Diff of the two buildlogs: -- --- b1/build.log 2024-10-28 01:48:32.714892257 +0000 +++ b2/build.log 2024-10-28 01:56:19.750308213 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Nov 29 20:06:26 -12 2025 -I: pbuilder-time-stamp: 1764489986 +I: Current time: Mon Oct 28 15:48:39 +14 2024 +I: pbuilder-time-stamp: 1730080119 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,53 +29,85 @@ dpkg-source: info: applying Makefile_config.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9407/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/12237/tmp/hooks/D01_modify_environment starting +debug: Running on infom07-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 28 01:48 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/12237/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/12237/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='7a93bbc7d13c4b248e81089d060f3690' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='9407' - PS1='# ' - PS2='> ' + INVOCATION_ID=6ac53d09de214422b3ad444415038f76 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=12237 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.kfjOv8hV/pbuilderrc_kFtC --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.kfjOv8hV/b1 --logfile b1/build.log qtltools_1.3.1+dfsg-4.dsc' - SUDO_GID='111' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.kfjOv8hV/pbuilderrc_MCBz --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kfjOv8hV/b2 --logfile b2/build.log qtltools_1.3.1+dfsg-4.dsc' + SUDO_GID=111 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom08-i386 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/9407/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/12237/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +259,7 @@ Get: 96 http://deb.debian.org/debian unstable/main i386 liblzma-dev i386 5.6.3-1 [328 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libhts-dev i386 1.20+ds-1 [1675 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 r-mathlib i386 4.4.1-3 [2594 kB] -Fetched 66.4 MB in 1s (84.0 MB/s) +Fetched 66.4 MB in 1s (78.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19933 files and directories currently installed.) @@ -636,7 +668,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/qtltools-1.3.1+dfsg/ && 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 > ../qtltools_1.3.1+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/12237/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/12237/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/qtltools-1.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../qtltools_1.3.1+dfsg-4_source.changes dpkg-buildpackage: info: source package qtltools dpkg-buildpackage: info: source version 1.3.1+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -649,7 +685,7 @@ make[1]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' rm -f debian/upstream.example/examples.tar.xz dh_auto_clean - make -j6 clean + make -j5 clean make[2]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' rm -f obj/*.o bin/QTLtools make[2]: Leaving directory '/build/reproducible-path/qtltools-1.3.1+dfsg' @@ -665,17 +701,17 @@ mkdir -p /build/reproducible-path/qtltools-1.3.1+dfsg/obj/ mkdir -p /build/reproducible-path/qtltools-1.3.1+dfsg/bin/ dh_auto_build - make -j6 "INSTALL=install --strip-program=true" + make -j5 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' g++ -std=c++0x -o obj/QTLtools.o -c src/QTLtools.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/data.o -c src/common/data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_main.o -c src/mode_ase/ase_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_management.o -c src/mode_ase/ase_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_read_blacklist.o -c src/mode_ase/ase_read_blacklist.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/ase_read_fasta.o -c src/mode_ase/ase_read_fasta.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, - from src/common/data.h:19, - from src/common/data.cpp:16: + from src/mode_ase/../common/data.h:19, + from src/mode_ase/ase_data.h:20, + from src/mode_ase/ase_management.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -689,9 +725,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' In file included from lib/OTools/otools.h:56, - from src/mode_ase/../common/data.h:19, - from src/mode_ase/ase_data.h:20, - from src/mode_ase/ase_management.cpp:16: + from src/mode_cis/../common/data.h:19, + from src/mode_cis/cis_data.h:33, + from src/QTLtools.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -705,9 +741,8 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' In file included from lib/OTools/otools.h:56, - from src/mode_cis/../common/data.h:19, - from src/mode_cis/cis_data.h:33, - from src/QTLtools.cpp:16: + from src/common/data.h:19, + from src/common/data.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -723,7 +758,7 @@ In file included from lib/OTools/otools.h:56, from src/mode_ase/../common/data.h:19, from src/mode_ase/ase_data.h:20, - from src/mode_ase/ase_read_fasta.cpp:16: + from src/mode_ase/ase_main.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -752,10 +787,13 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/ase_read_fasta.o -c src/mode_ase/ase_read_fasta.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/ase_read_genotypes.o -c src/mode_ase/ase_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/ase_read_gtf.o -c src/mode_ase/ase_read_gtf.