=>> Building biology/vcftools build started at Mon Sep 29 03:25:33 EDT 2025 port directory: /usr/ports/biology/vcftools package name: vcftools-0.1.17 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 419 Jun 29 20:14 /usr/ports/biology/vcftools/Makefile Ports top last git commit: a936fb9b16ba Ports top unclean checkout: no Port dir last git commit: 3ae8b09ca041 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500064 Jail OSVERSION: 1500064 Job Id: 15 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/15/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/vcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcftools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/vcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcftools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/vcftools" EXAMPLESDIR="share/examples/vcftools" DATADIR="share/vcftools" WWWDIR="www/vcftools" ETCDIR="etc/vcftools" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vcftools DOCSDIR=/usr/local/share/doc/vcftools EXAMPLESDIR=/usr/local/share/examples/vcftools WWWDIR=/usr/local/www/vcftools ETCDIR=/usr/local/etc/vcftools --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcftools-0.1.17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1.pkg [pkg.DaveG.ca] Installing pkg-2.3.1... [pkg.DaveG.ca] Extracting pkg-2.3.1: .......... done ===> vcftools-0.1.17 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcftools-0.1.17 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vcftools-0.1.17 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vcftools-0.1.17 for building => SHA256 Checksum OK for vcftools-vcftools-v0.1.17_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vcftools-0.1.17 for building ===> Extracting for vcftools-0.1.17 => SHA256 Checksum OK for vcftools-vcftools-v0.1.17_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for vcftools-0.1.17 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcftools-0.1.17 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> vcftools-0.1.17 depends on package: gmake>=4.4.1 - found ===> Returning to build of vcftools-0.1.17 ===> vcftools-0.1.17 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> vcftools-0.1.17 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of vcftools-0.1.17 ===> vcftools-0.1.17 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg.DaveG.ca] Installing autoconf-2.72... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing m4-1.4.19_1,1... [pkg.DaveG.ca] `-- Extracting m4-1.4.19_1,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72: .......... done ===> vcftools-0.1.17 depends on package: autoconf>=2.72 - found ===> Returning to build of vcftools-0.1.17 ===> vcftools-0.1.17 depends on package: automake>=1.17 - not found ===> Installing existing package /packages/All/automake-1.17.pkg [pkg.DaveG.ca] Installing automake-1.17... [pkg.DaveG.ca] Extracting automake-1.17: .......... done ===> vcftools-0.1.17 depends on package: automake>=1.17 - found ===> Returning to build of vcftools-0.1.17 ===> vcftools-0.1.17 depends on package: perl5>=5.42.r<5.43 - found ===> vcftools-0.1.17 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> vcftools-0.1.17 depends on file: /usr/local/bin/ccache - found ===> Returning to build of vcftools-0.1.17 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vcftools-0.1.17 configure.ac:16: installing './compile' configure.ac:12: installing './install-sh' configure.ac:12: installing './missing' src/cpp/Makefile.am: installing './depcomp' configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports nested variables... yes checking xargs -n works... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking for perl... (cached) /usr/local/bin/perl checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for arpa/inet.h... (cached) yes checking for fcntl.h... (cached) yes checking for limits.h... (cached) yes checking for netdb.h... (cached) yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/socket.h... (cached) yes checking for unistd.h... (cached) yes checking for _Bool... (cached) yes checking for stdbool.h that conforms to C99 or later... (cached) yes checking for inline... inline checking for int16_t... (cached) yes checking for int32_t... (cached) yes checking for int64_t... (cached) yes checking for int8_t... (cached) yes checking for off_t... (cached) yes checking for size_t... (cached) yes checking for ssize_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint8_t... (cached) yes checking for cc option to enable large file support... none needed checking for error_at_line... no checking for gethostbyaddr... yes checking for gethostbyname... (cached) yes checking for malloc... (cached) yes checking for memset... (cached) yes checking for pow... no checking for realloc... yes checking for select... (cached) yes checking for socket... yes checking for sqrt... no checking for strchr... (cached) yes checking for strdup... (cached) yes checking for strerror... (cached) yes checking for strstr... (cached) yes checking for strtol... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/cpp/Makefile config.status: creating src/perl/Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for vcftools-0.1.17 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17' Making all in src gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' Making all in cpp gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/cpp' c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-bcf_entry.o -MD -MP -MF .deps/vcftools-bcf_entry.Tpo -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-bcf_entry_setters.o -MD -MP -MF .deps/vcftools-bcf_entry_setters.Tpo -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-bcf_file.o -MD -MP -MF .deps/vcftools-bcf_file.Tpo -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-bgzf.o -MD -MP -MF .deps/vcftools-bgzf.Tpo -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-dgeev.o -MD -MP -MF .deps/vcftools-dgeev.Tpo -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-entry.o -MD -MP -MF .deps/vcftools-entry.Tpo -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-entry_filters.o -MD -MP -MF .deps/vcftools-entry_filters.Tpo -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-entry_getters.o -MD -MP -MF .deps/vcftools-entry_getters.Tpo -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-entry_setters.o -MD -MP -MF .deps/vcftools-entry_setters.Tpo -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-gamma.o -MD -MP -MF .deps/vcftools-gamma.Tpo -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-header.o -MD -MP -MF .deps/vcftools-header.Tpo -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-knetfile.o -MD -MP -MF .deps/vcftools-knetfile.Tpo -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-output_log.o -MD -MP -MF .deps/vcftools-output_log.Tpo -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-parameters.o -MD -MP -MF .deps/vcftools-parameters.Tpo -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-variant_file.o -MD -MP -MF .deps/vcftools-variant_file.Tpo -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-variant_file_diff.o -MD -MP -MF .deps/vcftools-variant_file_diff.Tpo -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp mv -f .deps/vcftools-dgeev.Tpo .deps/vcftools-dgeev.