Diff of the two buildlogs: -- --- b1/build.log 2025-10-24 08:33:14.765747799 +0000 +++ b2/build.log 2025-10-24 08:42:47.678437748 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Nov 26 02:52:20 -12 2026 -I: pbuilder-time-stamp: 1795704740 +I: Current time: Fri Oct 24 22:33:19 +14 2025 +I: pbuilder-time-stamp: 1761294799 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ dpkg-source: info: applying simde I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2955330/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2711647/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 24 08:34 /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/2711647/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2711647/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='46016786c8744f45bbc6423b95f7d90f' - 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='2955330' - PS1='# ' - PS2='> ' + INVOCATION_ID=a6a54399f1d14425b27445dc57d39d72 + 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=2711647 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.ZTxVM3CB/pbuilderrc_2Mf2 --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.ZTxVM3CB/b1 --logfile b1/build.log last-align_1645-1.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.ZTxVM3CB/pbuilderrc_bqV2 --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.ZTxVM3CB/b2 --logfile b2/build.log last-align_1645-1.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 ionos15-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/2955330/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2711647/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -197,7 +229,7 @@ Get: 78 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 32.6 MB in 0s (140 MB/s) +Fetched 32.6 MB in 1s (46.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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.) @@ -480,8 +512,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Nov 26 14:53:12 UTC 2026. -Universal Time is now: Thu Nov 26 14:53:12 UTC 2026. +Local time is now: Fri Oct 24 08:34:53 UTC 2025. +Universal Time is now: Fri Oct 24 08:34:53 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -550,7 +582,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/last-align-1645/ && 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 > ../last-align_1645-1_source.changes +I: user script /srv/workspace/pbuilder/2711647/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2711647/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/last-align-1645/ && 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 > ../last-align_1645-1_source.changes dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1645-1 dpkg-buildpackage: info: source distribution unstable @@ -563,37 +599,37 @@ make[1]: Entering directory '/build/reproducible-path/last-align-1645' for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ dh_auto_clean -- SFX=-${SIMD} ; done - make -j42 clean SFX=-avx2 + make -j40 clean SFX=-avx2 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-avx2 ../bin/lastal-avx2 ../bin/last-split-avx2 ../bin/last-merge-batches-avx2 ../bin/last-pair-probs-avx2 *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 clean SFX=-avx + make -j40 clean SFX=-avx make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-avx ../bin/lastal-avx ../bin/last-split-avx ../bin/last-merge-batches-avx ../bin/last-pair-probs-avx *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 clean SFX=-sse4.1 + make -j40 clean SFX=-sse4.1 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-sse4.1 ../bin/lastal-sse4.1 ../bin/last-split-sse4.1 ../bin/last-merge-batches-sse4.1 ../bin/last-pair-probs-sse4.1 *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 clean SFX=-ssse3 + make -j40 clean SFX=-ssse3 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-ssse3 ../bin/lastal-ssse3 ../bin/last-split-ssse3 ../bin/last-merge-batches-ssse3 ../bin/last-pair-probs-ssse3 *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 clean SFX=-sse3 + make -j40 clean SFX=-sse3 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-sse3 ../bin/lastal-sse3 ../bin/last-split-sse3 ../bin/last-merge-batches-sse3 ../bin/last-pair-probs-sse3 *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 clean SFX=-sse2 + make -j40 clean SFX=-sse2 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-sse2 ../bin/lastal-sse2 ../bin/last-split-sse2 ../bin/last-merge-batches-sse2 ../bin/last-pair-probs-sse2 *.o* */*.o* @@ -622,7 +658,7 @@ find . -name '*.o' -delete ; \ find . -name '*.o5' -delete ; \ done - make -j42 INSTALL="install --strip-program=true" all SFX=-avx2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx2" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2" + make -j40 INSTALL="install --strip-program=true" all SFX=-avx2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx2" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2" make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o Alphabet.o Alphabet.cc @@ -669,8 +705,6 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -678,6 +712,8 @@ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_basic.o alp/sls_basic.cpp @@ -695,6 +731,8 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -703,22 +741,19 @@ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ -alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] - 116 | virtual inline void copy (const DynProgProb &dynProgProb_) - | ^~~~ -alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ - 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) - | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp +alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] + 116 | virtual inline void copy (const DynProgProb &dynProgProb_) + | ^~~~ +alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ + 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) + | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/last-split-main.o split/last-split-main.cc In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -727,21 +762,19 @@ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ -alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] - 124 | virtual void copy ( - | ^~~~ -alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ - 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) - | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/last-split.o split/last-split.cc -cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx2 -c -o last-merge-batches.o last-merge-batches.c -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o last-pair-probs.o last-pair-probs.cc +alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] + 124 | virtual void copy ( + | ^~~~ +alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ + 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) + | ^~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/last-split-main.o split/last-split-main.cc In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -762,6 +795,9 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/last-split.o