Diff of the two buildlogs: -- --- b1/build.log 2024-04-12 01:37:03.624902761 +0000 +++ b2/build.log 2024-04-12 01:47:27.214338606 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 11 13:15:20 -12 2024 -I: pbuilder-time-stamp: 1712884520 +I: Current time: Fri Apr 12 15:37:39 +14 2024 +I: pbuilder-time-stamp: 1712885859 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ dpkg-source: info: applying PR53.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/27178/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/12510/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +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 Apr 12 01:38 /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/12510/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/12510/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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(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='3e7c0eda19e74474933b81447220b1bb' - 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='27178' - PS1='# ' - PS2='> ' + INVOCATION_ID=44c4a5f104bf408ebb5befeabc4d8d74 + 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=12510 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.uJfMekil/pbuilderrc_qRUw --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.uJfMekil/b1 --logfile b1/build.log unifrac-tools_1.4-3.dsc' - SUDO_GID='116' - SUDO_UID='112' - 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.uJfMekil/pbuilderrc_j79D --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.uJfMekil/b2 --logfile b2/build.log unifrac-tools_1.4-3.dsc' + SUDO_GID=113 + SUDO_UID=107 + 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 cbxi4b 6.1.0-18-armmp #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 11 11:27 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/27178/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 10 11:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/12510/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -220,7 +252,7 @@ Get: 84 http://deb.debian.org/debian trixie/main armhf libtmglib-dev armhf 3.12.0-3 [93.9 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf liblapacke-dev armhf 3.12.0-3 [293 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf liblz4-dev armhf 1.9.4-2 [75.0 kB] -Fetched 46.9 MB in 4s (10.5 MB/s) +Fetched 46.9 MB in 5s (9957 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19635 files and directories currently installed.) @@ -507,8 +539,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Apr 12 01:17:08 UTC 2024. -Universal Time is now: Fri Apr 12 01:17:08 UTC 2024. +Local time is now: Fri Apr 12 01:40:09 UTC 2024. +Universal Time is now: Fri Apr 12 01:40:09 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -594,7 +626,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/unifrac-tools-1.4/ && 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 > ../unifrac-tools_1.4-3_source.changes +I: user script /srv/workspace/pbuilder/12510/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/12510/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/unifrac-tools-1.4/ && 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 > ../unifrac-tools_1.4-3_source.changes dpkg-buildpackage: info: source package unifrac-tools dpkg-buildpackage: info: source version 1.4-3 dpkg-buildpackage: info: source distribution unstable @@ -1297,1609 +1333,26 @@ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/status_enum.hpp; cp status_enum.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make clean && make api -/bin/sh: 1: source: not found -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -rm -f *.o ssu_nv_avx2 faithpd_nv_avx2 test_su test_ska test_api libssu_nv_avx2.so -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c tree.cpp -o tree.o -tree.cpp: In member function 'void su::BPTree::newick_to_bp(std::string)': -tree.cpp:321:67: warning: 'last_structure' may be used uninitialized [-Wmaybe-uninitialized] - 321 | if(potential_single_descendent || (last_structure == ',')) { - | ~~~~~~~~~~~~~~~~^~~~~~~ -tree.cpp:300:10: note: 'last_structure' was declared here - 300 | char last_structure; - | ^~~~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c biom.cpp -o biom.o -biom.cpp: In constructor 'su::biom::biom(std::string)': -biom.cpp:32:51: warning: implicitly-declared 'H5::H5File& H5::H5File::operator=(const H5::H5File&)' is deprecated [-Wdeprecated-copy] - 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); - | ^ -In file included from /usr/include/hdf5/serial/H5Cpp.h:47, - from biom.hpp:14, - from biom.cpp:13: -/usr/include/hdf5/serial/H5File.h:104:5: note: because 'H5::H5File' has user-provided 'H5::H5File::H5File(const H5::H5File&)' - 104 | H5File(const H5File &original); - | ^~~~~~ -/usr/include/hdf5/serial/H5File.h: In member function 'H5::H5File& H5::H5File::operator=(const H5::H5File&)': -/usr/include/hdf5/serial/H5File.h:24:17: warning: implicitly-declared 'H5::Group& H5::Group::operator=(const H5::Group&)' is deprecated [-Wdeprecated-copy] - 24 | class H5_DLLCPP H5File : public Group { - | ^~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:46: -/usr/include/hdf5/serial/H5Group.h:62:5: note: because 'H5::Group' has user-provided 'H5::Group::Group(const H5::Group&)' - 62 | Group(const Group &original); - | ^~~~~ -biom.cpp: In constructor 'su::biom::biom(std::string)': -biom.cpp:32:51: note: synthesized method 'H5::H5File& H5::H5File::operator=(const H5::H5File&)' first required here - 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); - | ^ -biom.cpp: In member function 'void su::biom::load_ids(const char*, std::vector >&)': -biom.cpp:134:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 135 | sizeof(char*) * dims[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp: In member function 'void su::biom::load_indptr(const char*, std::vector&)': -biom.cpp:166:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp: In member function 'unsigned int su::biom::get_obs_data_direct(const std::string&, uint32_t*&, double*&)': -biom.cpp:206:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp:212:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 213 | sizeof(double) * count[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp: In member function 'unsigned int su::biom::get_sample_data_direct(const std::string&, uint32_t*&, double*&)': -biom.cpp:251:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp:257:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 258 | sizeof(double) * count[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c biom_inmem.cpp -o biom_inmem.o -biom_inmem.cpp: In constructor 'su::biom_inmem::biom_inmem(const char* const*, const char* const*, uint32_t*, uint32_t*, double*, int, int)': -biom_inmem.cpp:328:30: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 328 | for(int i = 0; i < n_obs; i++) { - | ~~^~~~~~~ -biom_inmem.cpp:333:30: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 333 | for(int i = 0; i < n_samples; i++) { - | ~~^~~~~~~~~~~ -biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = double]': -biom_inmem.cpp:99:60: required from here -biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", - | ~~^ - | | - | long int - | %d - 24 | bufsize, __FILE__, __LINE__); - | ~~~~~~~ - | | - | size_t {aka unsigned int} -biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int]': -biom_inmem.cpp:100:62: required from here -biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", - | ~~^ - | | - | long int - | %d - 24 | bufsize, __FILE__, __LINE__); - | ~~~~~~~ - | | - | size_t {aka unsigned int} -biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int*]': -biom_inmem.cpp:177:55: required from here -biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", - | ~~^ - | | - | long int - | %d - 24 | bufsize, __FILE__, __LINE__); - | ~~~~~~~ - | | - | size_t {aka unsigned int} -biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = double*]': -biom_inmem.cpp:178:55: required from here -biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", - | ~~^ - | | - | long int - | %d - 24 | bufsize, __FILE__, __LINE__); - | ~~~~~~~ - | | - | size_t {aka unsigned int} -biom_inmem.cpp: In instantiation of 'void su::biom_inmem::get_obs_data_range_TT(uint32_t, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; uint32_t = unsigned int]': -biom_inmem.cpp:427:34: required from 'void su::biom_inmem::get_obs_data_range_TT(const std::string&, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; std::string = std::__cxx11::basic_string]' -biom_inmem.cpp:431:36: required from here -biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'unsigned int' [-Wsign-compare] - 410 | if ((j>=start)&&(j=start)&&(j]' -biom_inmem.cpp:435:36: required from here -biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'unsigned int' [-Wsign-compare] - 410 | if ((j>=start)&&(j=start)&&(j::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(const typename _Container::value_type&) [with _Container = std::vector]' at /usr/include/c++/13/bits/stl_iterator.h:739:22, - inlined from '_OutputIterator std::partial_sum(_InputIterator, _InputIterator, _OutputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = back_insert_iterator >]' at /usr/include/c++/13/bits/stl_numeric.h:270:17, - inlined from 'void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = unsigned int]' at /usr/include/c++/13/bits/random.tcc:2671:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(const typename _Container::value_type&) [with _Container = std::vector]' at /usr/include/c++/13/bits/stl_iterator.h:739:22, - inlined from '_OutputIterator std::partial_sum(_InputIterator, _InputIterator, _OutputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = back_insert_iterator >]' at /usr/include/c++/13/bits/stl_numeric.h:274:16, - inlined from 'void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = unsigned int]' at /usr/include/c++/13/bits/random.tcc:2671:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c tsv.cpp -o tsv.o -tsv.cpp: In member function 'void su::indexed_tsv::read_grouping(const std::string&, uint32_t*, uint32_t&) const': -tsv.cpp:126:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 126 | for (int i=1; i< header_line.size(); i++) { - | ~^~~~~~~~~~~~~~~~~~~~ -tsv.cpp:138:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 138 | for (int i=1; i< n_filter_els; i++) grouping[i] = n_filter_els; - | ~^~~~~~~~~~~~~~ -tsv.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 173 | for (int i=1; i< n_filter_els; i++) { - | ~^~~~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac.cpp -o unifrac.o -In file included from unifrac.cpp:13: -affinity.hpp:1: warning: "_GNU_SOURCE" redefined - 1 | #define _GNU_SOURCE - | -: note: this is the location of the previous definition -affinity.hpp: In function 'int bind_to_core(int)': -affinity.hpp:118:62: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pthread_t' {aka 'long unsigned int'} [-Wformat=] - 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); - | ~^ ~~~~~~ - | | | - | int pthread_t {aka long unsigned int} - | %ld -affinity.hpp:99:12: warning: variable 'ret' set but not used [-Wunused-but-set-variable] - 99 | int j, ret; - | ^~~ -affinity.hpp: At global scope: -affinity.hpp:82:12: warning: 'int bind_to_core(int)' defined but not used [-Wunused-function] - 82 | static int bind_to_core(int core) { - | ^~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c cmd.cpp -o cmd.o -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c skbio_alt.cpp -o skbio_alt.o -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib api.cpp -c -o api.o -fPIC -api.cpp: In function 'compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:97:62: note: in expansion of macro 'PARSE_TREE_TABLE' - 97 | #define PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) PARSE_TREE_TABLE(tree_filename, table_filename) \ - | ^~~~~~~~~~~~~~~~ -api.cpp:474:5: note: in expansion of macro 'PARSE_SYNC_TREE_TABLE' - 474 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) - | ^~~~~~~~~~~~~~~~~~~~~ -api.cpp: In function 'compute_status faith_pd_one_off(const char*, const char*, r_vec**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:513:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 513 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In function 'compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:550:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 550 | PARSE_TREE_TABLE(tree_filename, table_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In function 'compute_status one_off_matrix_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp64_t**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:628:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 628 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In function 'compute_status one_off_matrix_fp32_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp32_t**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:650:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 650 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In function 'IOStatus read_partial_header_fd(int, TPMat&)': -api.cpp:1795:83: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare] - 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) - | ~~~~~~~~~~~~~~~~~~^~~ -api.cpp: In instantiation of 'compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = double; TMat = mat_full_fp64; hid_t = long long int]': -api.cpp:1400:59: required from here -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:1281:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In instantiation of 'compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = float; TMat = mat_full_fp32; hid_t = long long int]': -api.cpp:1408:58: required from here -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:1281:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In instantiation of 'IOStatus read_partial_header_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]': -api.cpp:1963:48: required from here -api.cpp:1795:83: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare] - 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) - | ~~~~~~~~~~~~~~~~~~^~~ -api.cpp:1821:15: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1821 | if (cnt != sample_id_length_compressed) {free(cmp_buf); return magic_incompatible;} - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp:1827:14: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1827 | if (cnt!