Diff of the two buildlogs: -- --- b1/build.log 2025-01-05 21:53:13.489726427 +0000 +++ b2/build.log 2025-01-05 22:55:19.264187619 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 5 09:08:19 -12 2025 -I: pbuilder-time-stamp: 1736111299 +I: Current time: Mon Jan 6 12:01:13 +14 2025 +I: pbuilder-time-stamp: 1736114473 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying fix_linking.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3429/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4460/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +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 5 22:01 /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/4460/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4460/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='8ae1099a4e6348e5ba7c6a943f3f31bd' - 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='3429' - PS1='# ' - PS2='> ' + INVOCATION_ID=cffbbfcc5cb54a38a9bfdabe0b745805 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=4460 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.rdpj0Dqm/pbuilderrc_33oK --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rdpj0Dqm/b1 --logfile b1/build.log mothur_1.48.1-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.rdpj0Dqm/pbuilderrc_SFqU --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rdpj0Dqm/b2 --logfile b2/build.log mothur_1.48.1-1.dsc' + SUDO_GID=110 + SUDO_UID=103 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32a 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3429/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/4460/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -91,7 +123,7 @@ Depends: debhelper-compat (= 13), gfortran, libboost-iostreams-dev, libreadline-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19679 files and directories currently installed.) +(Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -170,10 +202,10 @@ Get: 46 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-6 [146 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libreadline-dev armhf 8.2-6 [138 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] -Fetched 51.9 MB in 7s (7860 kB/s) +Fetched 51.9 MB in 7s (7196 kB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. -(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 ... 19679 files and directories currently installed.) +(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 ... 19675 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package sensible-utils. @@ -383,7 +415,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mothur-1.48.1/ && 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 > ../mothur_1.48.1-1_source.changes +I: user script /srv/workspace/pbuilder/4460/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/4460/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mothur-1.48.1/ && 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 > ../mothur_1.48.1-1_source.changes dpkg-buildpackage: info: source package mothur dpkg-buildpackage: info: source version 1.48.1-1 dpkg-buildpackage: info: source distribution unstable @@ -409,7 +445,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/mothur-1.48.1' dh_auto_build -- 64BIT_VERSION=no - make -j3 "INSTALL=install --strip-program=true" 64BIT_VERSION=no + make -j4 "INSTALL=install --strip-program=true" 64BIT_VERSION=no make[2]: Entering directory '/build/reproducible-path/mothur-1.48.1' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/accuracy.o source/calculators/accuracy.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ace.o source/calculators/ace.cpp @@ -421,57 +457,58 @@ from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/ace.h:16, - from source/calculators/ace.cpp:10: + from source/calculators/boneh.h:13, + from source/calculators/boneh.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput Ace::getValues(SAbundVector*)' at source/calculators/ace.cpp:16:14: + inlined from 'virtual EstOutput Boneh::getValues(SAbundVector*)' at source/calculators/boneh.cpp:40:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bootstrap.o source/calculators/bootstrap.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bstick.o source/calculators/bstick.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/bergerparker.h:12, - from source/calculators/bergerparker.cpp:10: + from source/calculators/ace.h:16, + from source/calculators/ace.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput BergerParker::getValues(SAbundVector*)' at source/calculators/bergerparker.cpp:16:14: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bootstrap.o source/calculators/bootstrap.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bstick.o source/calculators/bstick.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/boneh.h:13, - from source/calculators/boneh.cpp:10: + from source/calculators/bergerparker.h:12, + from source/calculators/bergerparker.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput Boneh::getValues(SAbundVector*)' at source/calculators/boneh.cpp:40:14: + inlined from 'virtual EstOutput BergerParker::getValues(SAbundVector*)' at source/calculators/bergerparker.cpp:16:14: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual EstOutput Ace::getValues(SAbundVector*)' at source/calculators/ace.cpp:16:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/calculator.o source/calculators/calculator.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/canberra.o source/calculators/canberra.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -490,7 +527,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/canberra.o source/calculators/canberra.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -503,13 +539,13 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/chao1.o source/calculators/chao1.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual EstOutput BStick::getValues(SAbundVector*)' at source/calculators/bstick.cpp:48:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/chao1.o source/calculators/chao1.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -529,6 +565,8 @@ 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/coverage.o source/calculators/coverage.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/diversityutils.o source/calculators/diversityutils.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/eachgapdist.o source/calculators/eachgapdist.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -547,8 +585,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/diversityutils.o source/calculators/diversityutils.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/eachgapdist.o source/calculators/eachgapdist.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/eachgapignore.o source/calculators/eachgapignore.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/efron.o source/calculators/efron.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -567,9 +605,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/eachgapignore.o source/calculators/eachgapignore.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/efron.o source/calculators/efron.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/erarefaction.o source/calculators/erarefaction.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/f1score.o source/calculators/f1score.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -588,7 +625,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/f1score.o source/calculators/f1score.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fdr.o source/calculators/fdr.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fn.o source/calculators/fn.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fp.o source/calculators/fp.cpp @@ -596,6 +632,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/geom.o source/calculators/geom.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/goodscoverage.o source/calculators/goodscoverage.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/gower.o source/calculators/gower.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hamming.o source/calculators/hamming.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -608,6 +645,13 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual EstOutput Geom::getValues(SAbundVector*)' at source/calculators/geom.cpp:44:14: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/heip.o source/calculators/heip.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -626,12 +670,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput Geom::getValues(SAbundVector*)' at source/calculators/geom.cpp:44:14: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hellinger.o source/calculators/hellinger.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -650,9 +689,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hamming.o source/calculators/hamming.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/heip.o source/calculators/heip.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hellinger.o source/calculators/hellinger.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/igabundance.o source/calculators/igabundance.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -671,21 +708,22 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ignoregaps.o source/calculators/ignoregaps.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/hellinger.h:14, - from source/calculators/hellinger.cpp:10: + from source/calculators/heip.h:13, + from source/calculators/heip.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput Hellinger::getValues(std::vector)' at source/calculators/hellinger.cpp:15:14: + inlined from 'virtual EstOutput Heip::getValues(SAbundVector*)' at source/calculators/heip.cpp:17:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -695,21 +733,20 @@ from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/heip.h:13, - from source/calculators/heip.cpp:10: + from source/calculators/hellinger.h:14, + from source/calculators/hellinger.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/igabundance.o source/calculators/igabundance.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput Heip::getValues(SAbundVector*)' at source/calculators/heip.cpp:17:14: + inlined from 'virtual EstOutput Hellinger::getValues(std::vector)' at source/calculators/hellinger.cpp:15:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ignoregaps.o source/calculators/ignoregaps.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/igrarefaction.o source/calculators/igrarefaction.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/invsimpson.o source/calculators/invsimpson.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -727,9 +764,9 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/invsimpson.o source/calculators/invsimpson.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/jackknife.o source/calculators/jackknife.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/kimura.o source/calculators/kimura.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/kmerdist.o source/calculators/kmerdist.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -748,6 +785,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnabundance.o source/calculators/lnabundance.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -760,16 +798,15 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/kmerdist.o source/calculators/kmerdist.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual EstOutput Jackknife::getValues(SAbundVector*)' at source/calculators/jackknife.cpp:68:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnabundance.o source/calculators/lnabundance.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnrarefaction.o source/calculators/lnrarefaction.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnshift.o source/calculators/lnshift.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/logsd.o source/calculators/logsd.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -787,8 +824,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/logsd.o source/calculators/logsd.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lsabundance.o source/calculators/lsabundance.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lsrarefaction.o source/calculators/lsrarefaction.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -806,7 +843,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lsrarefaction.o source/calculators/lsrarefaction.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/manhattan.o source/calculators/manhattan.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -825,7 +862,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/manhattan.o source/calculators/manhattan.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mcc.o source/calculators/mcc.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -843,8 +880,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mcc.o source/calculators/mcc.