Diff of the two buildlogs: -- --- b1/build.log 2025-10-27 22:22:10.915374721 +0000 +++ b2/build.log 2025-10-27 22:28:35.183837325 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Nov 29 16:34:08 -12 2026 -I: pbuilder-time-stamp: 1796013248 +I: Current time: Tue Oct 28 12:22:12 +14 2025 +I: pbuilder-time-stamp: 1761603732 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -24,53 +24,85 @@ 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/2819300/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2070644/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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 27 22:22 /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/2070644/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2070644/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fea6885d452e4cc5b5f58177031688ba' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2819300' - PS1='# ' - PS2='> ' + INVOCATION_ID=0a3e3c65de294aa3a58375ccb96f6e38 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=2070644 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.q432lmFf/pbuilderrc_FRYy --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.q432lmFf/b1 --logfile b1/build.log qtltools_1.3.1+dfsg-4.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.q432lmFf/pbuilderrc_Ftry --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.q432lmFf/b2 --logfile b2/build.log qtltools_1.3.1+dfsg-4.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2819300/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2070644/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -239,7 +271,7 @@ Get: 113 http://deb.debian.org/debian forky/main amd64 liblzma-dev amd64 5.8.1-2 [349 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 libhts-dev amd64 1.22.1+ds2-1 [1807 kB] Get: 115 http://deb.debian.org/debian forky/main amd64 r-mathlib amd64 4.5.1-1 [2735 kB] -Fetched 76.4 MB in 2s (45.4 MB/s) +Fetched 76.4 MB in 1s (128 MB/s) Preconfiguring packages ... 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 ... 19900 files and directories currently installed.) @@ -716,7 +748,11 @@ 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/2070644/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2070644/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 @@ -729,7 +765,7 @@ make[1]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' rm -f debian/upstream.example/examples.tar.xz dh_auto_clean - make -j42 clean + make -j40 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' @@ -745,7 +781,7 @@ 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 -j42 INSTALL="install --strip-program=true" + make -j40 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib @@ -787,12 +823,10 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_extract/../common/data.h:19, + from src/mode_extract/extract_data.h:20, + from src/mode_extract/extract_write.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) | ^ @@ -808,7 +842,7 @@ 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_chunking.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) | ^ @@ -824,7 +858,7 @@ 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_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) | ^ @@ -838,9 +872,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_fdensity/fdensity_read_annotation.cpp:16: + from src/mode_correct/../common/data.h:19, + from src/mode_correct/correct_data.h:24, + from src/mode_correct/correct_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) | ^ @@ -854,9 +888,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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_cis/../common/data.h:19, + from src/mode_cis/cis_data.h:33, + from src/mode_cis/cis_conditionnal_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) | ^ @@ -872,7 +906,7 @@ 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_main.cpp:16: + 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) | ^ @@ -886,41 +920,40 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_fenrich/fenrich_management.cpp:16: + from src/mode_cis/../common/data.h:19, + from src/mode_cis/cis_data.h:33, + from src/mode_cis/cis_chunking.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) | ^ lib/OTools/interval_tree.h:76:22: note: remove the '< >' -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, - from src/mode_fdensity/fdensity_process.cpp:17: -lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 76 | IntervalTree(void) - | ^ lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 82 | IntervalTree(const intervalTree& other) { | ^ lib/OTools/interval_tree.h:82:22: note: remove the '< >' -lib/OTools/interval_tree.h:76:22: note: remove the '< >' lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ +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/mode_cis/cis_main.cpp:17: +lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 76 | IntervalTree(void) + | ^ +lib/OTools/interval_tree.h:76:22: note: remove the '< >' lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 82 | IntervalTree(const intervalTree& other) { | ^ -lib/OTools/interval_tree.h:118:13: note: remove the '< >' lib/OTools/interval_tree.h:82:22: note: remove the '< >' lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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_annotations.