=sample_id_length) {free(samples_buf); free(cmp_buf); return magic_incompatible;} - | ~~~^~~~~~~~~~~~~~~~~~ -api.cpp:1831:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1831 | for(int i = 0; i < n_samples; i++) { - | ~~^~~~~~~~~~~ -api.cpp: In instantiation of 'IOStatus read_partial_data_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]': -api.cpp:1965:49: required from here -api.cpp:1864:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1864 | for(int i = 0; i < n_stripes; i++) { - | ~~^~~~~~~~~~~ -api.cpp:1868:19: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1868 | if ( (i+1)n_samples != n_samples) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -api.cpp:2077:54: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp:2092:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 2092 | if(stripe_count != partial_mats[0]->stripe_total) { - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp: In instantiation of 'MergeStatus check_partial(const TPMat* const*, int, bool) [with TPMat = partial_mat; MergeStatus = merge_status]': -api.cpp:2109:36: required from here -api.cpp:2042:39: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare] - 2042 | if(partial_mats[i]->n_samples != n_samples) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -api.cpp:2077:54: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp:2092:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 2092 | if(stripe_count != partial_mats[0]->stripe_total) { - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp: In function 'void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = double; TMat = mat_full_fp64]': -api.cpp:257:18: warning: ignoring return value of 'int ftruncate(int, __off64_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 257 | ftruncate(fd,msize); - | ~~~~~~~~~^~~~~~~~~~ -api.cpp: In function 'void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = float; TMat = mat_full_fp32]': -api.cpp:257:18: warning: ignoring return value of 'int ftruncate(int, __off64_t)' declared with attribute 'warn_unused_result' [-Wunused-result] -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac_internal.cpp -o unifrac_internal.o -In file included from unifrac_internal.cpp:12: -affinity.hpp:1: warning: "_GNU_SOURCE" redefined - 1 | #define _GNU_SOURCE - | -: note: this is the location of the previous definition -affinity.hpp: In function 'int bind_to_core(int)': -affinity.hpp:118:62: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pthread_t' {aka 'long unsigned int'} [-Wformat=] - 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); - | ~^ ~~~~~~ - | | | - | int pthread_t {aka long unsigned int} - | %ld -affinity.hpp:99:12: warning: variable 'ret' set but not used [-Wunused-but-set-variable] - 99 | int j, ret; - | ^~~ -affinity.hpp: At global scope: -affinity.hpp:82:12: warning: 'int bind_to_core(int)' defined but not used [-Wunused-function] - 82 | static int bind_to_core(int core) { - | ^~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac_cmp.cpp -o unifrac_cmp_cpu.o -In file included from unifrac_cmp.cpp:19: -unifrac_task.hpp:196: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 196 | #pragma acc enter data create(buf[:bsize]) - | -unifrac_task.hpp:357: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 357 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) - | -unifrac_task.hpp:395: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 395 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) - | -unifrac_task.hpp:438: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 438 | #pragma acc enter data create(zcheck[:n_samples],stripe_sums[:n_samples],sums[:bsize]) - | -In file included from unifrac_cmp.cpp:24: -unifrac_task.cpp:41: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 41 | #pragma acc loop seq - | -unifrac_task.cpp:558: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 558 | #pragma acc loop seq - | -unifrac_task.cpp:1008: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1008 | #pragma acc loop seq - | -unifrac_task.cpp:1081: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1081 | #pragma acc loop seq - | -unifrac_task.cpp:1159: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1159 | #pragma acc loop seq - | -unifrac_task.cpp:1544: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1544 | #pragma acc loop vector - | -unifrac_task.cpp:1573: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1573 | #pragma acc loop vector - | -unifrac_task.cpp:1586: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] - 1586 | #pragma acc wait - | -unifrac_task.cpp:1700: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1700 | #pragma acc loop seq - | -unifrac_task.cpp:1710: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1710 | #pragma acc loop seq - | -unifrac_cmp.cpp:97: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 97 | #pragma acc enter data create(lengths[:max_emb]) - | -unifrac_cmp.cpp:195: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] - 195 | #pragma acc wait - | -unifrac_cmp.cpp:204: warning: ignoring '#pragma acc parallel' [-Wunknown-pragmas] - 204 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) - | -unifrac_cmp.cpp:214: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] - 214 | #pragma acc exit data delete(lengths[:max_emb]) - | -unifrac_cmp.cpp:282: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 282 | #pragma acc enter data copyin(sample_total_counts[:n_samples_r]) - | -unifrac_cmp.cpp:293: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 293 | #pragma acc enter data create(lengths[:max_emb]) - | -unifrac_cmp.cpp:338: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] - 338 | #pragma acc wait - | -unifrac_cmp.cpp:339: warning: ignoring '#pragma acc update' [-Wunknown-pragmas] - 339 | #pragma acc update device(lengths[:filled_emb]) - | -unifrac_cmp.cpp:347: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] - 347 | #pragma acc wait - | -unifrac_cmp.cpp:355: warning: ignoring '#pragma acc parallel' [-Wunknown-pragmas] - 355 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) - | -unifrac_cmp.cpp:366: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] - 366 | #pragma acc exit data delete(lengths[:max_emb]) - | -unifrac_cmp.cpp:367: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] - 367 | #pragma acc exit data delete(sample_total_counts[:n_samples_r]) - | -unifrac_cmp.cpp: In instantiation of 'void initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = double]': -unifrac_cmp.cpp:281:29: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]' -unifrac_cmp.cpp:380:77: required from here -unifrac_cmp.cpp:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_cmp.cpp: In instantiation of 'void initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = float]': -unifrac_cmp.cpp:281:29: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]' -unifrac_cmp.cpp:392:77: required from here -unifrac_cmp.cpp:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = double; uint64_t = long long unsigned int]': -unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' -unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' -unifrac_cmp.cpp:285:11: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]' -unifrac_cmp.cpp:380:77: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = float; uint64_t = long long unsigned int]': -unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' -unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' -unifrac_cmp.cpp:285:11: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]' -unifrac_cmp.cpp:392:77: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = long long unsigned int; uint64_t = long long unsigned int]': -unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' -unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' -unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]' -unifrac_cmp.cpp:89:11: required from 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = double]' -unifrac_cmp.cpp:226:70: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = long long unsigned int; uint64_t = long long unsigned int]': -unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' -unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' -unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]' -unifrac_cmp.cpp:89:11: required from 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = float]' -unifrac_cmp.cpp:238:69: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = unsigned