Setting up libmagic1t64:armhf (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-2) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:armhf (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libncurses6:armhf (6.5-2+b1) ...
Setting up ruby-net-telnet (0.2.0-1) ...
Setting up autopoint (0.22.5-2) ...
Setting up autoconf (2.72-3) ...
Setting up ruby-webrick (1.8.1-1) ...
Setting up dwz (0.15-1+b2) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:armhf (0.0.8-1+b2) ...
Setting up antiword (0.37-16) ...
Setting up openssl (3.3.2-2) ...
Setting up ruby-xmlrpc (0.3.3-2) ...
Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up gettext (0.22.5-2) ...
Setting up libtool (2.4.7-8) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
146 added, 0 removed; done.
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-6) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up rubygems-integration (1.18) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.20) ...
Setting up rake (13.2.1-1) ...
Setting up ruby3.1 (3.1.2-8.4) ...
Setting up libruby3.1t64:armhf (3.1.2-8.4) ...
Setting up libruby:armhf (1:3.1+nmu1) ...
Setting up ruby (1:3.1+nmu1) ...
Setting up ruby-asciidoctor (2.0.23-1) ...
Setting up asciidoctor (2.0.23-1) ...
Setting up ruby-sdbm:armhf (1.0.0-5+b5) ...
Setting up ruby-rubygems (3.4.20-1) ...
Processing triggers for libc-bin (2.40-4) ...
Processing triggers for ca-certificates (20240203) ...
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 armhf
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 -j3 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 -j3 "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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosome.cpp -o src/TChromosome.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++
src/TChromosome.cpp: In member function 'void TChromosome::read_chromosome(std::string, std::string)':
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/global_functions.cpp: In function 'void load_all_chromosomes(std::string, std::vector<TChromosome>&, bool)':
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 ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.o
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
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 ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/reassemble.cpp -o src/reassemble.o
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
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/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 ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.o
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/mapcontigs.cpp -o src/mapcontigs.o
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++
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*, unsigned int)' writing between 17 and 2147483647 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/arm-linux-gnueabihf/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:509:28,
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-c3XSPsM5
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/88
objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/88/3f8b21cb7f1be3965ee7262c46c09d71c87773.debug
chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/88/3f8b21cb7f1be3965ee7262c46c09d71c87773.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/88/3f8b21cb7f1be3965ee7262c46c09d71c87773.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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
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=883f8b21cb7f1be3965ee7262c46c09d71c87773 -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_armhf.deb'.
dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-7_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-7_armhf.buildinfo
dpkg-genchanges --build=binary -O../snpomatic_1.0-7_armhf.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/18564 and its subdirectories
I: Current time: Sun Dec 15 02:37:17 -12 2024
I: pbuilder-time-stamp: 1734273437