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) | ^ @@ -936,7 +969,7 @@ 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_read_phenotypes.cpp:16: + from src/mode_cis/cis_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) | ^ @@ -952,7 +985,7 @@ 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_blacklist.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) | ^ @@ -966,9 +999,9 @@ | ^~~~~~~~~~~~~~ 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/mode_cis/cis_initilization.cpp:16: + from src/mode_ase/../common/data.h:19, + from src/mode_ase/ase_data.h:20, + 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) | ^ @@ -984,39 +1017,39 @@ 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_collapse_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) | ^ +lib/OTools/interval_tree.h:76:22: note: remove the '< >' +lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 82 | IntervalTree(const intervalTree& other) { + | ^ +lib/OTools/interval_tree.h:82:22: note: remove the '< >' +lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 118 | intervalVector& ivals, + | ^~~~~~~~~~~~~~ +lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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_ase/../common/data.h:19, + from src/mode_ase/ase_data.h:20, + 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) | ^ lib/OTools/interval_tree.h:76:22: note: remove the '< >' -lib/OTools/interval_tree.h:76:22: note: remove the '< >' lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 82 | IntervalTree(const intervalTree& other) { | ^ -lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 82 | IntervalTree(const intervalTree& other) { - | ^ -lib/OTools/interval_tree.h:82:22: note: remove the '< >' lib/OTools/interval_tree.h:82:22: note: remove the '< >' lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ -lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 118 | intervalVector& ivals, - | ^~~~~~~~~~~~~~ -lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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/mode_cis/cis_management.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) | ^ @@ -1030,9 +1063,9 @@ | ^~~~~~~~~~~~~~ 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/mode_cis/cis_read_covariates.cpp:16: + 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: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1046,9 +1079,9 @@ | ^~~~~~~~~~~~~~ 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/mode_cis/cis_conditionnal_pass.cpp:16: + from src/mode_fdensity/../common/data.h:19, + from src/mode_fdensity/fdensity_data.h:20, + from src/mode_fdensity/fdensity_read_annotation.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) | ^ @@ -1080,22 +1113,23 @@ 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, - from src/mode_fdensity/fdensity_main.cpp:16: + from src/mode_fdensity/fdensity_read_qtl.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) | ^ lib/OTools/interval_tree.h:76:22: note: remove the '< >' -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_processing.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) +lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 82 | IntervalTree(const intervalTree& other) { | ^ +lib/OTools/interval_tree.h:82:22: note: remove the '< >' +lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 118 | intervalVector& ivals, + | ^~~~~~~~~~~~~~ +lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_fenrich/fenrich_main.cpp:16: + from src/mode_fdensity/../common/data.h:19, + from src/mode_fdensity/fdensity_data.h:20, + from src/mode_fdensity/fdensity_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) | ^ @@ -1103,32 +1137,31 @@ lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 82 | IntervalTree(const intervalTree& other) { | ^ -lib/OTools/interval_tree.h:76:22: note: remove the '< >' lib/OTools/interval_tree.h:82:22: note: remove the '< >' -lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 82 | IntervalTree(const intervalTree& other) { +lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 118 | intervalVector& ivals, + | ^~~~~~~~~~~~~~ +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: +lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 76 | IntervalTree(void) | ^ +lib/OTools/interval_tree.h:76:22: note: remove the '< >' lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 82 | IntervalTree(const intervalTree& other) { | ^ lib/OTools/interval_tree.h:82:22: note: remove the '< >' -lib/OTools/interval_tree.h:82:22: note: remove the '< >' lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 118 | intervalVector& ivals, - | ^~~~~~~~~~~~~~ -lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 118 | intervalVector& ivals, - | ^~~~~~~~~~~~~~ -lib/OTools/interval_tree.h:118:13: note: remove the '< >' -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_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) | ^ @@ -1142,9 +1175,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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_managment.cpp:16: + from src/mode_cis/../common/data.h:19, + from src/mode_cis/cis_data.h:33, + from src/mode_cis/cis_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) | ^ @@ -1158,9 +1191,9 @@ | ^~~~~~~~~~~~~~ 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/mode_cis/cis_collapse_phenotypes.cpp:16: + from src/mode_correct/../common/data.h:19, + from src/mode_correct/correct_data.h:24, + from src/mode_correct/correct_processing.