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchi2.o source/calculators/memchi2.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchord.o source/calculators/memchord.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -863,8 +900,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchord.o source/calculators/memchord.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memeuclidean.o source/calculators/memeuclidean.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mempearson.o source/calculators/mempearson.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -883,7 +920,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mempearson.o source/calculators/mempearson.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metroig.o source/calculators/metroig.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -896,6 +933,13 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual EstOutput MemChord::getValues(std::vector)' at source/calculators/memchord.cpp:15:14: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metrolognormal.o source/calculators/metrolognormal.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -910,18 +954,10 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput MemChord::getValues(std::vector)' at source/calculators/memchord.cpp:15:14: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual EstOutput MemEuclidean::getValues(std::vector)' at source/calculators/memeuclidean.cpp:15:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metroig.o source/calculators/metroig.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metrolognormal.o source/calculators/metrolognormal.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -944,6 +980,8 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metrosichel.o source/calculators/metrosichel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npshannon.o source/calculators/npshannon.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npv.o source/calculators/npv.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/odum.o source/calculators/odum.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/onegapdist.o source/calculators/onegapdist.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -962,9 +1000,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/odum.o source/calculators/odum.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/onegapdist.o source/calculators/onegapdist.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/onegapignore.o source/calculators/onegapignore.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/parsimony.o source/calculators/parsimony.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -983,11 +1020,11 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/parsimony.o source/calculators/parsimony.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ppv.o source/calculators/ppv.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/prng.o source/calculators/prng.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/qstat.o source/calculators/qstat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sensitivity.o source/calculators/sensitivity.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannon.o source/calculators/shannon.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1006,9 +1043,9 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannon.o source/calculators/shannon.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannoneven.o source/calculators/shannoneven.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannonrange.o source/calculators/shannonrange.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedace.o source/calculators/sharedace.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1027,7 +1064,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedace.o source/calculators/sharedace.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedanderbergs.o source/calculators/sharedanderbergs.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1052,35 +1089,34 @@ from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/shannonrange.h:19, - from source/calculators/shannonrange.cpp:9: + from source/calculators/sharedace.h:15, + from source/calculators/sharedace.cpp:11: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput RangeShannon::getValues(SAbundVector*)' at source/calculators/shannonrange.cpp:15:20: + inlined from 'virtual EstOutput SharedAce::getValues(std::vector)' at source/calculators/sharedace.cpp:17:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedanderbergs.o source/calculators/sharedanderbergs.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedbraycurtis.o source/calculators/sharedbraycurtis.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/sharedace.h:15, - from source/calculators/sharedace.cpp:11: + from source/calculators/shannonrange.h:19, + from source/calculators/shannonrange.cpp:9: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedbraycurtis.o source/calculators/sharedbraycurtis.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput SharedAce::getValues(std::vector)' at source/calculators/sharedace.cpp:17:14: + inlined from 'virtual EstOutput RangeShannon::getValues(SAbundVector*)' at source/calculators/shannonrange.cpp:15:20: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1097,12 +1133,14 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjabund.o source/calculators/sharedjabund.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual EstOutput Anderberg::getValues(std::vector)' at source/calculators/sharedanderbergs.cpp:22:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjackknife.o source/calculators/sharedjackknife.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1121,8 +1159,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjabund.o source/calculators/sharedjabund.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjackknife.o source/calculators/sharedjackknife.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1142,6 +1178,7 @@ 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjclass.o source/calculators/sharedjclass.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjest.o source/calculators/sharedjest.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1165,7 +1202,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjest.o source/calculators/sharedjest.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjsd.o source/calculators/sharedjsd.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1184,7 +1221,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjsd.o source/calculators/sharedjsd.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1204,6 +1240,7 @@ 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkstest.o source/calculators/sharedkstest.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynski.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1232,7 +1269,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynski.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1252,71 +1288,65 @@ 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynskicody.o source/calculators/sharedkulczynskicody.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedlennon.o source/calculators/sharedlennon.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/sharedkstest.h:11, - from source/calculators/sharedkstest.cpp:10: + from source/calculators/sharedkulczynski.h:13, + from source/calculators/sharedkulczynski.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput KSTest::getValues(std::vector)' at source/calculators/sharedkstest.cpp:16:14: + inlined from 'virtual EstOutput Kulczynski::getValues(std::vector)' at source/calculators/sharedkulczynski.cpp:22:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedlennon.o source/calculators/sharedlennon.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/sharedkulczynski.h:13, - from source/calculators/sharedkulczynski.cpp:10: + from source/calculators/sharedkstest.h:11, + from source/calculators/sharedkstest.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmarczewski.o source/calculators/sharedmarczewski.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput Kulczynski::getValues(std::vector)' at source/calculators/sharedkulczynski.cpp:22:14: + inlined from 'virtual EstOutput KSTest::getValues(std::vector)' at source/calculators/sharedkstest.cpp:16:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmarczewski.o source/calculators/sharedmarczewski.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmorisitahorn.o source/calculators/sharedmorisitahorn.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/sharedkulczynskicody.h:14, - from source/calculators/sharedkulczynskicody.cpp:10: + from source/calculators/sharedlennon.h:14, + from source/calculators/sharedlennon.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput KulczynskiCody::getValues(std::vector)' at source/calculators/sharedkulczynskicody.cpp:22:14: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmorisitahorn.o source/calculators/sharedmorisitahorn.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/sharedlennon.h:14, - from source/calculators/sharedlennon.cpp:10: + from source/calculators/sharedkulczynskicody.h:14, + from source/calculators/sharedkulczynskicody.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: @@ -1327,6 +1357,14 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual EstOutput KulczynskiCody::getValues(std::vector)' at source/calculators/sharedkulczynskicody.cpp:22:14: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedochiai.o source/calculators/sharedochiai.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedrjsd.o source/calculators/sharedrjsd.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1345,8 +1383,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedochiai.o source/calculators/sharedochiai.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedrjsd.o source/calculators/sharedrjsd.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobs.o source/calculators/sharedsobs.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1365,7 +1402,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobs.o source/calculators/sharedsobs.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsobscollectsummary.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1396,7 +1433,6 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsobscollectsummary.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual EstOutput RJSD::getValues(std::vector)' at source/calculators/sharedrjsd.cpp:17:14: @@ -1404,6 +1440,7 @@ 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorabund.o source/calculators/sharedsorabund.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorclass.o source/calculators/sharedsorclass.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1422,7 +1459,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorclass.o source/calculators/sharedsorclass.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorest.o source/calculators/sharedsorest.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1446,7 +1483,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorest.o source/calculators/sharedsorest.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetan.o source/calculators/sharedthetan.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1459,13 +1496,6 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput SorAbund::getValues(std::vector)' at source/calculators/sharedsorabund.cpp:19:14: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetan.o source/calculators/sharedthetan.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1480,11 +1510,18 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual EstOutput SorAbund::getValues(std::vector)' at source/calculators/sharedsorabund.cpp:19:14: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual EstOutput SorClass::getValues(std::vector)' at source/calculators/sharedsorclass.cpp:22:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetayc.o source/calculators/sharedthetayc.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shen.o source/calculators/shen.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1531,64 +1568,63 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shen.o source/calculators/shen.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/siabundance.o source/calculators/siabundance.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpson.o source/calculators/simpson.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/sharedthetayc.h:16, - from source/calculators/sharedthetayc.cpp:10: + from source/calculators/shen.h:13, + from source/calculators/shen.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput ThetaYC::getValues(std::vector)' at source/calculators/sharedthetayc.cpp:15:14: + inlined from 'virtual EstOutput Shen::getValues(SAbundVector*)' at source/calculators/shen.cpp:19:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpson.o source/calculators/simpson.