=>> Building biology/p5-Bio-SCF build started at Sun Mar 15 13:32:08 EDT 2026 port directory: /usr/ports/biology/p5-Bio-SCF package name: p5-Bio-SCF-1.03_3 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: wen@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 459 Feb 17 19:06 /usr/ports/biology/p5-Bio-SCF/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: 6620ae9fa686 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 14 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 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_0_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_0_x64-HEAD-ALL/14/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_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-- wen@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- INSTALLDIRS="site" CC="cc" CCFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " LD="cc" PREFIX="/usr/local" INSTALLPRIVLIB="/usr/local/lib" INSTALLARCHLIB="/usr/local/lib" --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work/.cache HOME=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh PERL_EXTUTILS_AUTOINSTALL="--skipdeps" PERL_MM_USE_DEFAULT="YES" CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work/.cache HOME=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/p5-Bio-SCF/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/p5-Bio-SCF/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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=5.42.1 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/Bio-SCF" EXAMPLESDIR="share/examples/Bio-SCF" DATADIR="share/Bio-SCF" WWWDIR="www/Bio-SCF" ETCDIR="etc/Bio-SCF" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/Bio-SCF DOCSDIR=/usr/local/share/doc/Bio-SCF EXAMPLESDIR=/usr/local/share/examples/Bio-SCF WWWDIR=/usr/local/www/Bio-SCF ETCDIR=/usr/local/etc/Bio-SCF --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 ===> p5-Bio-SCF-1.03_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> p5-Bio-SCF-1.03_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-Bio-SCF-1.03_3 =========================================================================== =================================================== ===== 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 p5-Bio-SCF-1.03_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by p5-Bio-SCF-1.03_3 for building => SHA256 Checksum OK for Bio-SCF-1.03.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 p5-Bio-SCF-1.03_3 for building ===> Extracting for p5-Bio-SCF-1.03_3 => SHA256 Checksum OK for Bio-SCF-1.03.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 p5-Bio-SCF-1.03_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> p5-Bio-SCF-1.03_3 depends on file: /usr/local/include/io_lib/scf.h - not found ===> Installing existing package /packages/All/io_lib-1.15.1.pkg [pkg.DaveG.ca] Installing io_lib-1.15.1... [pkg.DaveG.ca] `-- Installing curl-8.17.0... [pkg.DaveG.ca] | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.17.0: .......... done [pkg.DaveG.ca] Extracting io_lib-1.15.1: .......... done ===> p5-Bio-SCF-1.03_3 depends on file: /usr/local/include/io_lib/scf.h - found ===> Returning to build of p5-Bio-SCF-1.03_3 ===> p5-Bio-SCF-1.03_3 depends on package: perl5>=5.42.r<5.43 - not found ===> Installing existing package /packages/All/perl5-5.42.1.pkg [pkg.DaveG.ca] Installing perl5-5.42.1... [pkg.DaveG.ca] Extracting perl5-5.42.1: .......... done ===> p5-Bio-SCF-1.03_3 depends on package: perl5>=5.42.r<5.43 - found ===> Returning to build of p5-Bio-SCF-1.03_3 ===> p5-Bio-SCF-1.03_3 depends on package: perl5>=5.42.r<5.43 - found ===> p5-Bio-SCF-1.03_3 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. ===> p5-Bio-SCF-1.03_3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of p5-Bio-SCF-1.03_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for p5-Bio-SCF-1.03_3 Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::SCF Writing MYMETA.yml and MYMETA.json =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for p5-Bio-SCF-1.03_3 --- blib/lib/Bio/.exists --- --- blib/arch/.exists --- --- blib/lib/auto/Bio/SCF/.exists --- --- blib/arch/auto/Bio/SCF/.exists --- --- blib/bin/.exists --- --- blib/script/.exists --- --- blib/man1/.exists --- --- blib/man3/.exists --- --- config --- --- subdirs --- --- dynamic --- --- SCF.c --- --- SCF.bs --- --- pm_to_blib --- --- SCF.bs --- Running Mkbootstrap for SCF () --- SCF.c --- "/usr/local/bin/perl5.42.1" "/usr/local/lib/perl5/5.42/ExtUtils/xsubpp" -typemap '/usr/local/lib/perl5/5.42/ExtUtils/typemap' SCF.xs > SCF.xsc --- blibdirs --- --- SCF.bs --- chmod 644 "SCF.bs" --- config --- --- blib/arch/auto/Bio/SCF/SCF.bs --- --- SCF.c --- Please specify prototyping behavior for SCF.xs (see perlxs manual) --- pm_to_blib --- cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm cp SCF.pm blib/lib/Bio/SCF.pm --- blib/arch/auto/Bio/SCF/SCF.bs --- "/usr/local/bin/perl5.42.1" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs blib/arch/auto/Bio/SCF/SCF.bs 644 --- SCF.c --- mv SCF.xsc SCF.c --- SCF.