int; uint64_t = long long unsigned int]': -unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' -unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' -unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' -unifrac_cmp.cpp:285:11: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]' -unifrac_cmp.cpp:380:77: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = unsigned int; uint64_t = long long unsigned int]': -unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' -unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' -unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' -unifrac_cmp.cpp:285:11: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]' -unifrac_cmp.cpp:392:77: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In constructor 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]': -unifrac_task.hpp:435:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:436:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:437:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]': -unifrac_task.hpp:393:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:394:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]': -unifrac_task.hpp:355:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:356:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]': -unifrac_task.hpp:435:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:436:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:437:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]': -unifrac_task.hpp:393:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:394:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]': -unifrac_task.hpp:355:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:356:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -h5c++ -shared -fopenmp -shlib -o libssu_nv_avx2.so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,libssu_nv_avx2.so.0 -llapacke -lblas -lgfortran -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5 -ln -sf libssu_nv_avx2.so.0 libssu_nv_avx2.so -# FIXME: Should build static lib as well -# h5c++ -shared -fopenmp -shlib -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -source ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make main -/bin/sh: 1: source: not found -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib su.cpp -o ssu_nv_avx2 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib faithpd.cpp -o faithpd_nv_avx2 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -source ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make install -/bin/sh: 1: source: not found -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu_nv_avx2.so; cp -a libssu_nv_avx2.so* /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ssu_nv_avx2; cp ssu_nv_avx2 /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/faithpd_nv_avx2; cp faithpd_nv_avx2 /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ -mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/task_parameters.hpp; cp task_parameters.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/api.hpp; cp api.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/status_enum.hpp; cp status_enum.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -source ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make clean && make api -/bin/sh: 1: source: not found -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -rm -f *.o ssu_nv faithpd_nv test_su test_ska test_api libssu_nv.so -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c tree.cpp -o tree.o -tree.cpp: In member function 'void su::BPTree::newick_to_bp(std::string)': -tree.cpp:321:67: warning: 'last_structure' may be used uninitialized [-Wmaybe-uninitialized] - 321 | if(potential_single_descendent || (last_structure == ',')) { - | ~~~~~~~~~~~~~~~~^~~~~~~ -tree.cpp:300:10: note: 'last_structure' was declared here - 300 | char last_structure; - | ^~~~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c biom.cpp -o biom.o -biom.cpp: In constructor 'su::biom::biom(std::string)': -biom.cpp:32:51: warning: implicitly-declared 'H5::H5File& H5::H5File::operator=(const H5::H5File&)' is deprecated [-Wdeprecated-copy] - 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); - | ^ -In file included from /usr/include/hdf5/serial/H5Cpp.h:47, - from biom.hpp:14, - from biom.cpp:13: -/usr/include/hdf5/serial/H5File.h:104:5: note: because 'H5::H5File' has user-provided 'H5::H5File::H5File(const H5::H5File&)' - 104 | H5File(const H5File &original); - | ^~~~~~ -/usr/include/hdf5/serial/H5File.h: In member function 'H5::H5File& H5::H5File::operator=(const H5::H5File&)': -/usr/include/hdf5/serial/H5File.h:24:17: warning: implicitly-declared 'H5::Group& H5::Group::operator=(const H5::Group&)' is deprecated [-Wdeprecated-copy] - 24 | class H5_DLLCPP H5File : public Group { - | ^~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:46: -/usr/include/hdf5/serial/H5Group.h:62:5: note: because 'H5::Group' has user-provided 'H5::Group::Group(const H5::Group&)' - 62 | Group(const Group &original); - | ^~~~~ -biom.cpp: In constructor 'su::biom::biom(std::string)': -biom.cpp:32:51: note: synthesized method 'H5::H5File& H5::H5File::operator=(const H5::H5File&)' first required here - 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); - | ^ -biom.cpp: In member function 'void su::biom::load_ids(const char*, std::vector >&)': -biom.cpp:134:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 135 | sizeof(char*) * dims[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp: In member function 'void su::biom::load_indptr(const char*, std::vector&)': -biom.cpp:166:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp: In member function 'unsigned int su::biom::get_obs_data_direct(const std::string&, uint32_t*&, double*&)': -biom.cpp:206:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp:212:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 213 | sizeof(double) * count[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp: In member function 'unsigned int su::biom::get_sample_data_direct(const std::string&, uint32_t*&, double*&)': -biom.cpp:251:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -biom.cpp:257:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] - 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 258 | sizeof(double) * count[0], __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | hsize_t {aka long long unsigned int} -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c biom_inmem.cpp -o biom_inmem.o -biom_inmem.cpp: In constructor 'su::biom_inmem::biom_inmem(const char* const*, const char* const*, uint32_t*, uint32_t*, double*, int, int)': -biom_inmem.cpp:328:30: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 328 | for(int i = 0; i < n_obs; i++) { - | ~~^~~~~~~ -biom_inmem.cpp:333:30: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 333 | for(int i = 0; i < n_samples; i++) { - | ~~^~~~~~~~~~~ -biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = double]': -biom_inmem.cpp:99:60: required from here -biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", - | ~~^ - | | - | long int - | %d - 24 | bufsize, __FILE__, __LINE__); - | ~~~~~~~ - | | - | size_t {aka unsigned int} -biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int]': -biom_inmem.cpp:100:62: required from here -biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", - | ~~^ - | | - | long int - | %d - 24 | bufsize, __FILE__, __LINE__); - | ~~~~~~~ - | | - | size_t {aka unsigned int} -biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int*]': -biom_inmem.cpp:177:55: required from here -biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", - | ~~^ - | | - | long int - | %d - 24 | bufsize, __FILE__, __LINE__); - | ~~~~~~~ - | | - | size_t {aka unsigned int} -biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = double*]': -biom_inmem.cpp:178:55: required from here -biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", - | ~~^ - | | - | long int - | %d - 24 | bufsize, __FILE__, __LINE__); - | ~~~~~~~ - | | - | size_t {aka unsigned int} -biom_inmem.cpp: In instantiation of 'void su::biom_inmem::get_obs_data_range_TT(uint32_t, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; uint32_t = unsigned int]': -biom_inmem.cpp:427:34: required from 'void su::biom_inmem::get_obs_data_range_TT(const std::string&, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; std::string = std::__cxx11::basic_string]' -biom_inmem.cpp:431:36: required from here -biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'unsigned int' [-Wsign-compare] - 410 | if ((j>=start)&&(j=start)&&(j]' -biom_inmem.cpp:435:36: required from here -biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'unsigned int' [-Wsign-compare] - 410 | if ((j>=start)&&(j=start)&&(j::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(const typename _Container::value_type&) [with _Container = std::vector]' at /usr/include/c++/13/bits/stl_iterator.h:739:22, - inlined from '_OutputIterator std::partial_sum(_InputIterator, _InputIterator, _OutputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = back_insert_iterator >]' at /usr/include/c++/13/bits/stl_numeric.h:270:17, - inlined from 'void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = unsigned int]' at /usr/include/c++/13/bits/random.tcc:2671:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(const typename _Container::value_type&) [with _Container = std::vector]' at /usr/include/c++/13/bits/stl_iterator.h:739:22, - inlined from '_OutputIterator std::partial_sum(_InputIterator, _InputIterator, _OutputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = back_insert_iterator >]' at /usr/include/c++/13/bits/stl_numeric.h:274:16, - inlined from 'void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = unsigned int]' at /usr/include/c++/13/bits/random.tcc:2671:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c tsv.cpp -o tsv.o -tsv.cpp: In member function 'void su::indexed_tsv::read_grouping(const std::string&, uint32_t*, uint32_t&) const': -tsv.cpp:126:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 126 | for (int i=1; i< header_line.size(); i++) { - | ~^~~~~~~~~~~~~~~~~~~~ -tsv.cpp:138:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 138 | for (int i=1; i< n_filter_els; i++) grouping[i] = n_filter_els; - | ~^~~~~~~~~~~~~~ -tsv.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 173 | for (int i=1; i< n_filter_els; i++) { - | ~^~~~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac.cpp -o unifrac.o -In file included from unifrac.cpp:13: -affinity.hpp:1: warning: "_GNU_SOURCE" redefined - 1 | #define _GNU_SOURCE - | -: note: this is the location of the previous definition -affinity.hpp: In function 'int bind_to_core(int)': -affinity.hpp:118:62: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pthread_t' {aka 'long unsigned int'} [-Wformat=] - 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); - | ~^ ~~~~~~ - | | | - | int pthread_t {aka long unsigned int} - | %ld -affinity.hpp:99:12: warning: variable 'ret' set but not used [-Wunused-but-set-variable] - 99 | int j, ret; - | ^~~ -affinity.hpp: At global scope: -affinity.hpp:82:12: warning: 'int bind_to_core(int)' defined but not used [-Wunused-function] - 82 | static int bind_to_core(int core) { - | ^~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c cmd.cpp -o cmd.o -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c skbio_alt.cpp -o skbio_alt.o -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib api.cpp -c -o api.o -fPIC -api.cpp: In function 'compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:97:62: note: in expansion of macro 'PARSE_TREE_TABLE' - 97 | #define PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) PARSE_TREE_TABLE(tree_filename, table_filename) \ - | ^~~~~~~~~~~~~~~~ -api.cpp:474:5: note: in expansion of macro 'PARSE_SYNC_TREE_TABLE' - 474 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) - | ^~~~~~~~~~~~~~~~~~~~~ -api.cpp: In function 'compute_status faith_pd_one_off(const char*, const char*, r_vec**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:513:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 513 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In function 'compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:550:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 550 | PARSE_TREE_TABLE(tree_filename, table_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In function 'compute_status one_off_matrix_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp64_t**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:628:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 628 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In function 'compute_status one_off_matrix_fp32_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp32_t**)': -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:650:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 650 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In function 'IOStatus read_partial_header_fd(int, TPMat&)': -api.cpp:1795:83: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare] - 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) - | ~~~~~~~~~~~~~~~~~~^~~ -api.cpp: In instantiation of 'compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = double; TMat = mat_full_fp64; hid_t = long long int]': -api.cpp:1400:59: required from here -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:1281:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In instantiation of 'compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = float; TMat = mat_full_fp32; hid_t = long long int]': -api.cpp:1408:58: required from here -api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ - | ~~~~~~~~~~~~~~~~^~~~ -api.cpp:1281:5: note: in expansion of macro 'PARSE_TREE_TABLE' - 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) - | ^~~~~~~~~~~~~~~~ -api.cpp: In instantiation of 'IOStatus read_partial_header_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]': -api.cpp:1963:48: required from here -api.cpp:1795:83: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare] - 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) - | ~~~~~~~~~~~~~~~~~~^~~ -api.cpp:1821:15: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1821 | if (cnt != sample_id_length_compressed) {free(cmp_buf); return magic_incompatible;} - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp:1827:14: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1827 | if (cnt!