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, - from source/calculators/diversitycalc.h:12, - from source/calculators/diversityutils.hpp:20, - from source/calculators/siabundance.hpp:12, - from source/calculators/siabundance.cpp:9: + from source/datastructures/datavector.hpp:4, + from source/datastructures/sabundvector.hpp:4, + from source/calculators/calculator.h:5, + from source/calculators/sharedthetayc.h:16, + from source/calculators/sharedthetayc.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual std::vector SIAbundance::getValues(int, std::vector&)' at source/calculators/siabundance.cpp:20:23: + inlined from 'virtual EstOutput ThetaYC::getValues(std::vector)' at source/calculators/sharedthetayc.cpp:15:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpsoneven.o source/calculators/simpsoneven.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sirarefaction.o source/calculators/sirarefaction.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, - from source/datastructures/datavector.hpp:4, - from source/datastructures/sabundvector.hpp:4, - from source/calculators/calculator.h:5, - from source/calculators/shen.h:13, - from source/calculators/shen.cpp:10: + from source/calculators/diversitycalc.h:12, + from source/calculators/diversityutils.hpp:20, + from source/calculators/siabundance.hpp:12, + from source/calculators/siabundance.cpp:9: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput Shen::getValues(SAbundVector*)' at source/calculators/shen.cpp:19:14: + inlined from 'virtual std::vector SIAbundance::getValues(int, std::vector&)' at source/calculators/siabundance.cpp:20:23: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpsoneven.o source/calculators/simpsoneven.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sirarefaction.o source/calculators/sirarefaction.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1608,6 +1644,7 @@ 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sishift.o source/calculators/sishift.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/smithwilson.o source/calculators/smithwilson.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1626,8 +1663,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/smithwilson.o source/calculators/smithwilson.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/soergel.o source/calculators/soergel.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/solow.o source/calculators/solow.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1639,13 +1676,6 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual std::vector SIShift::getValues(int, std::vector&)' at source/calculators/sishift.cpp:21:23: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/solow.o source/calculators/solow.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1660,10 +1690,18 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual std::vector SIShift::getValues(int, std::vector&)' at source/calculators/sishift.cpp:21:23: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual EstOutput SmithWilson::getValues(SAbundVector*)' at source/calculators/smithwilson.cpp:17:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/spearman.o source/calculators/spearman.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/speciesprofile.o source/calculators/speciesprofile.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1682,8 +1720,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/spearman.o source/calculators/spearman.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/speciesprofile.o source/calculators/speciesprofile.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1703,6 +1739,7 @@ 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/specificity.o source/calculators/specificity.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchi2.o source/calculators/structchi2.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1715,6 +1752,12 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual EstOutput SpeciesProfile::getValues(std::vector)' at source/calculators/speciesprofile.cpp:15:14: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1729,19 +1772,13 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput SpeciesProfile::getValues(std::vector)' at source/calculators/speciesprofile.cpp:15:14: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual EstOutput Spearman::getValues(std::vector)' at source/calculators/spearman.cpp:16:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchi2.o source/calculators/structchi2.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchord.o source/calculators/structchord.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structeuclidean.o source/calculators/structeuclidean.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structkulczynski.o source/calculators/structkulczynski.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1760,6 +1797,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structpearson.o source/calculators/structpearson.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1778,6 +1816,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tn.o source/calculators/tn.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -1790,34 +1829,31 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structkulczynski.o source/calculators/structkulczynski.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual EstOutput StructEuclidean::getValues(std::vector)' at source/calculators/structeuclidean.cpp:15:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structpearson.o source/calculators/structpearson.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tn.o source/calculators/tn.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tp.o source/calculators/tp.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/structpearson.h:15, - from source/calculators/structpearson.cpp:10: + from source/calculators/structkulczynski.h:14, + from source/calculators/structkulczynski.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput StructPearson::getValues(std::vector)' at source/calculators/structpearson.cpp:15:14: + inlined from 'virtual EstOutput StructKulczynski::getValues(std::vector)' at source/calculators/structkulczynski.cpp:15:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tp.o source/calculators/tp.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tptn.o source/calculators/tptn.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, @@ -1825,15 +1861,15 @@ from source/datastructures/datavector.hpp:4, from source/datastructures/sabundvector.hpp:4, from source/calculators/calculator.h:5, - from source/calculators/structkulczynski.h:14, - from source/calculators/structkulczynski.cpp:10: + from source/calculators/structpearson.h:15, + from source/calculators/structpearson.cpp:10: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput StructKulczynski::getValues(std::vector)' at source/calculators/structkulczynski.cpp:15:14: + inlined from 'virtual EstOutput StructPearson::getValues(std::vector)' at source/calculators/structpearson.cpp:15:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1848,6 +1884,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeraslayer.o source/chimera/chimeraslayer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/decalc.o source/chimera/decalc.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/maligner.o source/chimera/maligner.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/mothurchimera.o source/chimera/mothurchimera.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:71, from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, @@ -1864,6 +1901,7 @@ 157 | operator()(_Iterator1 __it1, _Iterator2 __it2) | ^~~~~~~~ /usr/include/c++/14/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/myPerseus.o source/chimera/myPerseus.cpp In file included from /usr/include/c++/14/vector:65, from source/mothur.h:41: /usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = data_struct*]': @@ -1904,7 +1942,15 @@ /usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/mothurchimera.o source/chimera/mothurchimera.cpp +In file included from /usr/include/c++/14/vector:72, + from source/mothur.h:41, + from source/mothurout.h:13, + from source/chimera/myPerseus.h:14, + from source/chimera/myPerseus.cpp:10: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1770 | __insertion_sort(_RandomAccessIterator __first, @@ -1915,6 +1961,12 @@ /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double Perseus::basicPairwiseAlignSeqs(std::string, std::string, std::string&, std::string&, pwModel)' at source/chimera/myPerseus.cpp:65:25: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/14/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, @@ -2012,29 +2064,15 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/myPerseus.o source/chimera/myPerseus.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/pintail.o source/chimera/pintail.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/slayer.o source/chimera/slayer.cpp -In file included from /usr/include/c++/14/vector:72, - from source/mothur.h:41, - from source/mothurout.h:13, - from source/chimera/myPerseus.h:14, - from source/chimera/myPerseus.cpp:10: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double Perseus::basicPairwiseAlignSeqs(std::string, std::string, std::string&, std::string&, pwModel)' at source/chimera/myPerseus.cpp:65:25: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double Perseus::modeledPairwiseAlignSeqs(std::string, std::string, std::string&, std::string&, std::vector >&)' at source/chimera/myPerseus.cpp:308:25: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/slayer.o source/chimera/slayer.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/alignnode.o source/classifier/alignnode.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/aligntree.o source/classifier/aligntree.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:71, from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, @@ -2052,20 +2090,20 @@ 157 | operator()(_Iterator1 __it1, _Iterator2 __it2) | ^~~~~~~~ /usr/include/c++/14/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/alignnode.o source/classifier/alignnode.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/bayesian.o source/classifier/bayesian.cpp In file included from /usr/include/c++/14/algorithm:61, from source/mothur.h:54: /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/aligntree.o source/classifier/aligntree.cpp /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/bayesian.o source/classifier/bayesian.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/classify.o source/classifier/classify.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmernode.o source/classifier/kmernode.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61: /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = data_struct; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -2130,6 +2168,7 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmertree.o source/classifier/kmertree.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(data_struct, data_struct)]' at /usr/include/c++/14/bits/stl_algo.h:4804:18, inlined from 'std::string Slayer::getResults(Sequence, std::vector)' at source/chimera/slayer.cpp:82:8: @@ -2150,9 +2189,6 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/classify.o source/classifier/classify.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmernode.o source/classifier/kmernode.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmertree.o source/classifier/kmertree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/knn.o source/classifier/knn.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylosummary.o source/classifier/phylosummary.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylotree.o source/classifier/phylotree.cpp @@ -2161,11 +2197,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/clearcut.o source/clearcut/clearcut.