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_ase/../common/data.h:19, from src/mode_ase/ase_data.h:20, - from src/mode_ase/ase_main.cpp:16: + from src/mode_ase/ase_read_fasta.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -768,12 +806,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/ase_read_genotypes.o -c src/mode_ase/ase_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/ase_read_gtf.o -c src/mode_ase/ase_read_gtf.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_ase/../common/data.h:19, from src/mode_ase/ase_data.h:20, - from src/mode_ase/ase_read_genotypes.cpp:16: + from src/mode_ase/ase_read_gtf.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -786,12 +822,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/ase_read_sequences.o -c src/mode_ase/ase_read_sequences.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/ase_run_analyses.o -c src/mode_ase/ase_run_analyses.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_ase/../common/data.h:19, from src/mode_ase/ase_data.h:20, - from src/mode_ase/ase_read_gtf.cpp:16: + from src/mode_ase/ase_read_genotypes.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -804,12 +838,12 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/bamstat_main.o -c src/mode_bamstat/bamstat_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/bamstat_read_annotations.o -c src/mode_bamstat/bamstat_read_annotations.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/ase_read_sequences.o -c src/mode_ase/ase_read_sequences.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/ase_run_analyses.o -c src/mode_ase/ase_run_analyses.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_ase/../common/data.h:19, from src/mode_ase/ase_data.h:20, - from src/mode_ase/ase_read_sequences.cpp:16: + from src/mode_ase/ase_run_analyses.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -825,7 +859,7 @@ In file included from lib/OTools/otools.h:56, from src/mode_ase/../common/data.h:19, from src/mode_ase/ase_data.h:20, - from src/mode_ase/ase_run_analyses.cpp:16: + from src/mode_ase/ase_read_sequences.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -838,6 +872,8 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/bamstat_main.o -c src/mode_bamstat/bamstat_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/bamstat_read_annotations.o -c src/mode_bamstat/bamstat_read_annotations.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_bamstat/../common/data.h:19, from src/mode_bamstat/bamstat_data.h:20, @@ -876,7 +912,7 @@ In file included from lib/OTools/otools.h:56, from src/mode_bamstat/../common/data.h:19, from src/mode_bamstat/bamstat_data.h:20, - from src/mode_bamstat/bamstat_read_bam.cpp:16: + from src/mode_bamstat/bamstat_write_output.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -892,7 +928,7 @@ In file included from lib/OTools/otools.h:56, from src/mode_bamstat/../common/data.h:19, from src/mode_bamstat/bamstat_data.h:20, - from src/mode_bamstat/bamstat_write_output.cpp:16: + from src/mode_bamstat/bamstat_read_bam.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -905,8 +941,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/cis_collapse_phenotypes.o -c src/mode_cis/cis_collapse_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/cis_conditionnal_pass.o -c src/mode_cis/cis_conditionnal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -923,7 +957,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/cis_collapse_phenotypes.o -c src/mode_cis/cis_collapse_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/cis_conditionnal_pass.o -c src/mode_cis/cis_conditionnal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_initilization.o -c src/mode_cis/cis_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/cis_learn_beta.o -c src/mode_cis/cis_learn_beta.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -972,7 +1009,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/cis_learn_beta.o -c src/mode_cis/cis_learn_beta.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -990,7 +1026,6 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/cis_learn_dof.o -c src/mode_cis/cis_learn_dof.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/cis_main.o -c src/mode_cis/cis_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -1007,6 +1042,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/cis_main.o -c src/mode_cis/cis_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -1024,10 +1060,11 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/cis_management.o -c src/mode_cis/cis_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/cis_nominal_pass.o -c src/mode_cis/cis_nominal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, - from src/mode_cis/cis_management.cpp:16: + from src/mode_cis/cis_nominal_pass.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1040,12 +1077,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/cis_nominal_pass.o -c src/mode_cis/cis_nominal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/cis_permutation_pass.o -c src/mode_cis/cis_permutation_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, - from src/mode_cis/cis_nominal_pass.cpp:16: + from src/mode_cis/cis_management.