=>> Building biology/subread build started at Tue Jan 20 06:57:59 EST 2026 port directory: /usr/ports/biology/subread package name: subread-2.1.0 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p7 FreeBSD 14.3-RELEASE-p7 1403000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 558 Mar 30 2025 /usr/ports/biology/subread/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 888c0b0e32d3 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 04 ---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/04/.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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/subread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/subread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/subread/work/.cache HOME=/wrkdirs/usr/ports/biology/subread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/subread/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/subread/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/subread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/subread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/subread/work/.cache HOME=/wrkdirs/usr/ports/biology/subread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/subread/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/subread/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 -fcommon -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 -fcommon -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=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/subread" EXAMPLESDIR="share/examples/subread" DATADIR="share/subread" WWWDIR="www/subread" ETCDIR="etc/subread" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/subread DOCSDIR=/usr/local/share/doc/subread EXAMPLESDIR=/usr/local/share/examples/subread WWWDIR=/usr/local/www/subread ETCDIR=/usr/local/etc/subread --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 ===> subread-2.1.0 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 ===> subread-2.1.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of subread-2.1.0 =========================================================================== =================================================== ===== 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 subread-2.1.0 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by subread-2.1.0 for building => SHA256 Checksum OK for subread-2.1.0-source.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 subread-2.1.0 for building ===> Extracting for subread-2.1.0 => SHA256 Checksum OK for subread-2.1.0-source.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 subread-2.1.0 ===> Applying FreeBSD patches for subread-2.1.0 from /usr/ports/biology/subread/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> subread-2.1.0 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 ===> subread-2.1.0 depends on package: gmake>=4.4.1 - found ===> Returning to build of subread-2.1.0 ===> subread-2.1.0 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. ===> subread-2.1.0 depends on file: /usr/local/bin/ccache - found ===> Returning to build of subread-2.1.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> subread-2.1.0 depends on shared library: libsysinfo.so - not found ===> Installing existing package /packages/All/libsysinfo-0.0.3_3.pkg [pkg.DaveG.ca] Installing libsysinfo-0.0.3_3... [pkg.DaveG.ca] Extracting libsysinfo-0.0.3_3: ...... done ===> subread-2.1.0 depends on shared library: libsysinfo.so - found (/usr/local/lib/libsysinfo.so) ===> Returning to build of subread-2.1.0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for subread-2.1.0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for subread-2.1.0 cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core.o core.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-junction.o core-junction.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-indel.o core-indel.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sambam-file.o sambam-file.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sublog.o sublog.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o gene-algorithms.o gene-algorithms.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o hashtable.o hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o input-files.o input-files.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sorted-hashtable.o sorted-hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o gene-value-index.o gene-value-index.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o exon-algorithms.o exon-algorithms.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o HelperFunctions.o HelperFunctions.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o interval_merge.o interval_merge.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o long-hashtable.o long-hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-bigtable.o core-bigtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o seek-zlib.o seek-zlib.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o input-blc.o input-blc.c HelperFunctions.c:1558:75: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] 1558 | SUBREADprintf("\t'%s'\t%016llX\t%llu\t%.9f\n", s, randv, randv, randv*1./0xffffffffffffffffllu); | ~^~~~~~~~~~~~~~~~~~~~~ ./subread.h:142:44: note: expanded from macro 'SUBREADprintf' 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) | ^~~~~~~~~~~ 1 warning generated. input-blc.c:356:2: warning: call to undeclared function 'close'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 356 | close(fp->cbcl_bin_fd); | ^ input-blc.c:489:11: warning: call to undeclared function 'read'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 489 | rrv=read(tfp -> cbcl_bin_fd,&btmp,1);// bits per call. | ^ input-blc.c:529:32: warning: call to undeclared function 'dup'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 529 | tfp -> gzblock_fp=gzdopen(dup(tfp -> cbcl_bin_fd),"rb"); | ^ input-blc.c:582:7: warning: call to undeclared function 'close'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 582 | close(tfp -> cbcl_bin_fd); | ^ 4 warnings generated. cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm echo " " > longread-one/make.version cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm rm -f longread-one/*.o cd longread-one && /usr/local/bin/gmake cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/subread/work/subread-2.1.0-source/src/longread-one' cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o LRMsorted-hashtable.o -c -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing LRMsorted-hashtable.c gen_rand_reads.c:208:68: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] 208 | double rand_01 = plain_txt_to_long_rand(grc->random_seeds, 16)*1./0xffffffffffffffffllu; | ~^~~~~~~~~~~~~~~~~~~~~ gen_rand_reads.c:216:62: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] 216 | rand_01 = plain_txt_to_long_rand(grc->random_seeds, 16)*1./0xffffffffffffffffllu; | ~^~~~~~~~~~~~~~~~~~~~~ cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o LRMbase-index.o -c -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing LRMbase-index.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o LRMchro-event.o -c -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing LRMchro-event.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o LRMhelper.o -c -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing LRMhelper.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o LRMseek-zlib.o -c -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing LRMseek-zlib.c 2 warnings generated. cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o LRMfile-io.o -c -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing LRMfile-io.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o LRMhashtable.o -c -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing LRMhashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm readSummary.c:2578:66: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] 2578 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); | ~~ ^~~~~~~~~~~~~~~ | %lu ./subread.h:142:44: note: expanded from macro 'SUBREADprintf' 142 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) | ^~~~~~~~~~~ 1 warning generated. cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.1.0"\" -D_FILE_OFFSET_BITS=64 -o LRM -O2 -pipe -fcommon -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/subread/work/subread-2.1.0-source/src/longread-one' mkdir -p ../bin/utilities mv longread-one/LRM longread-one/sublong mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for subread-2.1.0 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/subread/work/stage/usr/local/bin install -c \ ../bin/exactSNP \ ../bin/featureCounts \ ../bin/sub* \ ../bin/utilities/* \ /wrkdirs/usr/ports/biology/subread/work/stage/usr/local/bin strip /wrkdirs/usr/ports/biology/subread/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=2026-01-20T11:57:59+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=888c0b0e32d3' '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 subread-2.1.0 ===> Building subread-2.1.0 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for subread-2.1.0 build of biology/subread | subread-2.1.0 ended at Tue Jan 20 06:58:19 EST 2026 build time: 00:00:21