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp -source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)': -source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 456 | fscanf(fp, "%ld\n", &dmat->ntaxa); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ source/clearcut/distclearcut.cpp: In function 'DMAT* NJ_compute_dmat(NJ_ARGS*, NJ_alignment*)': source/clearcut/distclearcut.cpp:155:41: warning: 'char* __builtin_strncat(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 155 | *dmat->taxaname[i] = '\0'; strncat(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i])+1); @@ -2173,11 +2204,17 @@ source/clearcut/distclearcut.cpp:155:89: note: length computed here 155 | *dmat->taxaname[i] = '\0'; strncat(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i])+1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp +source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)': +source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 456 | fscanf(fp, "%ld\n", &dmat->ntaxa); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncheckcommand.o source/commands/aligncheckcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/alignmusclecommand.o source/commands/alignmusclecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp source/commands/alignmusclecommand.cpp: In member function 'void AlignMuscleCommand::wrapperFunction()': source/commands/alignmusclecommand.cpp:297:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 297 | system(commandString.c_str()); @@ -2197,9 +2234,10 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp In file included from /usr/include/c++/14/algorithm:61, from source/mothur.h:54, from source/commands/command.hpp:16, @@ -2247,9 +2285,6 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp In file included from /usr/include/c++/14/vector:65, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -2269,6 +2304,8 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Taxonomy*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Taxonomy*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Taxonomy*; _Tp = Taxonomy]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, @@ -2277,16 +2314,19 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)': source/commands/chimerauchimecommand.cpp:517:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 517 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp +source/commands/chimeravsearchcommand.cpp: In function 'void driver(vsearchData*)': +source/commands/chimeravsearchcommand.cpp:412:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 412 | system(commandString.c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:65, from source/mothur.h:41, from source/commands/chimeraslayercommand.h:13, @@ -2296,10 +2336,6 @@ 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -source/commands/chimeravsearchcommand.cpp: In function 'void driver(vsearchData*)': -source/commands/chimeravsearchcommand.cpp:412:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 412 | system(commandString.c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = data_struct*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = data_struct*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = data_struct*; _Tp = data_struct]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, @@ -2325,12 +2361,12 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)': source/commands/clustercommand.cpp:542:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 542 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:71, @@ -2353,6 +2389,35 @@ source/commands/clustersplitcommand.cpp:1050:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1050 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algo.h:61, + from /usr/include/c++/14/algorithm:61, + from source/mothur.h:54, + from source/commands/command.hpp:16, + from source/commands/clustersplitcommand.h:13, + from source/commands/clustersplitcommand.cpp:10: +/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1770 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1876 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/set:62, + from source/mothur.h:42: +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from source/mothur.h:54: /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': @@ -2453,36 +2518,9 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algo.h:61, - from /usr/include/c++/14/algorithm:61, - from source/mothur.h:54, - from source/commands/command.hpp:16, - from source/commands/clustersplitcommand.h:13, - from source/commands/clustersplitcommand.cpp:10: -/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1770 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1876 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/set:62, - from source/mothur.h:42: -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]', @@ -2523,7 +2561,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -2554,7 +2591,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -2576,6 +2612,9 @@ 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -2591,9 +2630,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp @@ -2604,22 +2640,8 @@ source/commands/distancecommand.cpp:323:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 323 | system(("gzip -v " + outputFile).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from source/mothur.h:41, - from source/commands/command.hpp:16, - from source/commands/distsharedcommand.h:12, - from source/commands/distsharedcommand.cpp:10: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput SharedNSeqs::getValues(std::vector)' at source/calculators/sharednseqs.h:22:14: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/fastaqinfocommand.o source/commands/fastaqinfocommand.cpp In file included from /usr/include/c++/14/vector:65, from source/mothur.h:41, from source/commands/distancecommand.h:13, @@ -2661,23 +2683,26 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from source/mothur.h:41, + from source/commands/command.hpp:16, + from source/commands/distsharedcommand.h:12, + from source/commands/distsharedcommand.cpp:10: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int process(distSharedData*)' at source/commands/distsharedcommand.cpp:458:90: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int DistSharedCommand::createProcesses(SharedRAbundVectors*&)' at source/commands/distsharedcommand.cpp:567:81: + inlined from 'virtual EstOutput SharedNSeqs::getValues(std::vector)' at source/calculators/sharednseqs.h:22:14: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int DistSharedCommand::createProcesses(SharedRAbundVectors*&)' at source/commands/distsharedcommand.cpp:571:84: + inlined from 'int process(distSharedData*)' at source/commands/distsharedcommand.cpp:458:90: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/fastaqinfocommand.o source/commands/fastaqinfocommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -2693,9 +2718,21 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int DistSharedCommand::createProcesses(SharedRAbundVectors*&)' at source/commands/distsharedcommand.cpp:567:81: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int DistSharedCommand::createProcesses(SharedRAbundVectors*&)' at source/commands/distsharedcommand.cpp:571:84: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -2705,14 +2742,13 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int GetCoreMicroBiomeCommand::createTable(SharedRAbundFloatVectors*&)' at source/commands/getcoremicrobiomecommand.cpp:239:65: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlabelcommand.o source/commands/getlabelcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlineagecommand.o source/commands/getlineagecommand.cpp @@ -2720,6 +2756,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmetacommunitycommand.o source/commands/getmetacommunitycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmimarkspackagecommand.o source/commands/getmimarkspackagecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getotuscommand.o source/commands/getotuscommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -2822,7 +2859,6 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getotuscommand.o source/commands/getotuscommand.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > GetMetaCommunityCommand::generateDistanceMatrix(SharedRAbundVectors*&)' at source/commands/getmetacommunitycommand.cpp:766:86: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -2845,8 +2881,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsharedotucommand.o source/commands/getsharedotucommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapsimcommand.o source/commands/heatmapsimcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/helpcommand.o source/commands/helpcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/homovacommand.o source/commands/homovacommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -2867,6 +2901,10 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/helpcommand.o source/commands/helpcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/homovacommand.o source/commands/homovacommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/indicatorcommand.o source/commands/indicatorcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -2882,9 +2920,18 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/indicatorcommand.o source/commands/indicatorcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/lefsecommand.o source/commands/lefsecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotuscommand.o source/commands/listotuscommand.cpp +In file included from /usr/include/c++/14/set:62, + from source/mothur.h:42, + from source/commands/command.hpp:16, + from source/commands/libshuffcommand.h:13, + from source/commands/libshuffcommand.cpp:16: +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/set:62, from source/mothur.h:42, from source/commands/command.hpp:16, @@ -2894,7 +2941,6 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': @@ -2909,53 +2955,46 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::map LefseCommand::runKruskalWallis(SharedRAbundFloatVectors*&, SharedCLRVectors*&, DesignMap&)' at source/commands/lefsecommand.cpp:497:63: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', + inlined from 'int LibShuffCommand::printCoverageFile()' at source/commands/libshuffcommand.cpp:322:53: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/set:62, - from source/mothur.h:42, - from source/commands/command.hpp:16, - from source/commands/libshuffcommand.h:13, - from source/commands/libshuffcommand.cpp:16: -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::map LefseCommand::runWilcoxon(SharedRAbundFloatVectors*&, SharedCLRVectors*&, std::map, std::map, std::set > >&, std::map, std::vector >&, std::map, std::__cxx11::basic_string >)' at source/commands/lefsecommand.cpp:533:50: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', + inlined from 'int LibShuffCommand::printCoverageFile()' at source/commands/libshuffcommand.cpp:323:51: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void LefseCommand::printResults(std::vector >, std::map, std::map, std::string, std::vector >, std::vector >, std::string)' at source/commands/lefsecommand.cpp:1044:53: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', + inlined from 'int LibShuffCommand::printCoverageFile()' at source/commands/libshuffcommand.cpp:326:51: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void LefseCommand::printResults(std::vector >, std::map, std::map, std::string, std::vector >, std::vector >, std::string)' at source/commands/lefsecommand.cpp:1045:92: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', + inlined from 'int LibShuffCommand::printCoverageFile()' at source/commands/libshuffcommand.cpp:327:51: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/map:63, + from source/mothur.h:43: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void LefseCommand::printResultsAll(std::vector >, std::map, std::map, std::string, std::vector >, std::vector >, std::string)' at source/commands/lefsecommand.cpp:1089:53: + inlined from 'std::map LefseCommand::runKruskalWallis(SharedRAbundFloatVectors*&, SharedCLRVectors*&, DesignMap&)' at source/commands/lefsecommand.cpp:497:63: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2964,7 +3003,7 @@ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void LefseCommand::printResultsAll(std::vector >, std::map, std::map, std::string, std::vector >, std::vector >, std::string)' at source/commands/lefsecommand.cpp:1090:92: + inlined from 'std::map LefseCommand::runWilcoxon(SharedRAbundFloatVectors*&, SharedCLRVectors*&, std::map, std::map, std::set > >&, std::map, std::vector >&, std::map, std::__cxx11::basic_string >)' at source/commands/lefsecommand.cpp:533:50: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2972,13 +3011,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector > LefseCommand::lda(std::vector >&, std::vector, std::map >&, std::vector >)' at source/commands/lefsecommand.cpp:926:47: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::map LefseCommand::testLDA(SharedRAbundFloatVectors*&, SharedCLRVectors*&, std::map, std::map, std::vector >&, std::map, std::vector >&)' at source/commands/lefsecommand.cpp:830:57: + inlined from 'void LefseCommand::printResults(std::vector >, std::map, std::map, std::string, std::vector >, std::vector >, std::string)' at source/commands/lefsecommand.cpp:1044:53: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2986,47 +3020,49 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/map:63, - from source/mothur.h:43: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', - inlined from 'int LibShuffCommand::printCoverageFile()' at source/commands/libshuffcommand.cpp:322:53: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void LefseCommand::printResults(std::vector >, std::map, std::map, std::string, std::vector >, std::vector >, std::string)' at source/commands/lefsecommand.cpp:1045:92: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', - inlined from 'int LibShuffCommand::printCoverageFile()' at source/commands/libshuffcommand.cpp:323:51: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void LefseCommand::printResultsAll(std::vector >, std::map, std::map, std::string, std::vector >, std::vector >, std::string)' at source/commands/lefsecommand.cpp:1089:53: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', - inlined from 'int LibShuffCommand::printCoverageFile()' at source/commands/libshuffcommand.cpp:326:51: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void LefseCommand::printResultsAll(std::vector >, std::map, std::map, std::string, std::vector >, std::vector >, std::string)' at source/commands/lefsecommand.cpp:1090:92: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', - inlined from 'int LibShuffCommand::printCoverageFile()' at source/commands/libshuffcommand.cpp:327:51: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listseqscommand.o source/commands/listseqscommand.