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-variant_file_filters.o -MD -MP -MF .deps/vcftools-variant_file_filters.Tpo -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp mv -f .deps/vcftools-knetfile.Tpo .deps/vcftools-knetfile.Po mv -f .deps/vcftools-bgzf.Tpo .deps/vcftools-bgzf.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-variant_file_format_convert.o -MD -MP -MF .deps/vcftools-variant_file_format_convert.Tpo -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-variant_file_output.o -MD -MP -MF .deps/vcftools-variant_file_output.Tpo -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp mv -f .deps/vcftools-gamma.Tpo .deps/vcftools-gamma.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-vcf_entry.o -MD -MP -MF .deps/vcftools-vcf_entry.Tpo -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp mv -f .deps/vcftools-variant_file.Tpo .deps/vcftools-variant_file.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-vcf_entry_setters.o -MD -MP -MF .deps/vcftools-vcf_entry_setters.Tpo -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp mv -f .deps/vcftools-output_log.Tpo .deps/vcftools-output_log.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-vcf_file.o -MD -MP -MF .deps/vcftools-vcf_file.Tpo -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp variant_file_filters.cpp:129:2: warning: 'random_shuffle>' is deprecated [-Wdeprecated-declarations] 129 | random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order | ^ /usr/include/c++/v1/__algorithm/shuffle.h:95:23: note: 'random_shuffle>' has been explicitly marked deprecated here 95 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_DEPRECATED_IN_CXX14 void | ^ /usr/include/c++/v1/__config:742:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' 742 | # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. mv -f .deps/vcftools-variant_file_filters.Tpo .deps/vcftools-variant_file_filters.Po mv -f .deps/vcftools-bcf_file.Tpo .deps/vcftools-bcf_file.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT vcftools-vcftools.o -MD -MP -MF .deps/vcftools-vcftools.Tpo -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp bcf_entry_setters.cpp:311:13: warning: implicit conversion from 'int' to 'float' changes value from 2139095041 to 2139095040 [-Wimplicit-const-int-float-conversion] 311 | if (tmp == 0x7F800001) | ~~ ^~~~~~~~~~ bcf_entry_setters.cpp:328:28: warning: implicit conversion from 'int' to 'float' changes value from 2139095041 to 2139095040 [-Wimplicit-const-int-float-conversion] 328 | if ( (in == -1) or (in == 0x7F800001) ) | ~~ ^~~~~~~~~~ 2 warnings generated. mv -f .deps/vcftools-bcf_entry_setters.Tpo .deps/vcftools-bcf_entry_setters.Po entry.cpp:601:12: warning: implicit conversion from 'int' to 'float' changes value from 2139095042 to 2139095040 [-Wimplicit-const-int-float-conversion] 601 | value = 0x7F800002; | ~ ^~~~~~~~~~ 1 warning generated. mv -f .deps/vcftools-entry.Tpo .deps/vcftools-entry.Po mv -f .deps/vcftools-entry_setters.Tpo .deps/vcftools-entry_setters.Po mv -f .deps/vcftools-bcf_entry.Tpo .deps/vcftools-bcf_entry.Po mv -f .deps/vcftools-entry_getters.Tpo .deps/vcftools-entry_getters.Po mv -f .deps/vcftools-entry_filters.Tpo .deps/vcftools-entry_filters.Po mv -f .deps/vcftools-header.Tpo .deps/vcftools-header.Po mv -f .deps/vcftools-parameters.Tpo .deps/vcftools-parameters.Po mv -f .deps/vcftools-vcftools.Tpo .deps/vcftools-vcftools.Po variant_file_format_convert.cpp:29:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 29 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:29:24: note: non-constexpr function 'size' cannot be used in a constant expression 29 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_format_convert.cpp:403:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 403 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:403:24: note: non-constexpr function 'size' cannot be used in a constant expression 403 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_format_convert.cpp:628:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 628 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:628:23: note: non-constexpr function 'size' cannot be used in a constant expression 628 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_format_convert.cpp:658:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 658 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:658:24: note: non-constexpr function 'size' cannot be used in a constant expression 658 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_format_convert.cpp:680:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 680 | char tmpname2[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:680:25: note: non-constexpr function 'size' cannot be used in a constant expression 680 | char tmpname2[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_format_convert.cpp:811:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 811 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:811:23: note: non-constexpr function 'size' cannot be used in a constant expression 811 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_format_convert.cpp:841:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 841 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:841:24: note: non-constexpr function 'size' cannot be used in a constant expression 841 