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) | ^ @@ -1174,9 +1207,9 @@ | ^~~~~~~~~~~~~~ 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_read_genotypes.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) | ^ @@ -1190,9 +1223,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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_main.cpp:16: + from src/mode_correct/../common/data.h:19, + from src/mode_correct/correct_data.h:24, + from src/mode_correct/correct_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) | ^ @@ -1208,7 +1241,7 @@ 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_permutation_pass.cpp:16: + from src/mode_cis/cis_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) | ^ @@ -1216,14 +1249,18 @@ lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 82 | IntervalTree(const intervalTree& other) { | ^ +lib/OTools/interval_tree.h:82:22: note: remove the '< >' +lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 118 | intervalVector& ivals, + | ^~~~~~~~~~~~~~ +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/mode_cis/cis_read_genotypes.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) | ^ -lib/OTools/interval_tree.h:82:22: note: remove the '< >' lib/OTools/interval_tree.h:76:22: note: remove the '< >' lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 82 | IntervalTree(const intervalTree& other) { @@ -1233,14 +1270,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 118 | intervalVector& ivals, - | ^~~~~~~~~~~~~~ -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/mode_cis/cis_read_thresholds.cpp:16: + from src/mode_cis/cis_permutation_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) | ^ @@ -1254,9 +1287,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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_read_data.cpp:16: + from src/mode_ase/../common/data.h:19, + from src/mode_ase/ase_data.h:20, + from src/mode_ase/ase_read_blacklist.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) | ^ @@ -1270,9 +1303,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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_write.cpp:16: + from src/mode_cis/../common/data.h:19, + from src/mode_cis/cis_data.h:33, + from src/mode_cis/cis_initilization.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) | ^ @@ -1286,9 +1319,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_fdensity/fdensity_read_qtl.cpp:16: + from src/mode_bamstat/../common/data.h:19, + from src/mode_bamstat/bamstat_data.h:20, + from src/mode_bamstat/bamstat_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) | ^ @@ -1302,13 +1335,21 @@ | ^~~~~~~~~~~~~~ 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/mode_cis/cis_main.cpp:17: + 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: +lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 76 | IntervalTree(void) + | ^ +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_read_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) | ^ lib/OTools/interval_tree.h:76:22: note: remove the '< >' +lib/OTools/interval_tree.h:76:22: note: remove the '< >' lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 82 | IntervalTree(const intervalTree& other) { | ^ @@ -1317,14 +1358,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -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_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) - | ^ -lib/OTools/interval_tree.h:76:22: note: remove the '< >' lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 82 | IntervalTree(const intervalTree& other) { | ^ @@ -1334,9 +1367,9 @@ | ^~~~~~~~~~~~~~ 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/mode_bamstat/../common/data.h:19, + from src/mode_bamstat/bamstat_data.h:20, + from src/mode_bamstat/bamstat_read_annotations.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) | ^ @@ -1352,7 +1385,7 @@ 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_learn_beta.cpp:16: + from src/mode_cis/cis_learn_dof.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) | ^ @@ -1366,9 +1399,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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_extract/../common/data.h:19, + from src/mode_extract/extract_data.h:20, + from src/mode_extract/extract_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) | ^ @@ -1382,9 +1415,9 @@ | ^~~~~~~~~~~~~~ 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_read_fasta.cpp:16: + from src/mode_fdensity/../common/data.h:19, + from src/mode_fdensity/fdensity_data.h:20, + from src/mode_fdensity/fdensity_process.cpp:17: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -1398,9 +1431,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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_main.cpp:16: + from src/mode_cis/../common/data.h:19, + from src/mode_cis/cis_data.h:33, + from src/mode_cis/cis_read_thresholds.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) | ^ @@ -1414,9 +1447,9 @@ | ^~~~~~~~~~~~~~ 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_read_sequences.cpp:16: + from src/mode_cis/../common/data.h:19, + from src/mode_cis/cis_data.h:33, + from src/mode_cis/cis_learn_beta.