Diff of the two buildlogs: -- --- b1/build.log 2025-01-16 12:01:29.413668313 +0000 +++ b2/build.log 2025-01-16 12:27:36.635027580 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 18 06:20:59 -12 2026 -I: pbuilder-time-stamp: 1771438859 +I: Current time: Fri Jan 17 02:01:33 +14 2025 +I: pbuilder-time-stamp: 1737028893 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2797824/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1821435/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 Jan 16 12:01 /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/1821435/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1821435/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(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=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='eb8558aca8354ecaa953d82e3a78e42e' - 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='2797824' - PS1='# ' - PS2='> ' + INVOCATION_ID=d72fe5fdbf6b4e24a03905a03ca7dc1b + 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=1821435 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.3NYXCveZ/pbuilderrc_T16M --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3NYXCveZ/b1 --logfile b1/build.log last-align_1608-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.3NYXCveZ/pbuilderrc_mhJJ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3NYXCveZ/b2 --logfile b2/build.log last-align_1608-1.dsc' + SUDO_GID=110 + 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 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2797824/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1821435/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -188,7 +220,7 @@ Get: 70 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.4.0-1.1 [522 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 34.3 MB in 5s (7307 kB/s) +Fetched 34.3 MB in 4s (9088 kB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (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 ... 19850 files and directories currently installed.) @@ -443,8 +475,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Feb 18 18:21:27 UTC 2026. -Universal Time is now: Wed Feb 18 18:21:27 UTC 2026. +Local time is now: Thu Jan 16 12:04:07 UTC 2025. +Universal Time is now: Thu Jan 16 12:04:07 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -504,7 +536,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/last-align-1608/ && 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_1608-1_source.changes +I: user script /srv/workspace/pbuilder/1821435/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1821435/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/last-align-1608/ && 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_1608-1_source.changes dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1608-1 dpkg-buildpackage: info: source distribution unstable @@ -517,37 +553,37 @@ make[1]: Entering directory '/build/reproducible-path/last-align-1608' for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ dh_auto_clean -- SFX=-${SIMD} ; done - make -j42 clean SFX=-avx2 + make -j20 clean SFX=-avx2 make[2]: Entering directory '/build/reproducible-path/last-align-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - make -j42 clean SFX=-avx + make -j20 clean SFX=-avx make[2]: Entering directory '/build/reproducible-path/last-align-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - make -j42 clean SFX=-sse4.1 + make -j20 clean SFX=-sse4.1 make[2]: Entering directory '/build/reproducible-path/last-align-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - make -j42 clean SFX=-ssse3 + make -j20 clean SFX=-ssse3 make[2]: Entering directory '/build/reproducible-path/last-align-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - make -j42 clean SFX=-sse3 + make -j20 clean SFX=-sse3 make[2]: Entering directory '/build/reproducible-path/last-align-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - make -j42 clean SFX=-sse2 + make -j20 clean SFX=-sse2 make[2]: Entering directory '/build/reproducible-path/last-align-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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* @@ -576,7 +612,7 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx2" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -j20 "INSTALL=install --strip-program=true" all SFX=-avx2 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx2" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -602,8 +638,19 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentWrite.o AlignmentWrite.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_alignment_path_adder.o mcf_alignment_path_adder.cc @@ -625,33 +672,18 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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; - | ~~~~~~~~^ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_localmaxstat.o alp/njn_localmaxstat.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -670,14 +702,10 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -696,6 +724,11 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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=] @@ -716,6 +749,9 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -747,8 +783,8 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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:656:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 656 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -765,7 +801,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -j20 "INSTALL=install --strip-program=true" all SFX=-avx "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -789,9 +825,20 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 Alignment.o 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentPot.o AlignmentPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentWrite.o AlignmentWrite.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc @@ -812,21 +859,10 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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; - | ~~~~~~~~^ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_localmaxstat.o alp/njn_localmaxstat.cpp @@ -836,8 +872,6 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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=] @@ -858,12 +892,11 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -882,10 +915,8 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx -c -o last-merge-batches.o last-merge-batches.c 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_) | ^~~~~~~~ @@ -904,6 +935,11 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 LastdbArguments.o LastdbArguments.cc @@ -933,8 +969,8 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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:656:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 656 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -951,7 +987,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - 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-1608=. -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -j20 "INSTALL=install --strip-program=true" all SFX=-sse4.1 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -975,29 +1011,6 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 Alignment.o 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentPot.o AlignmentPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentWrite.o AlignmentWrite.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_alignment_path_adder.o mcf_alignment_path_adder.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GreedyXdropAligner.o GreedyXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 QualityPssmMaker.o QualityPssmMaker.