split/last-split.cc +cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx2 -c -o last-merge-batches.o last-merge-batches.c +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o ScoreMatrix.o ScoreMatrix.cc @@ -775,10 +811,6 @@ lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 372 | std::cout.write((char *)m.qualityReader() + b, e - b); | ^~~~~~~~~~~~~~~~~~~~~~~~~ -alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: -alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] - 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; - | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, @@ -796,6 +828,10 @@ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ +alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: +alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] + 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; + | ^~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-avx2 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-avx2 Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz @@ -815,7 +851,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-avx2 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 INSTALL="install --strip-program=true" all SFX=-avx CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx" + make -j40 INSTALL="install --strip-program=true" all SFX=-avx CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx" make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o Alphabet.o Alphabet.cc @@ -860,8 +896,6 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -869,13 +903,15 @@ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] 190 | size_t saBeg, size_t saEnd) { | ~~~~~~~^~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp @@ -883,57 +919,54 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_random.o alp/njn_random.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_dynprogproblim.cpp:37: + from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ -alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] - 116 | virtual inline void copy (const DynProgProb &dynProgProb_) - | ^~~~ -alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ - 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) - | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/last-split-main.o split/last-split-main.cc +alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] + 116 | virtual inline void copy (const DynProgProb &dynProgProb_) + | ^~~~ +alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ + 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) + | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_random.o alp/njn_random.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstat.cpp:39: + from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ -alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] - 116 | virtual inline void copy (const DynProgProb &dynProgProb_) - | ^~~~ -alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ - 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) - | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] + 116 | virtual inline void copy (const DynProgProb &dynProgProb_) + | ^~~~ +alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ + 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) + | ^~~~ In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstatutil.cpp:39: + from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -952,6 +985,9 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx -c -o last-merge-batches.o last-merge-batches.c g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o last-pair-probs.o last-pair-probs.cc @@ -965,10 +1001,6 @@ lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 372 | std::cout.write((char *)m.qualityReader() + b, e - b); | ^~~~~~~~~~~~~~~~~~~~~~~~~ -alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: -alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] - 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; - | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, @@ -986,9 +1018,12 @@ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ +alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: +alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] + 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; + | ^~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-avx last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-avx Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -1002,10 +1037,11 @@ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-avx Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 INSTALL="install --strip-program=true" all SFX=-sse4.1 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse4.1" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1" + make -j40 INSTALL="install --strip-program=true" all SFX=-sse4.1 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse4.1" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1" make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o Alphabet.o Alphabet.cc @@ -1050,8 +1086,6 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -1059,96 +1093,92 @@ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp -In file included from tantan.cc:5: -mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: -mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] - 20 | static inline SimdInt simdZero() { - | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerFrame.cc:4: + from GappedXdropAlignerDna.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerPssm.cc:3: + from Centroid.hh:7, + from Alignment.hh:8, + from Alignment.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerDna.cc:4: +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp +In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner3frame.cc:53: + from GappedXdropAligner.cc:49: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, - from Centroid.cc:4: + from Alignment.hh:8, + from AlignmentPot.hh:8, + from AlignmentPot.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from Alignment.cc:3: + from GappedXdropAlignerFrame.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from AlignmentPot.hh:8, - from AlignmentPot.cc:3: + from GappedXdropAlignerPssm.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: -SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] - 190 | size_t saBeg, size_t saEnd) { - | ~~~~~~~^~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp.o alp/sls_alp.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_basic.o alp/sls_basic.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from AlignmentWrite.cc:3: + from GappedXdropAligner2qual.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner2qual.cc:3: + from Centroid.hh:7, + from Centroid.