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) | ^ @@ -1429,9 +1462,17 @@ 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/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_fenrich/../common/data.h:19, + from src/mode_fenrich/fenrich_data.h:20, + from src/mode_fenrich/fenrich_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) | ^ @@ -1445,9 +1486,9 @@ | ^~~~~~~~~~~~~~ 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/mode_cis/cis_learn_dof.cpp:16: + from src/mode_fenrich/../common/data.h:19, + from src/mode_fenrich/fenrich_data.h:20, + from src/mode_fenrich/fenrich_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) | ^ @@ -1460,13 +1501,6 @@ 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/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -1483,7 +1517,10 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -1500,8 +1537,6 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -1550,7 +1585,36 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +In file included from /usr/include/eigen3/Eigen/Core:341, + from /usr/include/eigen3/Eigen/Dense:1, + from lib/OTools/residualizer.h:36, + from lib/OTools/otools.h:60: +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] + 327 | internal::triangular_matrix_vector_product + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 328 | + | ~~~~~~~~~ + 332 | ::run(actualLhs.rows(),actualLhs.cols(), + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 333 | actualLhs.data(),actualLhs.outerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 334 | actualRhsPtr,1, + | ~~~~~~~~~~~~~~~ + 335 | dest.data(),dest.innerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 336 | actualAlpha); + | ~~~~~~~~~~~~ +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here + 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -1567,6 +1631,7 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -1585,10 +1650,71 @@ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_read_phenotypes.o -c src/mode_genrich/genrich_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/genrich_read_reference_genotypes.o -c src/mode_genrich/genrich_read_reference_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +In file included from /usr/include/eigen3/Eigen/Core:341, + from /usr/include/eigen3/Eigen/Dense:1, + from lib/OTools/residualizer.h:36, + from lib/OTools/otools.h:60: +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] + 327 | internal::triangular_matrix_vector_product + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 328 | + | ~~~~~~~~~ + 332 | ::run(actualLhs.rows(),actualLhs.cols(), + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 333 | actualLhs.data(),actualLhs.outerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 334 | actualRhsPtr,1, + | ~~~~~~~~~~~~~~~ + 335 | dest.data(),dest.innerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 336 | actualAlpha); + | ~~~~~~~~~~~~ +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here + 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/eigen3/Eigen/Core:341, + from /usr/include/eigen3/Eigen/Dense:1, + from lib/OTools/residualizer.h:36, + from lib/OTools/otools.h:60: +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] + 327 | internal::triangular_matrix_vector_product + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 328 | + | ~~~~~~~~~ + 332 | ::run(actualLhs.rows(),actualLhs.cols(), + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 333 | actualLhs.data(),actualLhs.outerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 334 | actualRhsPtr,1, + | ~~~~~~~~~~~~~~~ + 335 | dest.data(),dest.innerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 336 | actualAlpha); + | ~~~~~~~~~~~~ +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here + 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_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) | ^ @@ -1601,12 +1727,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/genrich_read_reference_genotypes.o -c src/mode_genrich/genrich_read_reference_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_phenotypes.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) | ^ @@ -1619,12 +1743,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_routines.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) | ^ @@ -1640,7 +1762,7 @@ 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_routines.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) | ^ @@ -1653,7 +1775,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -1670,6 +1791,7 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -1686,6 +1808,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib @@ -1705,13 +1828,44 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +In file included from /usr/include/eigen3/Eigen/Core:341, + from /usr/include/eigen3/Eigen/Dense:1, + from lib/OTools/residualizer.h:36, + from lib/OTools/otools.h:60: +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] + 327 | internal::triangular_matrix_vector_product + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 328 | + | ~~~~~~~~~ + 332 | ::run(actualLhs.rows(),actualLhs.cols(), + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 333 | actualLhs.data(),actualLhs.outerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 334 | actualRhsPtr,1, + | ~~~~~~~~~~~~~~~ + 335 | dest.data(),dest.innerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 336 | actualAlpha); + | ~~~~~~~~~~~~ +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here + 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_read_phenotypes.