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector > LefseCommand::lda(std::vector >&, std::vector, std::map >&, std::vector >)' at source/commands/lefsecommand.cpp:926:47: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makebiomcommand.o source/commands/makebiomcommand.cpp +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::map LefseCommand::testLDA(SharedRAbundFloatVectors*&, SharedCLRVectors*&, std::map, std::map, std::vector >&, std::map, std::vector >&)' at source/commands/lefsecommand.cpp:830:57: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotuscommand.o source/commands/listotuscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listseqscommand.o source/commands/listseqscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makebiomcommand.o source/commands/makebiomcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makeclrcommand.o source/commands/makeclrcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp In file included from /usr/include/c++/14/vector:65, @@ -3073,11 +3109,11 @@ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::string)': source/commands/makefilecommand.cpp:473:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 473 | system(findCommand.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makesharedcommand.o source/commands/makesharedcommand.cpp @@ -3125,6 +3161,16 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergetaxsummarycommand.o source/commands/mergetaxsummarycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/metastatscommand.o source/commands/metastatscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mgclustercommand.o source/commands/mgclustercommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mimarksattributescommand.o source/commands/mimarksattributescommand.cpp +In file included from /usr/include/c++/14/set:62, + from source/mothur.h:42, + from source/commands/command.hpp:16, + from source/commands/mgclustercommand.h:13, + from source/commands/mgclustercommand.cpp:10: +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, long long int>; _KeyOfValue = std::_Select1st, long long int> >; _Compare = std::less >; _Alloc = std::allocator, long long int> >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, std::less >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -3145,17 +3191,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/set:62, - from source/mothur.h:42, - from source/commands/command.hpp:16, - from source/commands/mgclustercommand.h:13, - from source/commands/mgclustercommand.cpp:10: -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, long long int>; _KeyOfValue = std::_Select1st, long long int> >; _Compare = std::less >; _Alloc = std::allocator, long long int> >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, std::less >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mimarksattributescommand.o source/commands/mimarksattributescommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long int; _Compare = std::less >; _Alloc = std::allocator, long long int> >]', @@ -3194,7 +3231,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/normalizesharedcommand.o source/commands/normalizesharedcommand.cpp In file included from /usr/include/c++/14/vector:72, @@ -3212,13 +3248,13 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > NMDSCommand::nmdsCalc(std::vector >&, std::vector >&, double&)' at source/commands/nmdscommand.cpp:280:52: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()': source/commands/pairwiseseqscommand.cpp:339:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3226,6 +3262,7 @@ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp In file included from /usr/include/c++/14/set:62, from source/mothur.h:42, from source/commands/command.hpp:16, @@ -3246,6 +3283,26 @@ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, + from source/mothur.h:41, + from source/commands/command.hpp:16, + from source/commands/pcacommand.h:13, + from source/commands/pcacommand.cpp:10: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int PCACommand::process(SharedRAbundFloatVectors*&)' at source/commands/pcacommand.cpp:283:20: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int PCACommand::process(SharedRAbundFloatVectors*&)' at source/commands/pcacommand.cpp:307:23: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -3316,27 +3373,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from source/mothur.h:41, - from source/commands/command.hpp:16, - from source/commands/pcacommand.h:13, - from source/commands/pcacommand.cpp:10: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int PCACommand::process(SharedRAbundFloatVectors*&)' at source/commands/pcacommand.cpp:283:20: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int PCACommand::process(SharedRAbundFloatVectors*&)' at source/commands/pcacommand.cpp:307:23: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp @@ -3344,6 +3380,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/quitcommand.o source/commands/quitcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactcommand.o source/commands/rarefactcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -3359,6 +3396,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp In file included from /usr/include/c++/14/vector:65: /usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Sequence*]': /usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3407,9 +3445,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removegroupscommand.o source/commands/removegroupscommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -3435,6 +3470,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removegroupscommand.o source/commands/removegroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removelineagecommand.o source/commands/removelineagecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeotuscommand.o source/commands/removeotuscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removerarecommand.o source/commands/removerarecommand.cpp @@ -3453,6 +3489,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffinfocommand.o source/commands/sffinfocommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffmultiplecommand.o source/commands/sffmultiplecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhercommand.o source/commands/shhhercommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/shhhercommand.h:13, @@ -3477,7 +3514,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sortseqscommand.o source/commands/sortseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitabundcommand.o source/commands/splitabundcommand.cpp @@ -3490,6 +3526,7 @@ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -3519,7 +3556,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp @@ -3527,6 +3563,8 @@ source/commands/systemcommand.cpp:97:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | system(command.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/translateseqscommand.o source/commands/translateseqscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treesharedcommand.o source/commands/treesharedcommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -3542,7 +3580,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/translateseqscommand.o source/commands/translateseqscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int SummarySharedCommand::process(SharedRAbundVectors*, std::string, std::string, std::vector >)' at source/commands/summarysharedcommand.cpp:719:89: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3558,23 +3596,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treesharedcommand.o source/commands/treesharedcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp -In file included from /usr/include/c++/14/vector:72, - from source/mothur.h:41, - from source/commands/command.hpp:16, - from source/commands/treesharedcommand.h:13, - from source/commands/treesharedcommand.cpp:10: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput SharedNSeqs::getValues(std::vector)' at source/calculators/sharednseqs.h:22:14: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:65, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -3613,6 +3634,22 @@ 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp +In file included from /usr/include/c++/14/vector:72, + from source/mothur.h:41, + from source/commands/command.hpp:16, + from source/commands/treesharedcommand.h:13, + from source/commands/treesharedcommand.cpp:10: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual EstOutput SharedNSeqs::getValues(std::vector)' at source/calculators/sharednseqs.h:22:14: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int process(treeSharedData*)' at source/commands/treesharedcommand.cpp:626:90: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3628,8 +3665,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/commands/command.hpp:16, @@ -3645,6 +3680,24 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int UnifracUnweightedCommand::runRandomCalcs(Tree*, std::vector)' at source/commands/unifracunweightedcommand.cpp:596:53: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual int UnifracUnweightedCommand::execute()' at source/commands/unifracunweightedcommand.cpp:275:53: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual int UnifracUnweightedCommand::execute()' at source/commands/unifracunweightedcommand.cpp:318:57: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/uniqueseqscommand.o source/commands/uniqueseqscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/venncommand.o source/commands/venncommand.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from source/mothur.h:54, @@ -3668,27 +3721,12 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int UnifracUnweightedCommand::runRandomCalcs(Tree*, std::vector)' at source/commands/unifracunweightedcommand.cpp:596:53: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/set:62, from source/mothur.h:42: /usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual int UnifracUnweightedCommand::execute()' at source/commands/unifracunweightedcommand.cpp:275:53: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual int UnifracUnweightedCommand::execute()' at source/commands/unifracunweightedcommand.cpp:318:57: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': @@ -3701,8 +3739,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/uniqueseqscommand.o source/commands/uniqueseqscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/venncommand.o source/commands/venncommand.cpp In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', @@ -3755,6 +3791,23 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from source/mothur.h:41, + from source/commands/command.hpp:16, + from source/commands/venncommand.h:12, + from source/commands/venncommand.cpp:10: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'virtual EstOutput Sobs::getValues(SAbundVector*)' at source/calculators/sobs.h:26:14: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'int UnifracWeightedCommand::runRandomCalcs(Tree*, CountTable*, std::vector, int, std::vector&, std::vector >)' at source/commands/unifracweightedcommand.cpp:561:17: @@ -3793,56 +3846,40 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from source/mothur.h:41, + from source/mothurout.h:13, + from source/communitytype/communitytype.h:15, + from source/communitytype/communitytype.cpp:9: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual int UnifracWeightedCommand::execute()' at source/commands/unifracweightedcommand.cpp:263:53: + inlined from 'int CommunityTypeFinder::findkMeans()' at source/communitytype/communitytype.cpp:375:95: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual int UnifracWeightedCommand::execute()' at source/commands/unifracweightedcommand.cpp:264:57: + inlined from 'virtual int UnifracWeightedCommand::execute()' at source/commands/unifracweightedcommand.cpp:263:53: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual int UnifracWeightedCommand::execute()' at source/commands/unifracweightedcommand.cpp:293:57: + inlined from 'virtual int UnifracWeightedCommand::execute()' at source/commands/unifracweightedcommand.cpp:264:57: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from source/mothur.h:41, - from source/commands/command.hpp:16, - from source/commands/venncommand.h:12, - from source/commands/venncommand.cpp:10: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'virtual EstOutput Sobs::getValues(SAbundVector*)' at source/calculators/sobs.h:26:14: + inlined from 'virtual int UnifracWeightedCommand::execute()' at source/commands/unifracweightedcommand.cpp:293:57: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/pam.o source/communitytype/pam.cpp -In file included from /usr/include/c++/14/vector:72, - from source/mothur.h:41, - from source/mothurout.h:13, - from source/communitytype/communitytype.h:15, - from source/communitytype/communitytype.cpp:9: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int CommunityTypeFinder::findkMeans()' at source/communitytype/communitytype.cpp:375:95: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/qFinderDMM.o source/communitytype/qFinderDMM.