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVERSION=\"1.03\" -DXS_VERSION=\"1.03\" -DPIC -fPIC "-I/usr/local/lib/perl5/5.42/mach/CORE" -DLITTLE_ENDIAN SCF.c SCF.xs:57:20: warning: cast to smaller integer type 'int' from 'Scf *' [-Wpointer-to-int-cast] 57 | ret_val = newSViv((int)scf_data); | ^~~~~~~~~~~~~ /usr/local/lib/perl5/5.42/mach/CORE/embed.h:443:68: note: expanded from macro 'newSViv' 443 | # define newSViv(a) Perl_newSViv(aTHX_ a) | ^ SCF.xs:80:20: warning: cast to smaller integer type 'int' from 'Scf *' [-Wpointer-to-int-cast] 80 | ret_val = newSViv((int)scf_data); | ^~~~~~~~~~~~~ /usr/local/lib/perl5/5.42/mach/CORE/embed.h:443:68: note: expanded from macro 'newSViv' 443 | # define newSViv(a) Perl_newSViv(aTHX_ a) | ^ SCF.xs:89:17: warning: cast to 'Scf *' from smaller integer type 'int' [-Wint-to-pointer-cast] 89 | scf_deallocate((Scf *)scf_pointer); | ^~~~~~~~~~~~~~~~~~ SCF.xs:95:18: warning: cast to 'Scf *' from smaller integer type 'int' [-Wint-to-pointer-cast] 95 | Scf *scf_data = (Scf *)scf_pointer; | ^~~~~~~~~~~~~~~~~~ SCF.xs:108:18: warning: cast to 'Scf *' from smaller integer type 'int' [-Wint-to-pointer-cast] 108 | Scf *scf_data = (Scf *)scf_pointer; | ^~~~~~~~~~~~~~~~~~ SCF.xs:121:18: warning: cast to 'Scf *' from smaller integer type 'int' [-Wint-to-pointer-cast] 121 | Scf *scf_data = (Scf *)scf_pointer; | ^~~~~~~~~~~~~~~~~~ SCF.xs:137:18: warning: cast to 'Scf *' from smaller integer type 'int' [-Wint-to-pointer-cast] 137 | Scf *scf_data = (Scf *)scf_pointer; | ^~~~~~~~~~~~~~~~~~ SCF.xs:159:18: warning: cast to 'Scf *' from smaller integer type 'int' [-Wint-to-pointer-cast] 159 | Scf *scf_data = (Scf *)scf_pointer; | ^~~~~~~~~~~~~~~~~~ SCF.xs:186:18: warning: cast to 'Scf *' from smaller integer type 'int' [-Wint-to-pointer-cast] 186 | Scf *scf_data = (Scf *)scf_pointer; | ^~~~~~~~~~~~~~~~~~ SCF.xs:242:18: warning: cast to 'Scf *' from smaller integer type 'int' [-Wint-to-pointer-cast] 242 | Scf *scf_data = (Scf *)scf_pointer; | ^~~~~~~~~~~~~~~~~~ SCF.xs:255:18: warning: cast to 'Scf *' from smaller integer type 'int' [-Wint-to-pointer-cast] 255 | Scf *scf_data = (Scf *)scf_pointer; | ^~~~~~~~~~~~~~~~~~ 11 warnings generated. --- blib/arch/auto/Bio/SCF/SCF.so --- rm -f blib/arch/auto/Bio/SCF/SCF.so LD_RUN_PATH="/usr/local/lib:/usr/lib" cc -shared -L/usr/local/lib/perl5/5.42/mach/CORE -lperl -L/usr/local/lib -fstack-protector-strong SCF.o -o blib/arch/auto/Bio/SCF/SCF.so -lstaden-read -lz chmod 755 blib/arch/auto/Bio/SCF/SCF.so --- dynamic --- --- linkext --- --- pure_all --- --- manifypods --- Manifying 1 pod document --- all --- =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> p5-Bio-SCF-1.03_3 depends on file: /usr/local/include/io_lib/scf.h - found ===> p5-Bio-SCF-1.03_3 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for p5-Bio-SCF-1.03_3 ===> Generating temporary packing list "/usr/local/bin/perl5.42.1" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs blib/arch/auto/Bio/SCF/SCF.bs 644 Manifying 1 pod document Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /wrkdirs/usr/ports/biology/p5-Bio-SCF/work/stage/usr/local/lib/perl5/site_perl/mach/5.42/auto/Bio/SCF/SCF.so Installing /wrkdirs/usr/ports/biology/p5-Bio-SCF/work/stage/usr/local/lib/perl5/site_perl/mach/5.42/Bio/SCF.pm Installing /wrkdirs/usr/ports/biology/p5-Bio-SCF/work/stage/usr/local/lib/perl5/site_perl/mach/5.42/Bio/SCF/Arrays.pm Installing /wrkdirs/usr/ports/biology/p5-Bio-SCF/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SCF.3 ====> 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=2026-03-15T17:32:08+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=6620ae9fa686' '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 p5-Bio-SCF-1.03_3 ===> Building p5-Bio-SCF-1.03_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for p5-Bio-SCF-1.03_3 build of biology/p5-Bio-SCF | p5-Bio-SCF-1.03_3 ended at Sun Mar 15 13:34:22 EDT 2026 build time: 00:02:18