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) | ^ @@ -1724,10 +1878,13 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_read_covariates.cpp:16: + from src/mode_gwas/gwas_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) | ^ @@ -1743,7 +1900,7 @@ 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_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) | ^ @@ -1756,10 +1913,15 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/quan_readGTF.o -c src/mode_quan/quan_readGTF.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/quan_writeResults.o -c src/mode_quan/quan_writeResults.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_match/match_managment.cpp:16: + from src/mode_match/match_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) | ^ @@ -1775,7 +1937,7 @@ 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, - from src/mode_match/match_process.cpp:16: + from src/mode_match/match_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) | ^ @@ -1788,13 +1950,11 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/quan_xxhash.o -c src/mode_quan/quan_xxhash.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_match/match_main.cpp:16: + from src/mode_match/match_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) | ^ @@ -1807,14 +1967,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_match/match_read_sequences.cpp:16: + from src/mode_match/match_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) | ^ @@ -1828,9 +1984,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_pca/pca_main.cpp:16: + from src/mode_match/../common/data.h:19, + from src/mode_match/match_data.h:20, + from src/mode_match/match_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) | ^ @@ -1843,10 +1999,12 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/rep_initilization.o -c src/mode_rep/rep_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +g++ -std=c++0x -o obj/rep_main.o -c src/mode_rep/rep_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_match/match_read_genotypes.cpp:16: + from src/mode_pca/../common/data.h:19, + from src/mode_pca/pca_data.h:22, + from src/mode_pca/pca_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) | ^ @@ -1859,8 +2017,6 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/quan_readGTF.o -c src/mode_quan/quan_readGTF.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -1877,45 +2033,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/quan_writeResults.o -c src/mode_quan/quan_writeResults.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/quan_xxhash.o -c src/mode_quan/quan_xxhash.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/rep_initilization.o -c src/mode_rep/rep_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/rep_main.o -c src/mode_rep/rep_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/rep_nominal_pass.o -c src/mode_rep/rep_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -In file included from /usr/include/eigen3/Eigen/Core:341, - from /usr/include/eigen3/Eigen/Dense:1, - from lib/OTools/residualizer.h:36, - from lib/OTools/otools.h:60: -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] - 327 | internal::triangular_matrix_vector_product - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 328 | - | ~~~~~~~~~ - 332 | ::run(actualLhs.rows(),actualLhs.cols(), - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 333 | actualLhs.data(),actualLhs.outerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 334 | actualRhsPtr,1, - | ~~~~~~~~~~~~~~~ - 335 | dest.data(),dest.innerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 336 | actualAlpha); - | ~~~~~~~~~~~~ -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here - 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, - from src/mode_pca/pca_read_data.cpp:16: + from src/mode_quan/../common/data.h:19, + from src/mode_quan/quan_data.h:21, + from src/mode_quan/quan_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) | ^ @@ -1928,12 +2049,11 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -g++ -std=c++0x -o obj/rep_read_covariates.o -c src/mode_rep/rep_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_pca/pca_pca.cpp:16: + from src/mode_pca/pca_data.h:22, + from src/mode_pca/pca_read_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) | ^ @@ -1949,7 +2069,7 @@ 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, - from src/mode_quan/quan_main.cpp:16: + from src/mode_quan/quan_readBAM.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) | ^ @@ -1965,7 +2085,7 @@ 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, - from src/mode_quan/quan_readBAM.cpp:16: + from src/mode_quan/quan_readGTF.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) | ^ @@ -1979,9 +2099,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_quan/quan_readGTF.cpp:16: + from src/mode_rep/../common/data.h:19, + from src/mode_rep/rep_data.h:31, + from src/mode_rep/rep_initilization.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) | ^ @@ -1995,9 +2115,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_rep/rep_initilization.cpp:16: + from src/mode_pca/../common/data.h:19, + from src/mode_pca/pca_pca.h:22, + from src/mode_pca/pca_pca.