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1058,7 +1093,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/cis_read_covariates.o -c src/mode_cis/cis_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/cis_permutation_pass.o -c src/mode_cis/cis_permutation_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -1075,6 +1110,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/cis_read_covariates.o -c src/mode_cis/cis_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -1092,6 +1128,8 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/cis_read_genotypes.o -c src/mode_cis/cis_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/cis_read_phenotypes.o -c src/mode_cis/cis_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/cis_read_thresholds.o -c src/mode_cis/cis_read_thresholds.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -1108,7 +1146,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/cis_read_phenotypes.o -c src/mode_cis/cis_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -1125,7 +1162,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/cis_read_thresholds.o -c src/mode_cis/cis_read_thresholds.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, @@ -1160,8 +1196,6 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/correct_management.o -c src/mode_correct/correct_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/correct_processing.o -c src/mode_correct/correct_processing.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/correct_read_covariates.o -c src/mode_correct/correct_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_correct/../common/data.h:19, from src/mode_correct/correct_data.h:24, @@ -1178,6 +1212,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/correct_processing.o -c src/mode_correct/correct_processing.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_correct/../common/data.h:19, from src/mode_correct/correct_data.h:24, @@ -1194,10 +1229,12 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/correct_read_covariates.o -c src/mode_correct/correct_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/extract_main.o -c src/mode_extract/extract_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, - from src/mode_correct/../common/data.h:19, - from src/mode_correct/correct_data.h:24, - from src/mode_correct/correct_read_covariates.cpp:16: + from src/mode_extract/../common/data.h:19, + from src/mode_extract/extract_data.h:20, + from src/mode_extract/extract_main.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1210,11 +1247,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/extract_main.o -c src/mode_extract/extract_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, - from src/mode_extract/../common/data.h:19, - from src/mode_extract/extract_data.h:20, - from src/mode_extract/extract_main.cpp:16: + from src/mode_correct/../common/data.h:19, + from src/mode_correct/correct_data.h:24, + from src/mode_correct/correct_read_covariates.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1228,6 +1264,7 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/extract_managment.o -c src/mode_extract/extract_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/extract_read_data.o -c src/mode_extract/extract_read_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_extract/../common/data.h:19, from src/mode_extract/extract_data.h:20, @@ -1244,11 +1281,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/extract_read_data.o -c src/mode_extract/extract_read_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -src/mode_correct/correct_processing.cpp: In member function 'void correct_data::processVCF(std::string, std::string)': -src/mode_correct/correct_processing.cpp:127:22: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 127 | bcf_hdr_write(fp, hdr_new); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from lib/OTools/otools.h:56, from src/mode_extract/../common/data.h:19, from src/mode_extract/extract_data.h:20, @@ -1265,7 +1297,13 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +src/mode_correct/correct_processing.cpp: In member function 'void correct_data::processVCF(std::string, std::string)': +src/mode_correct/correct_processing.cpp:127:22: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 127 | bcf_hdr_write(fp, hdr_new); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~ g++ -std=c++0x -o obj/extract_write.o -c src/mode_extract/extract_write.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/fdensity_main.o -c src/mode_fdensity/fdensity_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/fdensity_process.o -c src/mode_fdensity/fdensity_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_extract/../common/data.h:19, from src/mode_extract/extract_data.h:20, @@ -1282,7 +1320,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/fdensity_main.o -c src/mode_fdensity/fdensity_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_fdensity/../common/data.h:19, from src/mode_fdensity/fdensity_data.h:20, @@ -1299,7 +1336,8 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/fdensity_process.o -c src/mode_fdensity/fdensity_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/fdensity_read_annotation.o -c src/mode_fdensity/fdensity_read_annotation.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/fdensity_read_qtl.o -c src/mode_fdensity/fdensity_read_qtl.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_fdensity/../common/data.h:19, from src/mode_fdensity/fdensity_data.h:20, @@ -1316,8 +1354,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/fdensity_read_annotation.o -c src/mode_fdensity/fdensity_read_annotation.