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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; @@ -1005,82 +1018,91 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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 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 GappedXdropAligner2qual.cc:3: +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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerFrame.cc:4: + 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerDna.cc:4: + from Centroid.hh:7, + 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner3frame.cc:53: + 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__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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_alignment_path_adder.o mcf_alignment_path_adder.cc In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Centroid.cc:4: + 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner.cc:49: + 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 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 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() { | ^ 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() { | ^ -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)’: @@ -1093,6 +1115,12 @@ /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 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)’: @@ -1105,11 +1133,31 @@ /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 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_gap_costs.o mcf_gap_costs.cc +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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GreedyXdropAligner.o GreedyXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 QualityPssmMaker.o QualityPssmMaker.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -1117,25 +1165,14 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -1154,10 +1191,8 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -1176,8 +1211,10 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -1196,7 +1233,6 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -1255,7 +1291,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -j20 "INSTALL=install --strip-program=true" all SFX=-ssse3 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -1279,29 +1315,6 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 Alignment.o 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentPot.o AlignmentPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentWrite.o AlignmentWrite.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_alignment_path_adder.o mcf_alignment_path_adder.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GreedyXdropAligner.o GreedyXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 QualityPssmMaker.o QualityPssmMaker.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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; @@ -1309,135 +1322,155 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.cc:4: + 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 GappedXdropAligner2qual.cc:3: + from Centroid.hh:7, + 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 GappedXdropAlignerPssm.cc:3: +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.cc +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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerDna.cc:4: + 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.cc 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() { | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner3frame.cc:53: + 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc 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() { - | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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__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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_alignment_path_adder.o mcf_alignment_path_adder.cc 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc +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 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_gap_costs.o mcf_gap_costs.cc 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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() { | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GreedyXdropAligner.o GreedyXdropAligner.cc 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() { | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 QualityPssmMaker.o QualityPssmMaker.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -1458,7 +1491,6 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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=] @@ -1479,16 +1511,14 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 last-pair-probs.o last-pair-probs.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -1504,6 +1534,12 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 lastdb.o lastdb.cc @@ -1541,8 +1577,8 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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:656:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 656 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -1559,7 +1595,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse3" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -j20 "INSTALL=install --strip-program=true" all SFX=-sse3 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse3" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -1583,29 +1619,6 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 Alignment.o 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentPot.o AlignmentPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentWrite.o AlignmentWrite.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_alignment_path_adder.o mcf_alignment_path_adder.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GreedyXdropAligner.o GreedyXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 QualityPssmMaker.o QualityPssmMaker.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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; @@ -1613,126 +1626,157 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner2qual.cc:3: + from Centroid.hh:7, + 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 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() { | ^ 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() { | ^ 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() { + | ^ +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_alignment_path_adder.o mcf_alignment_path_adder.cc +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 Centroid.hh:7, - from Alignment.hh:8, - from Alignment.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 /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 GappedXdropAligner.cc:49: + 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 Centroid.hh:7, - from Centroid.cc:4: + 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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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__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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc 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) { +/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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GeneticCode.o GeneticCode.cc 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GreedyXdropAligner.o GreedyXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 QualityPssmMaker.o QualityPssmMaker.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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() { - | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -1753,20 +1797,6 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse3 -c -o last-merge-batches.o last-merge-batches.c 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=] @@ -1787,6 +1817,10 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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=] @@ -1807,6 +1841,8 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse3 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 LastdbArguments.o LastdbArguments.cc @@ -1845,8 +1881,8 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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:656:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 656 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -1863,7 +1899,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' - 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse2" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -j20 "INSTALL=install --strip-program=true" all SFX=-sse2 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse2" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -1887,29 +1923,6 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 Alignment.o 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentPot.o AlignmentPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentWrite.o AlignmentWrite.