=sample_id_length) {free(samples_buf); free(cmp_buf); return magic_incompatible;} - | ~~~^~~~~~~~~~~~~~~~~~ -api.cpp:1831:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1831 | for(int i = 0; i < n_samples; i++) { - | ~~^~~~~~~~~~~ -api.cpp: In instantiation of 'IOStatus read_partial_data_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]': -api.cpp:1965:49: required from here -api.cpp:1864:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1864 | for(int i = 0; i < n_stripes; i++) { - | ~~^~~~~~~~~~~ -api.cpp:1868:19: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 1868 | if ( (i+1)n_samples != n_samples) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -api.cpp:2077:54: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp:2092:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 2092 | if(stripe_count != partial_mats[0]->stripe_total) { - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp: In instantiation of 'MergeStatus check_partial(const TPMat* const*, int, bool) [with TPMat = partial_mat; MergeStatus = merge_status]': -api.cpp:2109:36: required from here -api.cpp:2042:39: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare] - 2042 | if(partial_mats[i]->n_samples != n_samples) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -api.cpp:2077:54: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp:2092:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] - 2092 | if(stripe_count != partial_mats[0]->stripe_total) { - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -api.cpp: In function 'void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = double; TMat = mat_full_fp64]': -api.cpp:257:18: warning: ignoring return value of 'int ftruncate(int, __off64_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 257 | ftruncate(fd,msize); - | ~~~~~~~~~^~~~~~~~~~ -api.cpp: In function 'void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = float; TMat = mat_full_fp32]': -api.cpp:257:18: warning: ignoring return value of 'int ftruncate(int, __off64_t)' declared with attribute 'warn_unused_result' [-Wunused-result] -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac_internal.cpp -o unifrac_internal.o -In file included from unifrac_internal.cpp:12: -affinity.hpp:1: warning: "_GNU_SOURCE" redefined - 1 | #define _GNU_SOURCE - | -: note: this is the location of the previous definition -affinity.hpp: In function 'int bind_to_core(int)': -affinity.hpp:118:62: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pthread_t' {aka 'long unsigned int'} [-Wformat=] - 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); - | ~^ ~~~~~~ - | | | - | int pthread_t {aka long unsigned int} - | %ld -affinity.hpp:99:12: warning: variable 'ret' set but not used [-Wunused-but-set-variable] - 99 | int j, ret; - | ^~~ -affinity.hpp: At global scope: -affinity.hpp:82:12: warning: 'int bind_to_core(int)' defined but not used [-Wunused-function] - 82 | static int bind_to_core(int core) { - | ^~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac_cmp.cpp -o unifrac_cmp_cpu.o -In file included from unifrac_cmp.cpp:19: -unifrac_task.hpp:196: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 196 | #pragma acc enter data create(buf[:bsize]) - | -unifrac_task.hpp:357: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 357 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) - | -unifrac_task.hpp:395: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 395 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) - | -unifrac_task.hpp:438: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 438 | #pragma acc enter data create(zcheck[:n_samples],stripe_sums[:n_samples],sums[:bsize]) - | -In file included from unifrac_cmp.cpp:24: -unifrac_task.cpp:41: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 41 | #pragma acc loop seq - | -unifrac_task.cpp:558: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 558 | #pragma acc loop seq - | -unifrac_task.cpp:1008: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1008 | #pragma acc loop seq - | -unifrac_task.cpp:1081: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1081 | #pragma acc loop seq - | -unifrac_task.cpp:1159: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1159 | #pragma acc loop seq - | -unifrac_task.cpp:1544: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1544 | #pragma acc loop vector - | -unifrac_task.cpp:1573: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1573 | #pragma acc loop vector - | -unifrac_task.cpp:1586: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] - 1586 | #pragma acc wait - | -unifrac_task.cpp:1700: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1700 | #pragma acc loop seq - | -unifrac_task.cpp:1710: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] - 1710 | #pragma acc loop seq - | -unifrac_cmp.cpp:97: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 97 | #pragma acc enter data create(lengths[:max_emb]) - | -unifrac_cmp.cpp:195: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] - 195 | #pragma acc wait - | -unifrac_cmp.cpp:204: warning: ignoring '#pragma acc parallel' [-Wunknown-pragmas] - 204 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) - | -unifrac_cmp.cpp:214: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] - 214 | #pragma acc exit data delete(lengths[:max_emb]) - | -unifrac_cmp.cpp:282: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 282 | #pragma acc enter data copyin(sample_total_counts[:n_samples_r]) - | -unifrac_cmp.cpp:293: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] - 293 | #pragma acc enter data create(lengths[:max_emb]) - | -unifrac_cmp.cpp:338: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] - 338 | #pragma acc wait - | -unifrac_cmp.cpp:339: warning: ignoring '#pragma acc update' [-Wunknown-pragmas] - 339 | #pragma acc update device(lengths[:filled_emb]) - | -unifrac_cmp.cpp:347: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] - 347 | #pragma acc wait - | -unifrac_cmp.cpp:355: warning: ignoring '#pragma acc parallel' [-Wunknown-pragmas] - 355 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) - | -unifrac_cmp.cpp:366: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] - 366 | #pragma acc exit data delete(lengths[:max_emb]) - | -unifrac_cmp.cpp:367: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] - 367 | #pragma acc exit data delete(sample_total_counts[:n_samples_r]) - | -unifrac_cmp.cpp: In instantiation of 'void initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = double]': -unifrac_cmp.cpp:281:29: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]' -unifrac_cmp.cpp:380:77: required from here -unifrac_cmp.cpp:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_cmp.cpp: In instantiation of 'void initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = float]': -unifrac_cmp.cpp:281:29: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]' -unifrac_cmp.cpp:392:77: required from here -unifrac_cmp.cpp:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = double; uint64_t = long long unsigned int]': -unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' -unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' -unifrac_cmp.cpp:285:11: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]' -unifrac_cmp.cpp:380:77: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = float; uint64_t = long long unsigned int]': -unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' -unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' -unifrac_cmp.cpp:285:11: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]' -unifrac_cmp.cpp:392:77: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = long long unsigned int; uint64_t = long long unsigned int]': -unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' -unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' -unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]' -unifrac_cmp.cpp:89:11: required from 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = double]' -unifrac_cmp.cpp:226:70: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = long long unsigned int; uint64_t = long long unsigned int]': -unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' -unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' -unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]' -unifrac_cmp.cpp:89:11: required from 