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/fdensity_read_qtl.o -c src/mode_fdensity/fdensity_read_qtl.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_fdensity/../common/data.h:19, from src/mode_fdensity/fdensity_data.h:20, @@ -1353,6 +1389,7 @@ g++ -std=c++0x -o obj/fenrich_main.o -c src/mode_fenrich/fenrich_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_management.o -c src/mode_fenrich/fenrich_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_process.o -c src/mode_fenrich/fenrich_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/fenrich_read_annotation.o -c src/mode_fenrich/fenrich_read_annotation.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_fenrich/../common/data.h:19, from src/mode_fenrich/fenrich_data.h:20, @@ -1385,6 +1422,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/fenrich_read_qtl.o -c src/mode_fenrich/fenrich_read_qtl.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_fenrich/../common/data.h:19, from src/mode_fenrich/fenrich_data.h:20, @@ -1401,9 +1439,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/fenrich_read_annotation.o -c src/mode_fenrich/fenrich_read_annotation.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/fenrich_read_qtl.o -c src/mode_fenrich/fenrich_read_qtl.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/fenrich_read_tss.o -c src/mode_fenrich/fenrich_read_tss.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_fenrich/../common/data.h:19, from src/mode_fenrich/fenrich_data.h:20, @@ -1436,6 +1471,8 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/fenrich_read_tss.o -c src/mode_fenrich/fenrich_read_tss.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/genrich_binning_process.o -c src/mode_genrich/genrich_binning_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_fenrich/../common/data.h:19, from src/mode_fenrich/fenrich_data.h:20, @@ -1452,12 +1489,11 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/genrich_binning_process.o -c src/mode_genrich/genrich_binning_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_main.o -c src/mode_genrich/genrich_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_genrich/../common/data.h:19, from src/mode_genrich/genrich_data.h:22, - from src/mode_genrich/genrich_main.cpp:16: + from src/mode_genrich/genrich_binning_process.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1470,12 +1506,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/genrich_process.o -c src/mode_genrich/genrich_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/genrich_read_auxillliary_data.o -c src/mode_genrich/genrich_read_auxillliary_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_genrich/../common/data.h:19, from src/mode_genrich/genrich_data.h:22, - from src/mode_genrich/genrich_binning_process.cpp:16: + from src/mode_genrich/genrich_main.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1488,10 +1522,12 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/genrich_process.o -c src/mode_genrich/genrich_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/genrich_read_auxillliary_data.o -c src/mode_genrich/genrich_read_auxillliary_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_genrich/../common/data.h:19, from src/mode_genrich/genrich_data.h:22, - from src/mode_genrich/genrich_read_auxillliary_data.cpp:16: + from src/mode_genrich/genrich_process.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1507,7 +1543,7 @@ In file included from lib/OTools/otools.h:56, from src/mode_genrich/../common/data.h:19, from src/mode_genrich/genrich_data.h:22, - from src/mode_genrich/genrich_process.cpp:16: + from src/mode_genrich/genrich_read_auxillliary_data.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1525,7 +1561,7 @@ In file included from lib/OTools/otools.h:56, from src/mode_genrich/../common/data.h:19, from src/mode_genrich/genrich_data.h:22, - from src/mode_genrich/genrich_read_phenotypes.cpp:16: + from src/mode_genrich/genrich_read_reference_genotypes.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1541,7 +1577,7 @@ In file included from lib/OTools/otools.h:56, from src/mode_genrich/../common/data.h:19, from src/mode_genrich/genrich_data.h:22, - from src/mode_genrich/genrich_read_reference_genotypes.cpp:16: + from src/mode_genrich/genrich_read_phenotypes.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1556,6 +1592,7 @@ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/genrich_routines.o -c src/mode_genrich/genrich_routines.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/gwas_analysis_pass.o -c src/mode_gwas/gwas_analysis_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/gwas_initilization.o -c src/mode_gwas/gwas_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_genrich/../common/data.h:19, from src/mode_genrich/genrich_data.h:22, @@ -1588,7 +1625,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/gwas_initilization.o -c src/mode_gwas/gwas_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_gwas/../common/data.h:19, from src/mode_gwas/gwas_data.h:20, @@ -1606,10 +1642,11 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/gwas_main.o -c src/mode_gwas/gwas_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/gwas_managment.o -c src/mode_gwas/gwas_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_gwas/../common/data.h:19, from src/mode_gwas/gwas_data.h:20, - from src/mode_gwas/gwas_main.cpp:16: + from src/mode_gwas/gwas_managment.