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_alignment_path_adder.o mcf_alignment_path_adder.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GreedyXdropAligner.o GreedyXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 QualityPssmMaker.o QualityPssmMaker.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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; @@ -1917,34 +1930,49 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.cc 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner3frame.cc:53: + from Centroid.hh:7, + 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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) { + | ~~~~~~~^~~~~ 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() { | ^ +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerPssm.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 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() { @@ -1955,38 +1983,44 @@ 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 /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 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 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_alignment_path_adder.o mcf_alignment_path_adder.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner.cc:49: + 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 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() { | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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)’: @@ -2005,45 +2039,48 @@ /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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -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 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() { - | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Alignment.hh:8, - from AlignmentPot.hh:8, - from AlignmentPot.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() { | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 mcf_gap_costs.o mcf_gap_costs.cc 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GreedyXdropAligner.o GreedyXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 QualityPssmMaker.o QualityPssmMaker.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -2064,11 +2101,9 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -2087,12 +2122,8 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse2 -c -o last-merge-batches.o last-merge-batches.c 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_) | ^~~~~~~~ @@ -2111,6 +2142,11 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse2 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 LastdbArguments.o LastdbArguments.cc @@ -2149,8 +2185,8 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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:656:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 656 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -2168,7 +2204,7 @@ make[3]: Leaving directory '/build/reproducible-path/last-align-1608/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1608' dh_auto_build -- all SFX=-plain CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -j20 "INSTALL=install --strip-program=true" all SFX=-plain "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 @@ -2192,29 +2228,6 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 Alignment.o 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentPot.o AlignmentPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 AlignmentWrite.o AlignmentWrite.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_alignment_path_adder.o mcf_alignment_path_adder.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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; @@ -2222,7 +2235,10 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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 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] @@ -2230,52 +2246,76 @@ | ^ 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 GappedXdropAligner.hh:52, + 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.o GappedXdropAligner.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerDna.o GappedXdropAlignerDna.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc +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() { | ^ +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAlignerFrame.cc:4: + from Centroid.hh:7, + 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner3frame.o GappedXdropAligner3frame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAlignerFrame.o GappedXdropAlignerFrame.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_alignment_path_adder.o mcf_alignment_path_adder.cc In file included from GappedXdropAligner.hh:52, - from GappedXdropAligner3frame.cc:53: + 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 GappedXdropAlignerPssm.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc 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() { - | ^ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.hh:52, - from GappedXdropAligner.cc:49: + 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() { @@ -2287,73 +2327,61 @@ 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, - from Centroid.hh:7, - from Centroid.cc:4: + 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__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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 GappedXdropAligner.hh:52, - from Centroid.hh:7, - 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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__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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPair.o SegmentPair.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 SegmentPairPot.o SegmentPairPot.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 TwoQualityScoreMatrix.o TwoQualityScoreMatrix.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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -2372,11 +2400,15 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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_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_) | ^~~~~~~~ @@ -2395,13 +2427,10 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -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-1608=. -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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_) | ^~~~~~~~ @@ -2420,6 +2449,13 @@ alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 +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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-plain last-merge-batches.o @@ -2454,8 +2490,8 @@ 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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-1608=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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 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:656:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 656 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); @@ -2585,12 +2621,14 @@ 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/1821435/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1821435/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/2797824 and its subdirectories -I: Current time: Wed Feb 18 06:24:26 -12 2026 -I: pbuilder-time-stamp: 1771439066 +I: removing directory /srv/workspace/pbuilder/1821435 and its subdirectories +I: Current time: Fri Jan 17 02:27:35 +14 2025 +I: pbuilder-time-stamp: 1737030455