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) | ^ @@ -2013,7 +2133,7 @@ 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, - from src/mode_quan/quan_writeResults.cpp:16: + from src/mode_quan/quan_xxhash.cpp:109: lib/OTools/interval_tree.h:76:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 76 | IntervalTree(void) | ^ @@ -2027,9 +2147,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_quan/quan_xxhash.cpp:109: + from src/mode_rep/../common/data.h:19, + from src/mode_rep/rep_data.h:31, + from src/mode_rep/rep_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) | ^ @@ -2043,9 +2163,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_rep/rep_main.cpp:16: + from src/mode_quan/../common/data.h:19, + from src/mode_quan/quan_data.h:21, + from src/mode_quan/quan_writeResults.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) | ^ @@ -2058,64 +2178,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -In file included from /usr/include/eigen3/Eigen/Core:341, - from /usr/include/eigen3/Eigen/Dense:1, - from lib/OTools/residualizer.h:36, - from lib/OTools/otools.h:60: -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] - 327 | internal::triangular_matrix_vector_product - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 328 | - | ~~~~~~~~~ - 332 | ::run(actualLhs.rows(),actualLhs.cols(), - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 333 | actualLhs.data(),actualLhs.outerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 334 | actualRhsPtr,1, - | ~~~~~~~~~~~~~~~ - 335 | dest.data(),dest.innerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 336 | actualAlpha); - | ~~~~~~~~~~~~ -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here - 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/eigen3/Eigen/Core:341, - from /usr/include/eigen3/Eigen/Dense:1, - from lib/OTools/residualizer.h:36, - from lib/OTools/otools.h:60: -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] - 327 | internal::triangular_matrix_vector_product - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 328 | - | ~~~~~~~~~ - 332 | ::run(actualLhs.rows(),actualLhs.cols(), - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 333 | actualLhs.data(),actualLhs.outerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 334 | actualRhsPtr,1, - | ~~~~~~~~~~~~~~~ - 335 | dest.data(),dest.innerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 336 | actualAlpha); - | ~~~~~~~~~~~~ -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here - 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -std=c++0x -o obj/rep_nominal_pass.o -c src/mode_rep/rep_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2132,6 +2195,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/rep_read_covariates.o -c src/mode_rep/rep_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2148,6 +2212,8 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2164,6 +2230,7 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2180,36 +2247,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -In file included from /usr/include/eigen3/Eigen/Core:341, - from /usr/include/eigen3/Eigen/Dense:1, - from lib/OTools/residualizer.h:36, - from lib/OTools/otools.h:60: -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] - 327 | internal::triangular_matrix_vector_product - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 328 | - | ~~~~~~~~~ - 332 | ::run(actualLhs.rows(),actualLhs.cols(), - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 333 | actualLhs.data(),actualLhs.outerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 334 | actualRhsPtr,1, - | ~~~~~~~~~~~~~~~ - 335 | dest.data(),dest.innerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 336 | actualAlpha); - | ~~~~~~~~~~~~ -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here - 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2226,7 +2263,6 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_chunking.o -c src/mode_rtc/rtc_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2278,6 +2314,12 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2294,18 +2336,11 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' -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/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_initilization.o -c src/mode_rtc/rtc_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_rtc/rtc_initilization.cpp:16: + from src/mode_rtc/rtc_gwas_cis.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) | ^ @@ -2318,10 +2353,11 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_rtc/rtc_gwas_cis.cpp:16: + from src/mode_rtc/rtc_gwas_trans.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) | ^ @@ -2337,7 +2373,7 @@ 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, - from src/mode_rtc/rtc_gwas_trans.cpp:16: + from src/mode_rtc/rtc_initilization.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) | ^ @@ -2350,7 +2386,6 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2367,11 +2402,14 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_rtc/rtc_management.cpp:16: + from src/mode_rtc/rtc_mergeQTL_cis.