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner.cc:49: + from Centroid.hh:7, + from Alignment.hh:8, + from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: +SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] + 190 | size_t saBeg, size_t saEnd) { + | ~~~~~~~^~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: @@ -1161,36 +1191,41 @@ /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp.o alp/sls_alp.cpp +In file included from GappedXdropAligner.hh:52, + from GappedXdropAligner3frame.cc:53: +mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: +mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] + 20 | static inline SimdInt simdZero() { + | ^ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_basic.o alp/sls_basic.cpp In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 297 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_random.o alp/njn_random.cpp -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_random.o alp/njn_random.cpp alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ @@ -1206,10 +1241,15 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/last-split-main.o split/last-split-main.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/last-split.o split/last-split.cc In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstat.cpp:39: + from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -1228,14 +1268,9 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/last-split-main.o split/last-split-main.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse4.1 -c -o last-merge-batches.o last-merge-batches.c -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o last-pair-probs.o last-pair-probs.cc In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstatutil.cpp:39: + from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -1254,16 +1289,13 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o lastdb.o lastdb.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o LastalArguments.o LastalArguments.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o lastal.o lastal.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse4.1 last-merge-batches.o -lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: -lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] - 372 | std::cout.write((char *)m.qualityReader() + b, e - b); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, @@ -1273,6 +1305,14 @@ mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: +lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] + 372 | std::cout.write((char *)m.qualityReader() + b, e - b); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: +alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] + 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; + | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, @@ -1290,13 +1330,6 @@ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ -alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: -alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] - 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; - | ^~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-sse4.1 last-pair-probs.o last-pair-probs-main.o -lz -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse4.1 Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -1310,10 +1343,13 @@ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-sse4.1 last-pair-probs.o last-pair-probs-main.o -lz +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse4.1 Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-sse4.1 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 INSTALL="install --strip-program=true" all SFX=-ssse3 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3" + make -j40 INSTALL="install --strip-program=true" all SFX=-ssse3 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3" make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o Alphabet.o Alphabet.cc @@ -1358,8 +1394,6 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -1367,70 +1401,99 @@ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner2qual.cc:3: + from GappedXdropAligner.cc:49: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerFrame.cc:4: + from GappedXdropAligner2qual.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner3frame.cc:53: + from GappedXdropAlignerFrame.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerDna.cc:4: + from GappedXdropAligner3frame.cc:53: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, - from Centroid.cc:4: + from Alignment.hh:8, + from AlignmentPot.hh:8, + from AlignmentPot.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp.o alp/sls_alp.cpp +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerPssm.cc:3: + from GappedXdropAlignerDna.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner.cc:49: + from Centroid.hh:7, + from Alignment.hh:8, + from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from AlignmentPot.hh:8, - from AlignmentPot.cc:3: + from GappedXdropAlignerPssm.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: +/usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 297 | simde__m256d_from_private(simde__m256d_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_basic.o alp/sls_basic.cpp In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, - from AlignmentWrite.cc:3: + from Alignment.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { @@ -1439,85 +1502,54 @@ SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] 190 | size_t saBeg, size_t saEnd) { | ~~~~~~~^~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp.o alp/sls_alp.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_basic.o alp/sls_basic.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, - from Alignment.hh:8, - from Alignment.cc:3: + from Centroid.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: -/usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 297 | simde__m256d_from_private(simde__m256d_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_random.o alp/njn_random.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_dynprogproblim.cpp:37: + from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ -alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] - 124 | virtual void copy ( - | ^~~~ -alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ - 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) - | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] + 124 | virtual void copy ( + | ^~~~ +alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ + 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) + | ^~~~ In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstatutil.cpp:39: + from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -1537,25 +1569,29 @@ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstat.cpp:39: + from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ -alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] - 124 | virtual void copy ( - | ^~~~ -alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ - 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) - | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] + 124 | virtual void copy ( + | ^~~~ +alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ + 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) + | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_random.o alp/njn_random.