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1622,12 +1659,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/gwas_managment.o -c src/mode_gwas/gwas_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/gwas_read_covariates.o -c src/mode_gwas/gwas_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_gwas/../common/data.h:19, from src/mode_gwas/gwas_data.h:20, - from src/mode_gwas/gwas_managment.cpp:16: + from src/mode_gwas/gwas_main.cpp:16: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1640,6 +1675,11 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/gwas_read_covariates.o -c src/mode_gwas/gwas_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +src/mode_gwas/gwas_analysis_pass.cpp: In member function 'void gwas_data::runGwasPassOnVCF(std::string, std::string)': +src/mode_gwas/gwas_analysis_pass.cpp:28:28: warning: ignoring return value of 'int bcf_hdr_set_samples(bcf_hdr_t*, const char*, int)' declared with attribute 'warn_unused_result' [-Wunused-result] + 28 | bcf_hdr_set_samples(hdr, concat_id.c_str(), 0); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from lib/OTools/otools.h:56, from src/mode_gwas/../common/data.h:19, from src/mode_gwas/gwas_data.h:20, @@ -1657,10 +1697,7 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/gwas_read_phenotypes.o -c src/mode_gwas/gwas_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -src/mode_gwas/gwas_analysis_pass.cpp: In member function 'void gwas_data::runGwasPassOnVCF(std::string, std::string)': -src/mode_gwas/gwas_analysis_pass.cpp:28:28: warning: ignoring return value of 'int bcf_hdr_set_samples(bcf_hdr_t*, const char*, int)' declared with attribute 'warn_unused_result' [-Wunused-result] - 28 | bcf_hdr_set_samples(hdr, concat_id.c_str(), 0); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -std=c++0x -o obj/match_main.o -c src/mode_match/match_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_gwas/../common/data.h:19, from src/mode_gwas/gwas_data.h:20, @@ -1677,8 +1714,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/match_main.o -c src/mode_match/match_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/match_managment.o -c src/mode_match/match_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_match/../common/data.h:19, from src/mode_match/match_data.h:20, @@ -1695,6 +1730,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/match_managment.o -c src/mode_match/match_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_match/../common/data.h:19, from src/mode_match/match_data.h:20, @@ -1712,6 +1748,7 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/match_process.o -c src/mode_match/match_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/match_read_genotypes.o -c src/mode_match/match_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_match/../common/data.h:19, from src/mode_match/match_data.h:20, @@ -1728,7 +1765,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/match_read_genotypes.o -c src/mode_match/match_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_match/../common/data.h:19, from src/mode_match/match_data.h:20, @@ -1746,6 +1782,7 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/match_read_sequences.o -c src/mode_match/match_read_sequences.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/pca_main.o -c src/mode_pca/pca_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_match/../common/data.h:19, from src/mode_match/match_data.h:20, @@ -1762,7 +1799,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/pca_main.o -c src/mode_pca/pca_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_pca/../common/data.h:19, from src/mode_pca/pca_data.h:22, @@ -1780,7 +1816,6 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/pca_management.o -c src/mode_pca/pca_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/pca_pca.o -c src/mode_pca/pca_pca.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_pca/../common/data.h:19, from src/mode_pca/pca_data.h:22, @@ -1797,7 +1832,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/pca_read_data.o -c src/mode_pca/pca_read_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/pca_pca.o -c src/mode_pca/pca_pca.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_pca/../common/data.h:19, from src/mode_pca/pca_pca.h:22, @@ -1814,6 +1849,8 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/pca_read_data.o -c src/mode_pca/pca_read_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/quan_main.o -c src/mode_quan/quan_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_pca/../common/data.h:19, from src/mode_pca/pca_data.h:22, @@ -1830,8 +1867,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/quan_main.o -c src/mode_quan/quan_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/quan_readBAM.o -c src/mode_quan/quan_readBAM.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_quan/../common/data.h:19, from src/mode_quan/quan_data.h:21, @@ -1848,6 +1883,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/quan_readBAM.o -c src/mode_quan/quan_readBAM.