=>> Building biology/vcftools build started at Fri Mar 29 14:38:28 GMT 2024 port directory: /usr/ports/biology/vcftools package name: vcftools-0.1.16_2 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 434 Mar 7 22:02 /usr/ports/biology/vcftools/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: ebba67d68e Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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=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=/ccache/libexec/ccache:/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 CCACHE_DIR="/root/.ccache" 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=/ccache/libexec/ccache:/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=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 " CCACHE_DIR="/root/.ccache" 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=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 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--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 --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-0.1.16_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> vcftools-0.1.16_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcftools-0.1.16_2 =========================================================================== =================================================== ===== 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-0.1.16_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vcftools-0.1.16_2 for building => SHA256 Checksum OK for vcftools-vcftools-v0.1.16_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-0.1.16_2 for building ===> Extracting for vcftools-0.1.16_2 => SHA256 Checksum OK for vcftools-vcftools-v0.1.16_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-0.1.16_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcftools-0.1.16_2 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> vcftools-0.1.16_2 depends on package: gmake>=4.4.1 - found ===> Returning to build of vcftools-0.1.16_2 ===> vcftools-0.1.16_2 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.1.1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.1.1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.1.1,1: .......... done ===> vcftools-0.1.16_2 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of vcftools-0.1.16_2 ===> vcftools-0.1.16_2 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg-builder.dan.net.uk] Installing autoconf-2.72... [pkg-builder.dan.net.uk] `-- Installing autoconf-switch-20220527... [pkg-builder.dan.net.uk] `-- Extracting autoconf-switch-20220527: ....... done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_1: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> vcftools-0.1.16_2 depends on package: autoconf>=2.72 - found ===> Returning to build of vcftools-0.1.16_2 ===> vcftools-0.1.16_2 depends on package: automake>=1.16.5 - not found ===> Installing existing package /packages/All/automake-1.16.5_1.pkg [pkg-builder.dan.net.uk] Installing automake-1.16.5_1... [pkg-builder.dan.net.uk] Extracting automake-1.16.5_1: .......... done ===> vcftools-0.1.16_2 depends on package: automake>=1.16.5 - found ===> Returning to build of vcftools-0.1.16_2 ===> vcftools-0.1.16_2 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== 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-0.1.16_2 configure.ac:16: installing './compile' configure.ac:66: installing './config.guess' configure.ac:66: installing './config.sub' 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 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 gmake sets $(MAKE)... yes checking whether gmake supports nested variables... 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 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 build system type... amd64-portbld-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 checking for GNU libc compatible malloc... (cached) yes checking for GNU libc compatible realloc... yes checking for gethostbyaddr... yes checking for gethostbyname... (cached) yes checking for memset... (cached) yes checking for pow... no 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-0.1.16_2 gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' Making all in src gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' Making all in cpp gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/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 mv -f .deps/vcftools-bcf_entry.Tpo .deps/vcftools-bcf_entry.Po 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 bcf_entry_setters.cpp:309:13: warning: implicit conversion from 'int' to 'float' changes value from 2139095041 to 2139095040 [-Wimplicit-const-int-float-conversion] if (tmp == 0x7F800001) ~~ ^~~~~~~~~~ bcf_entry_setters.cpp:326:28: warning: implicit conversion from 'int' to 'float' changes value from 2139095041 to 2139095040 [-Wimplicit-const-int-float-conversion] if ( (in == -1) or (in == 0x7F800001) ) ~~ ^~~~~~~~~~ 2 warnings generated. mv -f .deps/vcftools-bcf_entry_setters.Tpo .deps/vcftools-bcf_entry_setters.Po 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 mv -f .deps/vcftools-bcf_file.Tpo .deps/vcftools-bcf_file.Po 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 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-dgeev.o -MD -MP -MF .deps/vcftools-dgeev.Tpo -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.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-entry.o -MD -MP -MF .deps/vcftools-entry.Tpo -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp entry.cpp:601:12: warning: implicit conversion from 'int' to 'float' changes value from 2139095042 to 2139095040 [-Wimplicit-const-int-float-conversion] value = 0x7F800002; ~ ^~~~~~~~~~ 1 warning generated. mv -f .deps/vcftools-entry.Tpo .deps/vcftools-entry.Po 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 mv -f .deps/vcftools-entry_filters.Tpo .deps/vcftools-entry_filters.Po 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 mv -f .deps/vcftools-entry_getters.Tpo .deps/vcftools-entry_getters.Po 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 mv -f .deps/vcftools-entry_setters.Tpo .deps/vcftools-entry_setters.Po 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 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-header.o -MD -MP -MF .deps/vcftools-header.Tpo -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp mv -f .deps/vcftools-header.Tpo .deps/vcftools-header.Po 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 mv -f .deps/vcftools-knetfile.Tpo .deps/vcftools-knetfile.Po 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 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-parameters.o -MD -MP -MF .deps/vcftools-parameters.Tpo -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp mv -f .deps/vcftools-parameters.Tpo .deps/vcftools-parameters.Po 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 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-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-variant_file_diff.Tpo .deps/vcftools-variant_file_diff.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 variant_file_filters.cpp:129:2: warning: 'random_shuffle>' is deprecated [-Wdeprecated-declarations] random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order ^ /usr/include/c++/v1/__algorithm/shuffle.h:93:1: note: 'random_shuffle>' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX14 void ^ /usr/include/c++/v1/__config:1024:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 1 warning generated. mv -f .deps/vcftools-variant_file_filters.Tpo .deps/vcftools-variant_file_filters.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 mv -f .deps/vcftools-variant_file_format_convert.Tpo .deps/vcftools-variant_file_format_convert.Po 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-variant_file_output.Tpo .deps/vcftools-variant_file_output.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-vcf_entry.Tpo .deps/vcftools-vcf_entry.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-vcf_entry_setters.Tpo .deps/vcftools-vcf_entry_setters.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 mv -f .deps/vcftools-vcf_file.Tpo .deps/vcftools-vcf_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 mv -f .deps/vcftools-vcftools.Tpo .deps/vcftools-vcftools.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -fstack-protector-strong -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 -lz gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/cpp' Making all in perl gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/perl' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/perl' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcftools-0.1.16_2 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for vcftools-0.1.16_2 ===> Generating temporary packing list Making install in src gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' Making install in cpp gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/cpp' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/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-0.1.16/src/cpp' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/cpp' Making install in perl gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/perl' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/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-0.1.16/src/perl' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/perl' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/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-0.1.16/src' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' 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-0.1.16' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' ====> 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=2024-03-29T14:38:28+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=ebba67d68e' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for vcftools-0.1.16_2 ===> Building vcftools-0.1.16_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for vcftools-0.1.16_2 build of biology/vcftools | vcftools-0.1.16_2 ended at Fri Mar 29 14:40:26 GMT 2024 build time: 00:01:59