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/last-split-main.o split/last-split-main.cc @@ -1568,10 +1604,6 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o LastalArguments.o LastalArguments.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o lastal.o lastal.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-ssse3 last-merge-batches.o -lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: -lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] - 372 | std::cout.write((char *)m.qualityReader() + b, e - b); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, @@ -1581,6 +1613,10 @@ mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: +lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] + 372 | std::cout.write((char *)m.qualityReader() + b, e - b); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; @@ -1603,7 +1639,6 @@ 412 | char rStrand, qStrand; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-ssse3 last-pair-probs.o last-pair-probs-main.o -lz -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-ssse3 Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -1617,11 +1652,12 @@ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-ssse3 Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-ssse3 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 INSTALL="install --strip-program=true" all SFX=-sse3 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse3" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3" + make -j40 INSTALL="install --strip-program=true" all SFX=-sse3 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse3" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3" make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o Alphabet.o Alphabet.cc @@ -1666,8 +1702,12 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp +In file included from GappedXdropAligner.hh:52, + from GappedXdropAlignerFrame.cc:4: +mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: +mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] + 20 | static inline SimdInt simdZero() { + | ^ dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -1675,44 +1715,46 @@ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerFrame.cc:4: -mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: -mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] - 20 | static inline SimdInt simdZero() { - | ^ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerPssm.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerDna.cc:4: -mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: -mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] - 20 | static inline SimdInt simdZero() { - | ^ -In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner3frame.cc:53: -mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: -mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] - 20 | static inline SimdInt simdZero() { - | ^ -In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner2qual.cc:3: + from Centroid.hh:7, + from Alignment.hh:8, + from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: +SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] + 190 | size_t saBeg, size_t saEnd) { + | ~~~~~~~^~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Centroid.cc:4: @@ -1721,13 +1763,6 @@ 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner.cc:49: -mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: -mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] - 20 | static inline SimdInt simdZero() { - | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp.o alp/sls_alp.cpp -In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, @@ -1737,34 +1772,39 @@ 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from Alignment.cc:3: + from GappedXdropAligner2qual.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: -SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] - 190 | size_t saBeg, size_t saEnd) { - | ~~~~~~~^~~~~ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: +/usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 297 | simde__m256d_from_private(simde__m256d_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp.o alp/sls_alp.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_basic.o alp/sls_basic.cpp In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from AlignmentWrite.cc:3: + from GappedXdropAligner.cc:49: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_basic.o alp/sls_basic.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from GappedXdropAligner.hh:52, + from GappedXdropAlignerDna.cc:4: +mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: +mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] + 20 | static inline SimdInt simdZero() { + | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: @@ -1772,28 +1812,44 @@ /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: -/usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 297 | simde__m256d_from_private(simde__m256d_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from GappedXdropAligner.hh:52, + from GappedXdropAligner3frame.cc:53: +mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: +mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] + 20 | static inline SimdInt simdZero() { + | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp +In file included from GappedXdropAligner.hh:52, + from Centroid.hh:7, + from Alignment.hh:8, + from Alignment.cc:3: +mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: +mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] + 20 | static inline SimdInt simdZero() { + | ^ +In file included from alp/njn_dynprogproblim.hpp:39, + from alp/njn_dynprogproblim.cpp:37: +alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] + 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) + | ^~~~~~~~ +alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ + 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) + | ^~~~~~~~ +alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] + 116 | virtual inline void copy (const DynProgProb &dynProgProb_) + | ^~~~ +alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ + 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) + | ^~~~ +alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] + 124 | virtual void copy ( + | ^~~~ +alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ + 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) + | ^~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: @@ -1802,9 +1858,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_dynprogproblim.cpp:37: + from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -1823,9 +1878,11 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstatutil.cpp:39: + from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -1844,27 +1901,6 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ -In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstat.cpp:39: -alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] - 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) - | ^~~~~~~~ -alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ - 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) - | ^~~~~~~~ -alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] - 124 | virtual void copy ( - | ^~~~ -alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ - 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) - | ^~~~ -alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] - 116 | virtual inline void copy (const DynProgProb &dynProgProb_) - | ^~~~ -alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ - 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) - | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/last-split.o split/last-split.cc @@ -1911,7 +1947,6 @@ 412 | char rStrand, qStrand; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-sse3 last-pair-probs.o last-pair-probs-main.o -lz -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse3 Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] @@ -1926,10 +1961,11 @@ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse3 Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-sse3 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' - make -j42 INSTALL="install --strip-program=true" all SFX=-sse2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse2" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2" + make -j40 INSTALL="install --strip-program=true" all SFX=-sse2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse2" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2" make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o Alphabet.o Alphabet.cc @@ -1974,8 +2010,6 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -1983,22 +2017,15 @@ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerDna.cc:4: -mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: -mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] - 20 | static inline SimdInt simdZero() { - | ^ -In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerFrame.cc:4: + from Centroid.hh:7, + from Alignment.hh:8, + from Alignment.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { @@ -2010,110 +2037,115 @@ 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerPssm.cc:3: -mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: -mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] - 20 | static inline SimdInt simdZero() { - | ^ -In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner3frame.cc:53: + from Centroid.hh:7, + from Alignment.hh:8, + from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, - from Centroid.cc:4: + from Alignment.hh:8, + from AlignmentPot.hh:8, + from AlignmentPot.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from AlignmentPot.hh:8, - from AlignmentPot.cc:3: + from GappedXdropAligner3frame.cc:53: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: +/usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 297 | simde__m256d_from_private(simde__m256d_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from Alignment.cc:3: + from GappedXdropAlignerDna.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from AlignmentWrite.cc:3: + from GappedXdropAlignerPssm.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp.o alp/sls_alp.cpp In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner.cc:49: + from GappedXdropAlignerFrame.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: -SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] - 190 | size_t saBeg, size_t saEnd) { - | ~~~~~~~^~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_basic.o alp/sls_basic.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp +SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: +SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] + 190 | size_t saBeg, size_t saEnd) { + | ~~~~~~~^~~~~ +In file included from GappedXdropAligner.hh:52, + from GappedXdropAligner.cc:49: +mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: +mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] + 20 | static inline SimdInt simdZero() { + | ^ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from GappedXdropAligner.hh:52, + from Centroid.hh:7, + from Centroid.cc:4: +mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: +mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] + 20 | static inline SimdInt simdZero() { + | ^ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp.o alp/sls_alp.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_basic.o alp/sls_basic.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: -/usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 297 | simde__m256d_from_private(simde__m256d_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_random.o alp/njn_random.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_dynprogproblim.cpp:37: + from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -2132,8 +2164,9 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_random.o alp/njn_random.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstatutil.cpp:39: + from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -2152,9 +2185,10 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstat.cpp:39: + from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -2173,6 +2207,8 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/last-split.o split/last-split.cc @@ -2218,9 +2254,7 @@ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-sse2 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse2 Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -2234,11 +2268,13 @@ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-sse2 last-pair-probs.o last-pair-probs-main.o -lz +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse2 Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-sse2 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' dh_auto_build -- all SFX=-plain CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3" - make -j42 INSTALL="install --strip-program=true" all SFX=-plain CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3" + make -j40 INSTALL="install --strip-program=true" all SFX=-plain CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3" make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o Alphabet.o Alphabet.cc @@ -2273,6 +2309,13 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o GeneticCode.o GeneticCode.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc +dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: +dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; + | ~~~~~~~~^ +dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; + | ~~~~~~~~^ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc @@ -2282,80 +2325,86 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/last_split_options.o split/last_split_options.cc +SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: +SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] + 190 | size_t saBeg, size_t saEnd) { + | ~~~~~~~^~~~~ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp -dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: -dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; - | ~~~~~~~~^ -dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; - | ~~~~~~~~^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp -In file included from tantan.cc:5: -mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: -mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] - 20 | static inline SimdInt simdZero() { - | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner2qual.cc:3: + from GappedXdropAlignerDna.