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -3864,11 +3901,12 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/aminoacid.o source/datastructures/aminoacid.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/biom.o source/datastructures/biom.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/biomhdf5.o source/datastructures/biomhdf5.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/biomsimple.o source/datastructures/biomsimple.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/contigsreport.o source/datastructures/contigsreport.cpp In file included from /usr/include/c++/14/vector:65, from source/mothur.h:41, from source/mothurout.h:13, @@ -3896,8 +3934,7 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/biomsimple.o source/datastructures/biomsimple.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/contigsreport.o source/datastructures/contigsreport.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp In file included from /usr/include/c++/14/vector:65, from source/mothur.h:41, from source/mothurout.h:13, @@ -3918,7 +3955,6 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp In file included from /usr/include/c++/14/algorithm:61, @@ -4037,18 +4073,7 @@ /usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/set:62, - from source/mothur.h:42, - from source/mothurout.h:13, - from source/datastructures/optidata.hpp:12, - from source/datastructures/optirefmatrix.hpp:12, - from source/datastructures/optirefmatrix.cpp:9: -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, long long int>; _KeyOfValue = std::_Select1st, long long int> >; _Compare = std::less >; _Alloc = std::allocator, long long int> >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, std::less >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', @@ -4096,12 +4121,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp -In file included from /usr/include/c++/14/map:63, - from source/mothur.h:43: -/usr/include/c++/14/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]': +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:65:82: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4109,8 +4130,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long int; _Compare = std::less >; _Alloc = std::allocator, long long int> >]': -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, std::less >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:83:82: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), @@ -4118,7 +4140,7 @@ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:65:82: + inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:103:37: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4127,7 +4149,7 @@ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:83:82: + inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:138:45: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4136,7 +4158,7 @@ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:103:37: + inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:147:62: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4145,7 +4167,7 @@ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:138:45: + inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:148:62: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4154,7 +4176,7 @@ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:147:62: + inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:166:45: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4163,7 +4185,7 @@ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:148:62: + inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:174:62: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4172,7 +4194,7 @@ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:166:45: + inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:175:62: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4180,8 +4202,26 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:174:62: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/picrust.o source/datastructures/picrust.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/protein.o source/datastructures/protein.cpp +In file included from /usr/include/c++/14/set:62, + from source/mothur.h:42, + from source/mothurout.h:13, + from source/datastructures/optidata.hpp:12, + from source/datastructures/optirefmatrix.hpp:12, + from source/datastructures/optirefmatrix.cpp:9: +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, long long int>; _KeyOfValue = std::_Select1st, long long int> >; _Compare = std::less >; _Alloc = std::allocator, long long int> >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, std::less >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/proteindb.o source/datastructures/proteindb.cpp +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +In file included from /usr/include/c++/14/map:63, + from source/mothur.h:43: +/usr/include/c++/14/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4189,9 +4229,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int OptiMatrix::readPhylip()' at source/datastructures/optimatrix.cpp:175:62: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +/usr/include/c++/14/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long int; _Compare = std::less >; _Alloc = std::allocator, long long int> >]': +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, std::less >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), @@ -4297,6 +4336,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:65, + from source/mothur.h:41, + from source/mothurout.h:13, + from source/datastructures/protein.hpp:12, + from source/datastructures/protein.cpp:9: +/usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]': +/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map OptiRefMatrix::readPhylipSingletons(std::vector&, std::string, long long int&, std::map, long long int>&)' at source/datastructures/optirefmatrix.cpp:818:29: /usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -4324,6 +4373,54 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1624:35, + inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:238:44: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'std::vector Protein::getAligned()' at source/datastructures/protein.cpp:538:49: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'std::vector Protein::getPairwise()' at source/datastructures/protein.cpp:567:50: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'std::vector Protein::getUnaligned()' at source/datastructures/protein.cpp:571:51: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'std::string Protein::getInlineProtein()' at source/datastructures/protein.cpp:559:34: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void Protein::printProtein(std::ostream&)' at source/datastructures/protein.cpp:592:28: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'int OptiRefMatrix::readFiles(std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string)' at source/datastructures/optirefmatrix.cpp:682:37: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -4342,8 +4439,97 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/picrust.o source/datastructures/picrust.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/protein.o source/datastructures/protein.cpp +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void Protein::printUnAlignedProtein(std::ostream&)' at source/datastructures/protein.cpp:599:28: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void Protein::printProtein(OutputWriter*)' at source/datastructures/protein.cpp:584:58: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:65, + from source/mothur.h:41, + from source/mothurout.h:13, + from source/datastructures/protein.hpp:12, + from source/datastructures/proteindb.hpp:12, + from source/datastructures/proteindb.cpp:9: +/usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]': +/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1624:35, + inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:238:44: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(const Protein&)' at source/datastructures/protein.hpp:21:7: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(const Protein&)' at source/datastructures/protein.hpp:21:7: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(const Protein&)' at source/datastructures/protein.hpp:21:7: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void Protein::filterToPos(int)' at source/datastructures/protein.cpp:638:17: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void Protein::filterFromPos(int)' at source/datastructures/protein.cpp:656:17: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void Protein::setAligned(std::vector)' at source/datastructures/protein.cpp:507:17: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void Protein::setAligned(std::string)' at source/datastructures/protein.cpp:497:15: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long int; _Compare = std::less >; _Alloc = std::allocator, long long int> >]', inlined from 'int OptiRefMatrix::readFiles(std::string, std::string, std::string, std::string, std::unordered_set >&)' at source/datastructures/optirefmatrix.cpp:551:37: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, std::less >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 @@ -4362,6 +4548,73 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void Protein::trim(int)' at source/datastructures/protein.cpp:709:19: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = Protein; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::string, std::vector)' at source/datastructures/protein.cpp:25:21: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::string, std::vector)' at source/datastructures/protein.cpp:26:19: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::string, std::string)' at source/datastructures/protein.cpp:48:21: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::string, std::string)' at source/datastructures/protein.cpp:49:19: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = Protein; _Alloc = std::allocator]', + inlined from 'ProteinDB::ProteinDB(int)' at source/datastructures/proteindb.cpp:20:69: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::istringstream&)' at source/datastructures/protein.cpp:85:23: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::istringstream&)' at source/datastructures/protein.cpp:86:25: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'virtual OptiData* OptiRefMatrix::extractRefMatrix()' at source/datastructures/optirefmatrix.cpp:96:31: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -4452,6 +4705,39 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::ifstream&)' at source/datastructures/protein.cpp:126:23: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::ifstream&)' at source/datastructures/protein.cpp:127:25: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::ifstream&, std::string&, bool)' at source/datastructures/protein.cpp:216:23: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'Protein::Protein(std::ifstream&, std::string&, bool)' at source/datastructures/protein.cpp:217:25: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'virtual OptiData* OptiRefMatrix::extractMatrixSubset(std::set&)' at