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_format_convert.cpp:995:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 995 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:995:23: note: non-constexpr function 'size' cannot be used in a constant expression 995 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_format_convert.cpp:1026:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1026 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:1026:24: note: non-constexpr function 'size' cannot be used in a constant expression 1026 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_format_convert.cpp:1048:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1048 | char tmpname2[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_format_convert.cpp:1048:25: note: non-constexpr function 'size' cannot be used in a constant expression 1048 | char tmpname2[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ 10 warnings generated. mv -f .deps/vcftools-variant_file_format_convert.Tpo .deps/vcftools-variant_file_format_convert.Po mv -f .deps/vcftools-vcf_entry.Tpo .deps/vcftools-vcf_entry.Po mv -f .deps/vcftools-vcf_entry_setters.Tpo .deps/vcftools-vcf_entry_setters.Po mv -f .deps/vcftools-variant_file_diff.Tpo .deps/vcftools-variant_file_diff.Po mv -f .deps/vcftools-vcf_file.Tpo .deps/vcftools-vcf_file.Po variant_file_output.cpp:1442:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1442 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_output.cpp:1442:23: note: non-constexpr function 'size' cannot be used in a constant expression 1442 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_output.cpp:1619:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1619 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_output.cpp:1619:23: note: non-constexpr function 'size' cannot be used in a constant expression 1619 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_output.cpp:1793:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1793 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_output.cpp:1793:23: note: non-constexpr function 'size' cannot be used in a constant expression 1793 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_output.cpp:1958:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1958 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_output.cpp:1958:23: note: non-constexpr function 'size' cannot be used in a constant expression 1958 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_output.cpp:2115:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2115 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_output.cpp:2115:23: note: non-constexpr function 'size' cannot be used in a constant expression 2115 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_output.cpp:2320:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2320 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_output.cpp:2320:23: note: non-constexpr function 'size' cannot be used in a constant expression 2320 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_output.cpp:2329:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2329 | char tmpname2[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_output.cpp:2329:24: note: non-constexpr function 'size' cannot be used in a constant expression 2329 | char tmpname2[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_output.cpp:2561:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2561 | char tmpname[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_output.cpp:2561:23: note: non-constexpr function 'size' cannot be used in a constant expression 2561 | char tmpname[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ variant_file_output.cpp:2570:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2570 | char tmpname2[new_tmp.size()]; | ^~~~~~~~~~~~~~ variant_file_output.cpp:2570:24: note: non-constexpr function 'size' cannot be used in a constant expression 2570 | char tmpname2[new_tmp.size()]; | ^ /usr/include/c++/v1/string:1283:65: note: declared here 1283 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 size_type size() const _NOEXCEPT { | ^ 9 warnings generated. mv -f .deps/vcftools-variant_file_output.Tpo .deps/vcftools-variant_file_output.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -L/lib -lz gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/cpp' Making all in perl gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/perl' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/perl' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcftools-0.1.17 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for vcftools-0.1.17 ===> Generating temporary packing list Making install in src gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' Making install in cpp gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/cpp' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/cpp' /bin/mkdir -p '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/bin' install -s -m 555 vcftools '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/share/man/man1' install -m 0644 vcftools.1 '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/share/man/man1' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/cpp' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/cpp' Making install in perl gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/perl' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/perl' /bin/mkdir -p '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/bin' install -m 555 fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/lib/perl5/site_perl' install -m 0644 FaSlice.pm Vcf.pm VcfStats.pm '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/lib/perl5/site_perl' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/perl' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src/perl' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17/src' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.17' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-09-29T07:25:33+0000' 'PKG_NOTE_ports_top_git_hash=a936fb9b16ba' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=3ae8b09ca041' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for vcftools-0.1.17 ===> Building vcftools-0.1.17 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for vcftools-0.1.17 build of biology/vcftools | vcftools-0.1.17 ended at Mon Sep 29 03:26:42 EDT 2025 build time: 00:01:12