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner3frame.cc:53: + from GappedXdropAligner.cc:49: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerDna.cc:4: + from GappedXdropAligner3frame.cc:53: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerPssm.cc:3: + from GappedXdropAlignerFrame.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerFrame.cc:4: +In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, - from Alignment.hh:8, - from AlignmentPot.hh:8, - from AlignmentPot.cc:3: + from Centroid.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/simde/x86/avx2.h:33, + from mcf_simd.hh:8: +/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: +/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 281 | simde__m256i_from_private(simde__m256i_private v) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, - from Alignment.cc:3: + from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Centroid.cc:4: + from GappedXdropAligner2qual.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner.cc:49: + from Centroid.hh:7, + from Alignment.hh:8, + from Alignment.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { @@ -2363,25 +2412,24 @@ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, - from AlignmentWrite.cc:3: + from AlignmentPot.hh:8, + from AlignmentPot.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp.o alp/sls_alp.cpp -SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: -SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] - 190 | size_t saBeg, size_t saEnd) { - | ~~~~~~~^~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_basic.o alp/sls_basic.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from GappedXdropAligner.hh:52, + from GappedXdropAlignerPssm.cc:3: +mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: +mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] + 20 | static inline SimdInt simdZero() { + | ^ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: @@ -2390,37 +2438,27 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { +/usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: +/usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 + 297 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp.o alp/sls_alp.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_basic.o alp/sls_basic.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: -/usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 297 | simde__m256d_from_private(simde__m256d_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp -In file included from /usr/include/simde/x86/avx2.h:33, - from mcf_simd.hh:8: -/usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: -/usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 - 281 | simde__m256i_from_private(simde__m256i_private v) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_dynprogproblim.cpp:37: + from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -2439,11 +2477,8 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstat.cpp:39: + from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ @@ -2462,32 +2497,33 @@ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/last-split-main.o split/last-split-main.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/last-split.o split/last-split.cc +cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o last-merge-batches.o last-merge-batches.c +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o last-pair-probs.o last-pair-probs.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc In file included from alp/njn_dynprogproblim.hpp:39, - from alp/njn_localmaxstatutil.cpp:39: + from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ -alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] - 124 | virtual void copy ( - | ^~~~ -alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ - 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) - | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/last-split.o split/last-split.cc -cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o last-merge-batches.o last-merge-batches.c -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o last-pair-probs.o last-pair-probs.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc +alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] + 124 | virtual void copy ( + | ^~~~ +alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ + 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) + | ^~~~ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o lastdb.o lastdb.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o LastalArguments.o LastalArguments.cc @@ -2506,10 +2542,6 @@ mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ -alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: -alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] - 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; - | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, @@ -2527,9 +2559,11 @@ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ +alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: +alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] + 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; + | ^~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-plain last-pair-probs.o last-pair-probs-main.o -lz -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-plain Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-plain Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -2543,6 +2577,8 @@ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-plain Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-plain Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-plain Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' @@ -2650,8 +2686,8 @@ make[1]: Leaving directory '/build/reproducible-path/last-align-1645' dh_md5sums dh_builddeb -dpkg-deb: building package 'last-align' in '../last-align_1645-1_amd64.deb'. dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_1645-1_amd64.deb'. +dpkg-deb: building package 'last-align' in '../last-align_1645-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../last-align_1645-1_amd64.buildinfo dpkg-genchanges --build=binary -O../last-align_1645-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2659,12 +2695,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2711647/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2711647/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/2955330 and its subdirectories -I: Current time: Thu Nov 26 02:56:12 -12 2026 -I: pbuilder-time-stamp: 1795704972 +I: removing directory /srv/workspace/pbuilder/2711647 and its subdirectories +I: Current time: Fri Oct 24 22:42:47 +14 2025 +I: pbuilder-time-stamp: 1761295367