source/datastructures/optirefmatrix.cpp:186:31: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -4542,257 +4828,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:65, - from source/mothur.h:41, - from source/mothurout.h:13, - from source/datastructures/protein.hpp:12, - from source/datastructures/protein.cpp:9: -/usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]': -/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1624:35, - inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:238:44: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'std::vector Protein::getAligned()' at source/datastructures/protein.cpp:538:49: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'std::vector Protein::getPairwise()' at source/datastructures/protein.cpp:567:50: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'std::vector Protein::getUnaligned()' at source/datastructures/protein.cpp:571:51: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'std::string Protein::getInlineProtein()' at source/datastructures/protein.cpp:559:34: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void Protein::printProtein(std::ostream&)' at source/datastructures/protein.cpp:592:28: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/proteindb.o source/datastructures/proteindb.cpp -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void Protein::printUnAlignedProtein(std::ostream&)' at source/datastructures/protein.cpp:599:28: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void Protein::printProtein(OutputWriter*)' at source/datastructures/protein.cpp:584:58: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void Protein::filterToPos(int)' at source/datastructures/protein.cpp:638:17: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void Protein::filterFromPos(int)' at source/datastructures/protein.cpp:656:17: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void Protein::setAligned(std::vector)' at source/datastructures/protein.cpp:507:17: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void Protein::setAligned(std::string)' at source/datastructures/protein.cpp:497:15: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void Protein::trim(int)' at source/datastructures/protein.cpp:709:19: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::string, std::vector)' at source/datastructures/protein.cpp:25:21: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::string, std::vector)' at source/datastructures/protein.cpp:26:19: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::string, std::string)' at source/datastructures/protein.cpp:48:21: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::string, std::string)' at source/datastructures/protein.cpp:49:19: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::istringstream&)' at source/datastructures/protein.cpp:85:23: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::istringstream&)' at source/datastructures/protein.cpp:86:25: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::ifstream&)' at source/datastructures/protein.cpp:126:23: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::ifstream&)' at source/datastructures/protein.cpp:127:25: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::ifstream&, std::string&, bool)' at source/datastructures/protein.cpp:216:23: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(std::ifstream&, std::string&, bool)' at source/datastructures/protein.cpp:217:25: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:65, - from source/mothur.h:41, - from source/mothurout.h:13, - from source/datastructures/protein.hpp:12, - from source/datastructures/proteindb.hpp:12, - from source/datastructures/proteindb.cpp:9: -/usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]': -/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1624:35, - inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:238:44: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(const Protein&)' at source/datastructures/protein.hpp:21:7: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(const Protein&)' at source/datastructures/protein.hpp:21:7: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = AminoAcid*; _Tp = AminoAcid]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'Protein::Protein(const Protein&)' at source/datastructures/protein.hpp:21:7: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = Protein; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundfloatvector.o source/datastructures/rabundfloatvector.cpp -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = Protein; _Alloc = std::allocator]', - inlined from 'ProteinDB::ProteinDB(int)' at source/datastructures/proteindb.cpp:20:69: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/report.o source/datastructures/report.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp @@ -4811,13 +4847,13 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sffread.o source/datastructures/sffread.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = Sequence; _Alloc = std::allocator]', inlined from 'SequenceDB::SequenceDB(int)' at source/datastructures/sequencedb.cpp:25:70: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sffread.o source/datastructures/sffread.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedclrvector.o source/datastructures/sharedclrvector.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedclrvectors.o source/datastructures/sharedclrvectors.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp @@ -4841,6 +4877,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readblast.o source/read/readblast.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcluster.o source/read/readcluster.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -4861,6 +4898,11 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector MothurMetastats::permuted_pvalues(std::vector >&, std::vector&, std::vector >&)' at source/metastats/mothurmetastats.cpp:254:78: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from source/mothur.h:54, from source/read/readblast.h:12, @@ -4887,12 +4929,7 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcluster.o source/read/readcluster.cpp -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector MothurMetastats::permuted_pvalues(std::vector >&, std::vector&, std::vector >&)' at source/metastats/mothurmetastats.cpp:254:78: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcolumn.o source/read/readcolumn.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(seqDist, seqDist)]' at /usr/include/c++/14/bits/stl_algo.h:4804:18, inlined from 'int ReadBlast::read(NameAssignment*)' at source/read/readblast.cpp:241:13: @@ -4963,7 +5000,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcolumn.o source/read/readcolumn.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylip.o source/read/readphylip.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readtree.o source/read/readtree.cpp @@ -4971,6 +5007,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/treereader.o source/read/treereader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/svm/svm.o source/svm/svm.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/alignreport.o source/alignreport.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/averagelinkage.o source/averagelinkage.cpp In file included from /usr/include/c++/14/map:62, from source/svm/svm.hpp:18, from source/svm/svm.cpp:17: @@ -4978,7 +5015,7 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/averagelinkage.o source/averagelinkage.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp In file included from /usr/include/c++/14/map:63: /usr/include/c++/14/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 @@ -4988,6 +5025,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'void SmoTrainer::assignNumericLabels(std::vector&, const LabeledObservationVector&, NumericClassToLabel&)' at source/svm/svm.cpp:674:59: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 @@ -4997,8 +5035,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clusterclassic.o source/clusterclassic.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'ParameterSetBuilder::ParameterSetBuilder(const ParameterRangeMap&)' at source/svm/svm.hpp:296:47: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 @@ -5017,7 +5054,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clusterclassic.o source/clusterclassic.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/collect.o source/collect.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandfactory.o source/commandfactory.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandoptionparser.o source/commandoptionparser.cpp @@ -5034,6 +5070,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/linearalgebra.o source/linearalgebra.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothur.o source/mothur.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothurout.o source/mothurout.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/myseqdist.o source/myseqdist.cpp In file included from /usr/include/c++/14/set:62, from source/mothur.h:42, from source/mothurout.h:13, @@ -5043,9 +5080,23 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/myseqdist.o source/myseqdist.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nast.o source/nast.cpp In file included from /usr/include/c++/14/vector:72, + from source/mothur.h:41, + from source/mothurout.h:13, + from source/myseqdist.h:14, + from source/myseqdist.cpp:10: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double getDist(std::vector&, std::vector&, std::vector >&, MothurOut*)' at source/myseqdist.cpp:183:34: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -5072,21 +5123,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from source/mothur.h:41, - from source/mothurout.h:13, - from source/myseqdist.h:14, - from source/myseqdist.cpp:10: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double getDist(std::vector&, std::vector&, std::vector >&, MothurOut*)' at source/myseqdist.cpp:183:34: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > LinearAlgebra::lda(std::vector >&, std::vector >, std::vector >&, bool&)' at source/linearalgebra.cpp:2074:90: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -5099,6 +5135,28 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/needlemanoverlap.o source/needlemanoverlap.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/noalign.o source/noalign.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/opticluster.o source/opticluster.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optifitcluster.o source/optifitcluster.cpp +In file included from /usr/include/c++/14/vector:72, + from source/mothur.h:41, + from source/mothurout.h:13, + from source/datastructures/alignmentcell.hpp:15, + from source/needlemanoverlap.cpp:20: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AminoAcid&}; _Tp = AminoAcid; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:452:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 452 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = AminoAcid; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:133:5: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 + 133 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/vector.tcc:170:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 170 | _M_realloc_insert(begin() + (__position - cbegin()), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +source/needlemanoverlap.cpp: In member function 'virtual void NeedlemanOverlap::align(Sequence, Protein)': +source/needlemanoverlap.cpp:124:20: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 + 124 | seqB.insert(seqB.begin(), dummy); lB = seqB.size(); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', @@ -5164,29 +5222,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from source/mothur.h:41, - from source/mothurout.h:13, - from source/datastructures/alignmentcell.hpp:15, - from source/needlemanoverlap.cpp:20: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AminoAcid&}; _Tp = AminoAcid; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:452:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 452 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = AminoAcid; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:133:5: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 - 133 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/vector.tcc:170:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 170 | _M_realloc_insert(begin() + (__position - cbegin()), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/opticluster.o source/opticluster.cpp -source/needlemanoverlap.cpp: In member function 'virtual void NeedlemanOverlap::align(Sequence, Protein)': -source/needlemanoverlap.cpp:124:20: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 - 124 | seqB.insert(seqB.begin(), dummy); lB = seqB.size(); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optifitcluster.o source/optifitcluster.