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) | ^ @@ -2384,13 +2422,10 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_rtc/rtc_mergeQTL_cis.cpp:16: + from src/mode_rtc/rtc_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) | ^ @@ -2403,9 +2438,6 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2422,8 +2454,8 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2440,10 +2472,12 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_rtc/rtc_read_get_hotspots.cpp:16: + from src/mode_rtc/rtc_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) | ^ @@ -2459,7 +2493,7 @@ 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, - from src/mode_rtc/rtc_read_genotypes.cpp:16: + from src/mode_rtc/rtc_read_get_hotspots.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) | ^ @@ -2472,6 +2506,8 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2488,7 +2524,6 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2505,6 +2540,7 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, @@ -2574,57 +2610,6 @@ g++ -std=c++0x -o obj/trans_main.o -c src/mode_trans/trans_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_managment.o -c src/mode_trans/trans_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_read_covariates.o -c src/mode_trans/trans_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/trans_read_phenotypes.o -c src/mode_trans/trans_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/trans_read_samples.o -c src/mode_trans/trans_read_samples.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_trans/trans_learn_beta.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) - | ^ -lib/OTools/interval_tree.h:76:22: note: remove the '< >' -lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 82 | IntervalTree(const intervalTree& other) { - | ^ -lib/OTools/interval_tree.h:82:22: note: remove the '< >' -lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 118 | intervalVector& ivals, - | ^~~~~~~~~~~~~~ -lib/OTools/interval_tree.h:118:13: note: remove the '< >' -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, - from src/mode_trans/trans_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) - | ^ -lib/OTools/interval_tree.h:76:22: note: remove the '< >' -lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 82 | IntervalTree(const intervalTree& other) { - | ^ -lib/OTools/interval_tree.h:82:22: note: remove the '< >' -lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 118 | intervalVector& ivals, - | ^~~~~~~~~~~~~~ -lib/OTools/interval_tree.h:118:13: note: remove the '< >' -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, - from src/mode_trans/trans_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) - | ^ -lib/OTools/interval_tree.h:76:22: note: remove the '< >' -lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 82 | IntervalTree(const intervalTree& other) { - | ^ -lib/OTools/interval_tree.h:82:22: note: remove the '< >' -lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 118 | intervalVector& ivals, - | ^~~~~~~~~~~~~~ -lib/OTools/interval_tree.h:118:13: note: remove the '< >' In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, @@ -2657,7 +2642,7 @@ 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, - from src/mode_trans/trans_read_phenotypes.cpp:16: + from src/mode_trans/trans_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) | ^ @@ -2673,7 +2658,7 @@ 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, - from src/mode_trans/trans_read_covariates.cpp:16: + from src/mode_trans/trans_learn_beta.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) | ^ @@ -2686,10 +2671,11 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/trans_read_phenotypes.o -c src/mode_trans/trans_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_trans/trans_read_samples.cpp:16: + from src/mode_trans/trans_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) | ^ @@ -2703,9 +2689,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_union/union_initilization.cpp:16: + from src/mode_trans/../common/data.h:19, + from src/mode_trans/trans_data.h:26, + from src/mode_trans/trans_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) | ^ @@ -2718,13 +2704,13 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +g++ -std=c++0x -o obj/trans_read_samples.o -c src/mode_trans/trans_read_samples.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_union/union_main.cpp:16: + from src/mode_trans/../common/data.h:19, + from src/mode_trans/trans_data.h:26, + from src/mode_trans/trans_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) | ^ @@ -2738,9 +2724,9 @@ | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' 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, - from src/mode_union/union_management.cpp:16: + from src/mode_trans/../common/data.h:19, + from src/mode_trans/trans_data.h:26, + from src/mode_trans/trans_read_samples.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) | ^ @@ -2753,14 +2739,10 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib -g++ -std=c++0x -o obj/union_union.o -c src/mode_union/union_union.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_union/union_read_covariates.cpp:16: + from src/mode_union/union_initilization.