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = float]' -unifrac_cmp.cpp:238:69: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = unsigned int; uint64_t = long long unsigned int]': -unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' -unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' -unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' -unifrac_cmp.cpp:285:11: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]' -unifrac_cmp.cpp:380:77: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = unsigned int; uint64_t = long long unsigned int]': -unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' -unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' -unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' -unifrac_cmp.cpp:285:11: required from 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]' -unifrac_cmp.cpp:392:77: required from here -unifrac_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] - 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", - | ~~^ - | | - | int - | %lld - 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | long long unsigned int -unifrac_task.hpp: In constructor 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]': -unifrac_task.hpp:435:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:436:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:437:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]': -unifrac_task.hpp:393:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:394:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]': -unifrac_task.hpp:355:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:356:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]': -unifrac_task.hpp:435:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:436:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:437:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]': -unifrac_task.hpp:393:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:394:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp: In constructor 'su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]': -unifrac_task.hpp:355:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unifrac_task.hpp:356:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -h5c++ -shared -fopenmp -shlib -o libssu_nv.so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,libssu_nv.so.0 -llapacke -lblas -lgfortran -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5 -ln -sf libssu_nv.so.0 libssu_nv.so -# FIXME: Should build static lib as well -# h5c++ -shared -fopenmp -shlib -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -source ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make main -/bin/sh: 1: source: not found -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib su.cpp -o ssu_nv tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib faithpd.cpp -o faithpd_nv tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -source ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make install -/bin/sh: 1: source: not found -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu_nv.so; cp -a libssu_nv.so* /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ssu_nv; cp ssu_nv /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/faithpd_nv; cp faithpd_nv /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ -mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/task_parameters.hpp; cp task_parameters.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/api.hpp; cp api.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/status_enum.hpp; cp status_enum.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -cd combined && make api -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/combined' -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c libssu.c -fPIC -cc -shared -o libssu.so libssu.o -fPIC -ldl -Wl,-z,relro -Wl,-z,now -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/combined' -cd combined && make install -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/combined' -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu.so; cp libssu.so /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ssu; cp ssu /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/faithpd; cp faithpd /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/combined' -source ./setup_nv_h5.sh; export BUILD_VARIANT=nv ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make test_binaries -/bin/sh: 1: source: not found -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib test_su.cpp -o test_su tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o skbio_alt.o api.o -llz4 -llapacke -lblas -lgfortran -lpthread -test_su.cpp: In function 'void test_bptree_postorder()': -test_su.cpp:302:14: warning: ISO C++ forbids variable length array 'obs' [-Wvla] - 302 | uint32_t obs[tree.nparens / 2]; - | ^~~ -test_su.cpp: In function 'void test_bptree_preorder()': -test_su.cpp:320:14: warning: ISO C++ forbids variable length array 'obs' [-Wvla] - 320 | uint32_t obs[tree.nparens / 2]; - | ^~~ -test_su.cpp: In function 'void test_bptree_parent()': -test_su.cpp:340:14: warning: ISO C++ forbids variable length array 'obs' [-Wvla] - 340 | uint32_t obs[tree.nparens - 2]; - | ^~~ -In file included from /usr/include/c++/13/vector:72, - from api.hpp:5, - from test_su.cpp:1: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector _double_array_to_vector(double*, unsigned int)' at test_helper.hpp:67:22, - inlined from 'void test_bptree_constructor_single_descendent()' at test_su.cpp:184:86: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector _double_array_to_vector(double*, unsigned int)' at test_helper.hpp:67:22, - inlined from 'void test_bptree_constructor_semicolon()' at test_su.cpp:229:86: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector _double_array_to_vector(double*, unsigned int)' at test_helper.hpp:67:22, - inlined from 'void test_bptree_constructor_complex()' at test_su.cpp:207:86: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const su::task_parameters&}; _Tp = su::task_parameters; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void test_bptree_mask()' at test_su.cpp:159:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void test_bptree_constructor_simple()' at test_su.cpp:49:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void test_bptree_constructor_simple()' at test_su.cpp:51:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void test_bptree_cstyle_constructor()' at test_su.cpp:1869:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void test_bptree_cstyle_constructor()' at test_su.cpp:1871:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void test_bptree_constructor_from_existing()' at test_su.cpp:106:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void test_bptree_constructor_from_existing()' at test_su.cpp:108:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = su::task_parameters; _Alloc = std::allocator]', - inlined from 'void test_unnormalized_weighted_unifrac()' at test_su.cpp:1235:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = su::task_parameters; _Alloc = std::allocator]', - inlined from 'void test_generalized_unifrac()' at test_su.cpp:1276:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = su::task_parameters; _Alloc = std::allocator]', - inlined from 'void test_generalized_unifrac()' at test_su.cpp:1308:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = su::task_parameters; _Alloc = std::allocator]', - inlined from 'void test_generalized_unifrac()' at test_su.cpp:1340:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = su::task_parameters; _Alloc = std::allocator]', - inlined from 'void test_vaw_unifrac_weighted_normalized()' at