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optionparser.o source/optionparser.cpp In file included from /usr/include/c++/14/set:62, from source/mothur.h:42, from source/datastructures/sparsedistancematrix.h:12, @@ -5211,6 +5246,7 @@ 2161 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:2161:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optionparser.o source/optionparser.cpp In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', @@ -5240,6 +5276,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/overlap.o source/overlap.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'int OptiCluster::initialize(double&, bool, std::string)' at source/opticluster.cpp:28:23: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -5279,9 +5316,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/overlap.o source/overlap.cpp /usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/raredisplay.o source/raredisplay.cpp In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', @@ -5311,7 +5348,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/raredisplay.o source/raredisplay.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarefact.o source/rarefact.cpp In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -5324,52 +5361,6 @@ 2161 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:2161:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarefact.o source/rarefact.cpp -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', - inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:422:38: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', - inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:424:38: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', - inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:442:38: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', - inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:444:38: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', - inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:517:55: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from source/mothur.h:54, @@ -5415,6 +5406,52 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/refchimeratest.o source/refchimeratest.cpp +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', + inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:422:38: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', + inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:424:38: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', + inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:442:38: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', + inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:444:38: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = std::__cxx11::basic_string; _Compare = std::less; _Alloc = std::allocator > >]', + inlined from 'ListVector* OptiFitCluster::getFittedList(std::string, bool)' at source/optifitcluster.cpp:517:55: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'virtual bool OptiFitCluster::update(double&)' at source/optifitcluster.cpp:170:149: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -5442,7 +5479,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/refchimeratest.o source/refchimeratest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/sensspeccalc.o source/sensspeccalc.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, @@ -5454,13 +5490,13 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/seqnoise.o source/seqnoise.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double RefChimeraTest::alignQueryToReferences(std::string, std::string, std::string&, std::string&, double&)' at source/refchimeratest.cpp:271:25: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/seqnoise.o source/seqnoise.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/singlelinkage.o source/singlelinkage.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/slibshuff.o source/slibshuff.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/subsample.o source/subsample.cpp @@ -5473,6 +5509,12 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int seqNoise::countDiffs(std::vector, std::vector)' at source/seqnoise.cpp:613:25: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from source/mothur.h:54, @@ -5483,17 +5525,12 @@ /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/summary.o source/summary.cpp /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int seqNoise::countDiffs(std::vector, std::vector)' at source/seqnoise.cpp:613:25: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -5570,8 +5607,35 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/summary.o source/summary.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trialSwap2.o source/trialSwap2.cpp +In file included from /usr/include/c++/14/vector:72, + from source/mothur.h:41, + from source/mothurout.h:13, + from source/trialswap2.h:13, + from source/trialSwap2.cpp:1: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trimoligos.o source/trimoligos.cpp +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double TrialSwap2::calc_c_score(std::vector >&, std::vector, int, int)' at source/trialSwap2.cpp:17:54: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/utils.o source/utils.cpp +In file included from /usr/include/c++/14/set:62, + from source/mothur.h:42, + from source/mothurout.h:13, + from source/summary.hpp:12, + from source/summary.cpp:9: +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = float; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 In file included from /usr/include/c++/14/set:62, from source/mothur.h:42, from source/mothurout.h:13, @@ -5610,32 +5674,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/set:62, - from source/mothur.h:42, - from source/mothurout.h:13, - from source/summary.hpp:12, - from source/summary.cpp:9: -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = float; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 -In file included from /usr/include/c++/14/vector:72, - from source/mothur.h:41, - from source/mothurout.h:13, - from source/trialswap2.h:13, - from source/trialSwap2.cpp:1: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double TrialSwap2::calc_c_score(std::vector >&, std::vector, int, int)' at source/trialSwap2.cpp:17:54: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: /usr/include/c++/14/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]': @@ -5646,7 +5684,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trimoligos.o source/trimoligos.cpp +source/utils.cpp: In member function 'bool Utils::findTool(std::string&, std::string&, std::vector >&, std::vector > >)': +source/utils.cpp:952:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 952 | system(versionTestCommand.c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +source/utils.cpp: In member function 'std::string Utils::sortFile(std::string, std::string)': +source/utils.cpp:1514:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1514 | system(command.c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = float; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void driverAlignSummarySummarize(seqSumData*)' at source/summary.cpp:896:87: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -5665,7 +5710,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/utils.o source/utils.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'long long int Summary::summarizeFasta(std::string, std::string)' at source/summary.cpp:389:44: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -5720,6 +5764,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validcalculator.o source/validcalculator.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'long long int Summary::summarizeFastaSummary(std::string)' at source/summary.cpp:596:44: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -5855,15 +5900,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -source/utils.cpp: In member function 'bool Utils::findTool(std::string&, std::string&, std::vector >&, std::vector > >)': -source/utils.cpp:952:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 952 | system(versionTestCommand.c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -source/utils.cpp: In member function 'std::string Utils::sortFile(std::string, std::string)': -source/utils.cpp:1514:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1514 | system(command.c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validcalculator.o source/validcalculator.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from source/mothur.h:54, @@ -5893,6 +5929,7 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, std::less >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'double Utils::median(std::vector)' at source/utils.cpp:4781:17: @@ -5973,8 +6010,9 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp In file included from /usr/include/c++/14/map:63, from source/mothur.h:43: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long int; _Compare = std::less >; _Alloc = std::allocator, long long int> >]', @@ -5995,27 +6033,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, - inlined from 'std::vector > Utils::getAverages(std::vector > >&, std::string)' at source/utils.cpp:6256:25: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, - inlined from 'std::vector > Utils::getAverages(std::vector > >&, std::string)' at source/utils.cpp:6256:25: -/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1822 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp +cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd .. +make[3]: Entering directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src' +make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +make[3]: Leaving directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src' +make[3]: Entering directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src' +make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o addtargets2.o addtargets2.cpp +g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alignchime.o alignchime.cpp In file included from /usr/include/c++/14/vector:72, from source/mothur.h:41, from source/mothurout.h:13, @@ -6044,6 +6070,28 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alignchimel.o alignchimel.cpp +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, + inlined from 'std::vector > Utils::getAverages(std::vector > >&, std::string)' at source/utils.cpp:6256:25: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, + inlined from 'std::vector > Utils::getAverages(std::vector > >&, std::string)' at source/utils.cpp:6256:25: +/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1822 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alnparams.o alnparams.cpp /usr/include/c++/14/bits/stl_algo.h: In function 'void std::shuffle(_RAIter, _RAIter, _UGenerator&&) [with _RAIter = __gnu_cxx::__normal_iterator >; _UGenerator = mersenne_twister_engine&]': /usr/include/c++/14/bits/stl_algo.h:3696:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 3696 | shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last, @@ -6062,18 +6110,6 @@ source/utils.cpp:125:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 125 | shuffle (randomize.begin(), randomize.end(), mersenne_twister_engine); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp -cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd .. -make[3]: Entering directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src' -make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. -make[3]: Leaving directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src' -make[3]: Entering directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src' -make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. -g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o addtargets2.o addtargets2.cpp -g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alignchime.o alignchime.cpp -g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alignchimel.o alignchimel.cpp -g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alnparams.o alnparams.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alpha.o alpha.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alpha2.o alpha2.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o fractid.o fractid.cpp @@ -6239,12 +6275,14 @@ 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/4460/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4460/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/3429 and its subdirectories -I: Current time: Sun Jan 5 09:52:53 -12 2025 -I: pbuilder-time-stamp: 1736113973 +I: removing directory /srv/workspace/pbuilder/4460 and its subdirectories +I: Current time: Mon Jan 6 12:55:14 +14 2025 +I: pbuilder-time-stamp: 1736117714