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) | ^ @@ -2773,10 +2755,12 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ lib/OTools/interval_tree.h:118:13: note: remove the '< >' +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_union/union_read_genotypes.cpp:16: + from src/mode_union/union_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) | ^ @@ -2789,10 +2773,13 @@ 118 | intervalVector& ivals, | ^~~~~~~~~~~~~~ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, - from src/mode_union/union_read_get_hotspots.cpp:16: + from src/mode_union/union_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) | ^ @@ -2808,7 +2795,7 @@ 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, - from src/mode_union/union_union.cpp:16: + from src/mode_union/union_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) | ^ @@ -2824,7 +2811,7 @@ 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, - from src/mode_union/union_read_phenotypes.cpp:16: + from src/mode_union/union_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) | ^ @@ -2866,6 +2853,7 @@ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -std=c++0x -o obj/union_union.o -c src/mode_union/union_union.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from src/mode_pca/pca_pca.h:21: @@ -2894,11 +2882,59 @@ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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, + from src/mode_union/union_read_get_hotspots.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) + | ^ +lib/OTools/interval_tree.h:76:22: note: remove the '< >' +lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 82 | IntervalTree(const intervalTree& other) { + | ^ +lib/OTools/interval_tree.h:82:22: note: remove the '< >' +lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 118 | intervalVector& ivals, + | ^~~~~~~~~~~~~~ +lib/OTools/interval_tree.h:118:13: note: remove the '< >' +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, + from src/mode_union/union_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) + | ^ +lib/OTools/interval_tree.h:76:22: note: remove the '< >' +lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 82 | IntervalTree(const intervalTree& other) { + | ^ +lib/OTools/interval_tree.h:82:22: note: remove the '< >' +lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 118 | intervalVector& ivals, + | ^~~~~~~~~~~~~~ +lib/OTools/interval_tree.h:118:13: note: remove the '< >' +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, + from src/mode_union/union_union.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) + | ^ +lib/OTools/interval_tree.h:76:22: note: remove the '< >' +lib/OTools/interval_tree.h:82:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 82 | IntervalTree(const intervalTree& other) { + | ^ +lib/OTools/interval_tree.h:82:22: note: remove the '< >' +lib/OTools/interval_tree.h:118:13: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 118 | intervalVector& ivals, + | ^~~~~~~~~~~~~~ +lib/OTools/interval_tree.h:118:13: note: remove the '< >' In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60: -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2920,14 +2956,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60: -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2949,7 +2985,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:341, @@ -3046,14 +3082,14 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j42 install DESTDIR=/build/reproducible-path/qtltools-1.3.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + make -j40 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_cis.R scripts/qtltools_runFDR_atrans.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_runFDR_ftrans.R scripts/qtltools_plotTrans.R scripts/qtltools_runFDR_cis.R scripts/qtltools_runFDR_atrans.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-ase.1 doc/QTLtools-rtc-union.1 doc/QTLtools-correct.1 doc/QTLtools-trans.1 doc/QTLtools.1 doc/QTLtools-gwas.1 doc/QTLtools-cis.1 doc/QTLtools-pca.1 doc/QTLtools-fenrich.1 doc/QTLtools-quan.1 doc/QTLtools-rtc.1 doc/QTLtools-rep.1 doc/QTLtools-extract.1 doc/QTLtools-fdensity.1 doc/QTLtools-bamstat.1 doc/QTLtools-mbv.1 /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/share/man/man1 +install --strip-program=true -m 644 doc/QTLtools-mbv.1 doc/QTLtools-gwas.1 doc/QTLtools-rtc-union.1 doc/QTLtools-pca.1 doc/QTLtools-extract.1 doc/QTLtools-bamstat.1 doc/QTLtools-fenrich.1 doc/QTLtools-fdensity.1 doc/QTLtools.1 doc/QTLtools-quan.1 doc/QTLtools-ase.1 doc/QTLtools-rep.1 doc/QTLtools-trans.1 doc/QTLtools-correct.1 doc/QTLtools-rtc.1 doc/QTLtools-cis.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 @@ -3089,8 +3125,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'qtltools-dbgsym' in '../qtltools-dbgsym_1.3.1+dfsg-4_amd64.deb'. 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_amd64.deb'. dpkg-deb: building package 'qtltools' in '../qtltools_1.3.1+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../qtltools_1.3.1+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../qtltools_1.3.1+dfsg-4_amd64.changes @@ -3099,12 +3135,14 @@ 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/2070644/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2070644/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/2819300 and its subdirectories -I: Current time: Sun Nov 29 16:45:09 -12 2026 -I: pbuilder-time-stamp: 1796013909 +I: removing directory /srv/workspace/pbuilder/2070644 and its subdirectories +I: Current time: Tue Oct 28 12:28:34 +14 2025 +I: pbuilder-time-stamp: 1761604114