=>> Building biology/stringtie build started at Tue Jan 20 02:16:18 EST 2026 port directory: /usr/ports/biology/stringtie package name: stringtie-2.1.1 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p7 FreeBSD 14.3-RELEASE-p7 1403000 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 554 Aug 27 2024 /usr/ports/biology/stringtie/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: fb16dfecae4a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p7 1403000 UNAME_r=14.3-RELEASE-p7 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_14_3_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_14_3_x64-HEAD-ALL/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_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-- mzaki@e-mail.ne.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/stringtie/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stringtie/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/stringtie/work/.cache HOME=/wrkdirs/usr/ports/biology/stringtie/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/stringtie/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/stringtie/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/stringtie/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stringtie/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/stringtie/work/.cache HOME=/wrkdirs/usr/ports/biology/stringtie/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/stringtie/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/stringtie/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/stringtie" EXAMPLESDIR="share/examples/stringtie" DATADIR="share/stringtie" WWWDIR="www/stringtie" ETCDIR="etc/stringtie" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/stringtie DOCSDIR=/usr/local/share/doc/stringtie EXAMPLESDIR=/usr/local/share/examples/stringtie WWWDIR=/usr/local/www/stringtie ETCDIR=/usr/local/etc/stringtie --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 ===> stringtie-2.1.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> stringtie-2.1.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of stringtie-2.1.1 =========================================================================== =================================================== ===== 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 stringtie-2.1.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by stringtie-2.1.1 for building => SHA256 Checksum OK for stringtie-2.1.1.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 stringtie-2.1.1 for building ===> Extracting for stringtie-2.1.1 => SHA256 Checksum OK for stringtie-2.1.1.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 stringtie-2.1.1 ===> Applying FreeBSD patches for stringtie-2.1.1 from /usr/ports/biology/stringtie/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> stringtie-2.1.1 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-0.26... [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-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> stringtie-2.1.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of stringtie-2.1.1 ===> stringtie-2.1.1 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. ===> stringtie-2.1.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of stringtie-2.1.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for stringtie-2.1.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for stringtie-2.1.1 cd ./samtools-0.1.18 && /usr/local/bin/gmake lib c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GBase.cpp -o gclib/GBase.o gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/stringtie/work/stringtie-2.1.1/samtools-0.1.18' cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam.c -o bam.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam.c -o sam.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. razf.c -o razf.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GArgs.cpp -o gclib/GArgs.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GStr.cpp -o gclib/GStr.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GBam.cpp -o gclib/GBam.o cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gdna.cpp -o gclib/gdna.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/codons.cpp -o gclib/codons.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gff.cpp -o gclib/gff.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GThreads.cpp -o gclib/GThreads.o bgzf.c:270:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 139 to -117 [-Wconstant-conversion] 270 | buffer[1] = GZIP_ID2; | ~ ^~~~~~~~ bgzf.c:278:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 255 to -1 [-Wconstant-conversion] 278 | buffer[9] = OS_UNKNOWN; | ~ ^~~~~~~~~~ 2 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c rlink.cpp -o rlink.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tablemaker.cpp -o tablemaker.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tmerge.cpp -o tmerge.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c stringtie.cpp -o stringtie.o warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stringtie/work/stringtie-2.1.1/samtools-0.1.18' warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] gclib/GBam.cpp:257:5: warning: variable 'rpos' set but not used [-Wunused-but-set-variable] 257 | int rpos = 0; | ^ gclib/GBam.cpp:258:5: warning: variable 'gpos' set but not used [-Wunused-but-set-variable] 258 | int gpos = aln_start; | ^ gclib/GBam.cpp:259:5: warning: variable 'num_mismatches' set but not used [-Wunused-but-set-variable] 259 | int num_mismatches=0; //NM tag value = edit distance | ^ 4 warnings generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] tablemaker.cpp:205:22: warning: 'bind2nd, double>' is deprecated [-Wdeprecated-declarations] 205 | bind2nd( minus(), avg)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, double>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ tablemaker.cpp:212:22: warning: 'bind2nd, double>' is deprecated [-Wdeprecated-declarations] 212 | bind2nd( minus(), mavg)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, double>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 3 warnings generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] stringtie.cpp:1119:4: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 1119 | s=args.getOpt('C'); | ^ stringtie.cpp:1108:3: note: previous statement is here 1108 | if ((ballgown || !ballgown_dir.is_empty()) && !guided) | ^ 2 warnings generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. warning: unknown warning option '-Wno-class-memaccess'; did you mean '-Wno-class-varargs'? [-Wunknown-warning-option] 1 warning generated. c++ -L./samtools-0.1.18 -o stringtie gclib/GBase.o gclib/GArgs.o gclib/GStr.o gclib/GBam.o gclib/gdna.o gclib/codons.o gclib/GFastaIndex.o gclib/GFaSeqGet.o gclib/gff.o gclib/GThreads.o rlink.o tablemaker.o tmerge.o stringtie.o -pthread -lbam -lz =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for stringtie-2.1.1 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/stringtie/work/stringtie-2.1.1/stringtie /wrkdirs/usr/ports/biology/stringtie/work/stage/usr/local/bin ====> 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=2026-01-20T07:16:18+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=fb16dfecae4a' '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 stringtie-2.1.1 ===> Building stringtie-2.1.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for stringtie-2.1.1 build of biology/stringtie | stringtie-2.1.1 ended at Tue Jan 20 02:16:53 EST 2026 build time: 00:00:37