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_quan/../common/data.h:19, from src/mode_quan/quan_data.h:21, @@ -1933,7 +1969,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/rep_management.o -c src/mode_rep/rep_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rep/../common/data.h:19, from src/mode_rep/rep_data.h:31, @@ -1950,6 +1985,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/rep_management.o -c src/mode_rep/rep_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rep/../common/data.h:19, from src/mode_rep/rep_data.h:31, @@ -1984,7 +2020,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/rep_read_genotypes.o -c src/mode_rep/rep_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rep/../common/data.h:19, from src/mode_rep/rep_data.h:31, @@ -2001,6 +2036,8 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/rep_read_genotypes.o -c src/mode_rep/rep_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/rep_read_phenotypes.o -c src/mode_rep/rep_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rep/../common/data.h:19, from src/mode_rep/rep_data.h:31, @@ -2017,7 +2054,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/rep_read_phenotypes.o -c src/mode_rep/rep_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rep_read_qtls.o -c src/mode_rep/rep_read_qtls.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rep/../common/data.h:19, @@ -2069,8 +2105,6 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/rtc_collapse_phenotypes.o -c src/mode_rtc/rtc_collapse_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/rtc_common.o -c src/mode_rtc/rtc_common.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/rtc_gwas_cis.o -c src/mode_rtc/rtc_gwas_cis.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2087,6 +2121,9 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/rtc_common.o -c src/mode_rtc/rtc_common.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/rtc_gwas_cis.o -c src/mode_rtc/rtc_gwas_cis.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/rtc_gwas_trans.o -c src/mode_rtc/rtc_gwas_trans.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2119,7 +2156,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/rtc_gwas_trans.o -c src/mode_rtc/rtc_gwas_trans.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2154,6 +2190,7 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/rtc_main.o -c src/mode_rtc/rtc_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/rtc_management.o -c src/mode_rtc/rtc_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2170,7 +2207,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/rtc_management.o -c src/mode_rtc/rtc_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2188,7 +2224,6 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/rtc_mergeQTL_cis.o -c src/mode_rtc/rtc_mergeQTL_cis.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/rtc_mergeQTL_trans.o -c src/mode_rtc/rtc_mergeQTL_trans.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2205,6 +2240,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/rtc_mergeQTL_trans.o -c src/mode_rtc/rtc_mergeQTL_trans.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2222,7 +2258,6 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/rtc_read_covariates.o -c src/mode_rtc/rtc_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/rtc_read_genotypes.o -c src/mode_rtc/rtc_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2239,6 +2274,8 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/rtc_read_genotypes.o -c src/mode_rtc/rtc_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/rtc_read_get_hotspots.o -c src/mode_rtc/rtc_read_get_hotspots.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2255,7 +2292,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/rtc_read_get_hotspots.o -c src/mode_rtc/rtc_read_get_hotspots.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/rtc_read_phenotypes.o -c src/mode_rtc/rtc_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2272,7 +2309,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/rtc_read_phenotypes.o -c src/mode_rtc/rtc_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2290,8 +2326,6 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/rtc_sampling.o -c src/mode_rtc/rtc_sampling.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/trans_adjust.o -c src/mode_trans/trans_adjust.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/trans_analysis_pass.o -c src/mode_trans/trans_analysis_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, @@ -2308,6 +2342,8 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/trans_adjust.o -c src/mode_trans/trans_adjust.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/trans_analysis_pass.o -c src/mode_trans/trans_analysis_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_trans/../common/data.h:19, from src/mode_trans/trans_data.h:26, @@ -2324,7 +2360,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/trans_chunking.o -c src/mode_trans/trans_chunking.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_trans/../common/data.h:19, from src/mode_trans/trans_data.h:26, @@ -2341,6 +2376,8 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/trans_chunking.o -c src/mode_trans/trans_chunking.