test_su.cpp:1395:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = su::task_parameters; _Alloc = std::allocator]', - inlined from 'void test_unweighted_unifrac()' at test_su.cpp:1498:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = su::task_parameters; _Alloc = std::allocator]', - inlined from 'void test_unweighted_unifrac_fast()' at test_su.cpp:1537:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = su::task_parameters; _Alloc = std::allocator]', - inlined from 'void test_normalized_weighted_unifrac()' at test_su.cpp:1577:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib test_ska.cpp -o test_ska skbio_alt.o tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o api.o -llz4 -llapacke -lblas -lgfortran -lpthread -test_ska.cpp: In function 'void test_pcoa_big()': -test_ska.cpp:271:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 271 | fscanf(fptr,"# unifrac %u\n",&n_samples); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -test_ska.cpp:278:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 278 | fscanf(fptr,"%lf\n",&(matrix[i])); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -test_ska.cpp:281:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 281 | fscanf(fptr,"# pcoa %u\n",&n_dims); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -test_ska.cpp:286:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fscanf(fptr,"%lf\n",&(exp1[i])); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -test_ska.cpp:290:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 290 | fscanf(fptr,"%lf\n",&(exp2[i])); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -test_ska.cpp:294:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 294 | fscanf(fptr,"%lf\n",&(exp3[i])); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib test_api.cpp -o test_api tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o skbio_alt.o api.o -llz4 -llapacke -lblas -lgfortran -lpthread -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -# use the default compiler for the test subdir as it tests the combined shlib -cd test && make test_binaries -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/test' -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c99 -O0 -g capi_test.c -I../src -lssu -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -Wl,-rpath,/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -Wl,-z,relro -Wl,-z,now -o capi_test -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/test' +/bin/sh: line 1: ./setup_nv_h5.sh: No such file or directory +make[2]: *** [Makefile:43: api_nv_avx2] Error 1 make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' -chmod +x /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/* -make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' -export PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin ; \ -cd ci ; \ -./crawford_test.sh -All tests succeeded +dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr returned exit code 2 +make[1]: *** [debian/rules:15: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' - create-stamp debian/debhelper-build-stamp - dh_testroot -O--no-parallel - dh_prep -O--no-parallel - debian/rules override_dh_auto_install -make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' -mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin -mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -dh_auto_install -- PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr - make -j1 install DESTDIR=/build/reproducible-path/unifrac-tools-1.4/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr -make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' -cd src && make install -make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' -h5c++ -shared -fopenmp -shlib -o libssu.so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,libssu.so.0 -llapacke -lblas -lgfortran -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5 -ln -sf libssu.so.0 libssu.so -# FIXME: Should build static lib as well -# h5c++ -shared -fopenmp -shlib -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib su.cpp -o ssu tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread -h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib faithpd.cpp -o faithpd tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu.so; cp -a libssu.so* /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ssu; cp ssu /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/faithpd; cp faithpd /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ -mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/task_parameters.hpp; cp task_parameters.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/api.hpp; cp api.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ -rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/status_enum.hpp; cp status_enum.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ -make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' -make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' -make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' - debian/rules override_dh_install -make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' -chrpath -d debian/tmp/usr/bin/ssu -chrpath -d debian/tmp/usr/bin/faithpd -chrpath -d debian/tmp/usr/lib/libssu.so* -dh_install -make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' - dh_installdocs -O--no-parallel - dh_installchangelogs -O--no-parallel - dh_installman -O--no-parallel - dh_installsystemduser -O--no-parallel - dh_perl -O--no-parallel - dh_link -O--no-parallel - dh_strip_nondeterminism -O--no-parallel - dh_compress -O--no-parallel - dh_fixperms -O--no-parallel - dh_missing -O--no-parallel - dh_dwz -a -O--no-parallel - dh_strip -a -O--no-parallel - dh_makeshlibs -a -O--no-parallel - dh_shlibdeps -a -O--no-parallel -dpkg-shlibdeps: warning: debian/unifrac-tools/usr/bin/ssu contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/unifrac-tools/usr/bin/faithpd contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libssu0/usr/lib/arm-linux-gnueabihf/libssu.so.0 found in none of the libraries - dh_installdeb -O--no-parallel - dh_gencontrol -O--no-parallel -dpkg-gencontrol: warning: Depends field of package libssu-dev: substitution variable ${shlibs:Depends} used, but is not defined - dh_md5sums -O--no-parallel - dh_builddeb -O--no-parallel -dpkg-deb: building package 'unifrac-tools' in '../unifrac-tools_1.4-3_armhf.deb'. -dpkg-deb: building package 'libssu0' in '../libssu0_1.4-3_armhf.deb'. -dpkg-deb: building package 'libssu-dev' in '../libssu-dev_1.4-3_armhf.deb'. -dpkg-deb: building package 'libssu0-dbgsym' in '../libssu0-dbgsym_1.4-3_armhf.deb'. -dpkg-deb: building package 'unifrac-tools-dbgsym' in '../unifrac-tools-dbgsym_1.4-3_armhf.deb'. - dpkg-genbuildinfo --build=binary -O../unifrac-tools_1.4-3_armhf.buildinfo - dpkg-genchanges --build=binary -O../unifrac-tools_1.4-3_armhf.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: not including original source code in upload +make: *** [debian/rules:10: binary] Error 2 +dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration +E: Failed autobuilding of package +I: user script /srv/workspace/pbuilder/12510/tmp/hooks/C01_cleanup starting +debug output: disk usage on i-capture-the-hostname at Fri Apr 12 01:47:19 UTC 2024 +Filesystem Size Used Avail Use% Mounted on +tmpfs 3.4G 0 3.4G 0% /dev/shm + +I: user script /srv/workspace/pbuilder/12510/tmp/hooks/C01_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/27178 and its subdirectories -I: Current time: Thu Apr 11 13:36:54 -12 2024 -I: pbuilder-time-stamp: 1712885814 +I: removing directory /srv/workspace/pbuilder/12510 and its subdirectories