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/trans_initilization.o -c src/mode_trans/trans_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_trans/../common/data.h:19, from src/mode_trans/trans_data.h:26, @@ -2357,7 +2394,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/trans_initilization.o -c src/mode_trans/trans_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_trans/../common/data.h:19, from src/mode_trans/trans_data.h:26, @@ -2477,6 +2513,8 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/union_initilization.o -c src/mode_union/union_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/union_main.o -c src/mode_union/union_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/union_management.o -c src/mode_union/union_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_union/../common/data.h:19, from src/mode_union/union_data.h:20, @@ -2493,9 +2531,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/union_main.o -c src/mode_union/union_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/union_management.o -c src/mode_union/union_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/union_read_covariates.o -c src/mode_union/union_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_union/../common/data.h:19, from src/mode_union/union_data.h:20, @@ -2528,6 +2563,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/union_read_covariates.o -c src/mode_union/union_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_union/../common/data.h:19, from src/mode_union/union_data.h:20, @@ -2545,7 +2581,6 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' g++ -std=c++0x -o obj/union_read_genotypes.o -c src/mode_union/union_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/union_read_get_hotspots.o -c src/mode_union/union_read_get_hotspots.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_union/../common/data.h:19, from src/mode_union/union_data.h:20, @@ -2562,6 +2597,8 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/union_read_get_hotspots.o -c src/mode_union/union_read_get_hotspots.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/union_read_phenotypes.o -c src/mode_union/union_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_union/../common/data.h:19, from src/mode_union/union_data.h:20, @@ -2578,7 +2615,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/union_read_phenotypes.o -c src/mode_union/union_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from lib/OTools/otools.h:56, from src/mode_union/../common/data.h:19, from src/mode_union/union_data.h:20, @@ -2619,14 +2655,14 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j6 install DESTDIR=/build/reproducible-path/qtltools-1.3.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j5 install DESTDIR=/build/reproducible-path/qtltools-1.3.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' mkdir -p -m 755 /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/bin /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/share/man/man1 /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/etc/bash_completion.d install --strip-program=true bin/QTLtools /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/bin install: WARNING: ignoring --strip-program option as -s option was not specified -install --strip-program=true -m 755 scripts/qtltools_runFDR_ftrans.R scripts/qtltools_runFDR_atrans.R scripts/qtltools_runFDR_cis.R scripts/qtltools_plotTrans.R /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/bin +install --strip-program=true -m 755 scripts/qtltools_plotTrans.R scripts/qtltools_runFDR_cis.R scripts/qtltools_runFDR_atrans.R scripts/qtltools_runFDR_ftrans.R /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/bin install: WARNING: ignoring --strip-program option as -s option was not specified -install --strip-program=true -m 644 doc/QTLtools-trans.1 doc/QTLtools-extract.1 doc/QTLtools-rtc-union.1 doc/QTLtools-pca.1 doc/QTLtools.1 doc/QTLtools-rtc.1 doc/QTLtools-rep.1 doc/QTLtools-cis.1 doc/QTLtools-fenrich.1 doc/QTLtools-mbv.1 doc/QTLtools-bamstat.1 doc/QTLtools-gwas.1 doc/QTLtools-correct.1 doc/QTLtools-ase.1 doc/QTLtools-quan.1 doc/QTLtools-fdensity.1 /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/share/man/man1 +install --strip-program=true -m 644 doc/QTLtools-gwas.1 doc/QTLtools-rtc-union.1 doc/QTLtools-cis.1 doc/QTLtools-quan.1 doc/QTLtools-extract.1 doc/QTLtools-fenrich.1 doc/QTLtools-trans.1 doc/QTLtools-fdensity.1 doc/QTLtools-bamstat.1 doc/QTLtools-rep.1 doc/QTLtools-correct.1 doc/QTLtools-ase.1 doc/QTLtools-mbv.1 doc/QTLtools.1 doc/QTLtools-pca.1 doc/QTLtools-rtc.1 /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/share/man/man1 install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -m 644 doc/QTLtools_bash_autocomplete.bash /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/etc/bash_completion.d install: WARNING: ignoring --strip-program option as -s option was not specified @@ -2663,9 +2699,9 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'qtltools-example' in '../qtltools-example_1.3.1+dfsg-4_all.deb'. dpkg-deb: building package 'qtltools-dbgsym' in '../qtltools-dbgsym_1.3.1+dfsg-4_i386.deb'. dpkg-deb: building package 'qtltools' in '../qtltools_1.3.1+dfsg-4_i386.deb'. -dpkg-deb: building package 'qtltools-example' in '../qtltools-example_1.3.1+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../qtltools_1.3.1+dfsg-4_i386.buildinfo dpkg-genchanges --build=binary -O../qtltools_1.3.1+dfsg-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2673,12 +2709,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/12237/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/12237/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/9407 and its subdirectories -I: Current time: Sat Nov 29 20:11:29 -12 2025 -I: pbuilder-time-stamp: 1764490289 +I: removing directory /srv/workspace/pbuilder/12237 and its subdirectories +I: Current time: Mon Oct 28 15:56:18 +14 2024 +I: pbuilder-time-stamp: 1730080578