=>> Building biology/tRNAscan-SE build started at Tue Apr 2 14:49:08 BST 2024 port directory: /usr/ports/biology/tRNAscan-SE package name: tRNAscan-SE-2.0.11 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 504 Mar 8 2023 /usr/ports/biology/tRNAscan-SE/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 20 ---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 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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 ===> tRNAscan-SE-2.0.11 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 ===> tRNAscan-SE-2.0.11 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of tRNAscan-SE-2.0.11 =========================================================================== =================================================== ===== 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 tRNAscan-SE-2.0.11 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by tRNAscan-SE-2.0.11 for building => SHA256 Checksum OK for trnascan-se-2.0.11.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 tRNAscan-SE-2.0.11 for building ===> Extracting for tRNAscan-SE-2.0.11 => SHA256 Checksum OK for trnascan-se-2.0.11.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 tRNAscan-SE-2.0.11 ===> Applying FreeBSD patches for tRNAscan-SE-2.0.11 from /usr/ports/biology/tRNAscan-SE/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> tRNAscan-SE-2.0.11 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 indexinfo-0.3.1... [pkg-builder.dan.net.uk] `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [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. ===> tRNAscan-SE-2.0.11 depends on package: autoconf>=2.72 - found ===> Returning to build of tRNAscan-SE-2.0.11 ===> tRNAscan-SE-2.0.11 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 ===> tRNAscan-SE-2.0.11 depends on package: automake>=1.16.5 - found ===> Returning to build of tRNAscan-SE-2.0.11 ===> tRNAscan-SE-2.0.11 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 tRNAscan-SE-2.0.11 configure.ac:21: installing './compile' configure.ac:50: installing './config.guess' configure.ac:50: installing './config.sub' configure: loading site script /usr/ports/Templates/config.site checking for gcc... cc 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 cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking for a BSD-compatible install... /usr/bin/install -c checking for perl... (cached) /usr/local/bin/perl checking for Perl version 5.0.0 or later... 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 size_t... (cached) yes checking for working alloca.h... no checking for alloca... yes checking for limits.h... (cached) yes checking for memory.h... (cached) yes checking for stddef.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.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 size_t... (cached) yes 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 bzero... (cached) yes checking for memset... (cached) yes checking for re_comp... no checking for regcomp... yes checking for strcasecmp... (cached) yes checking for strchr... (cached) yes checking for strstr... (cached) yes checking for library containing sqrt... -lm 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 make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of cc... gcc3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for tRNAscan-SE-2.0.11 /usr/bin/make all-am depbase=`echo src/alignio.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/alignio.o -MD -MP -MF $depbase.Tpo -c -o src/alignio.o src/alignio.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sqerror.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/sqerror.o -MD -MP -MF $depbase.Tpo -c -o src/sqerror.o src/sqerror.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sqio.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/sqio.o -MD -MP -MF $depbase.Tpo -c -o src/sqio.o src/sqio.c && mv -f $depbase.Tpo $depbase.Po src/sqio.c:1030:9: warning: comparison of array 'sp' equal to a null pointer is always false [-Wtautological-pointer-compare] if (sp==NULL || *sp=='\0') ^~ ~~~~ 1 warning generated. depbase=`echo src/iupac.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/iupac.o -MD -MP -MF $depbase.Tpo -c -o src/iupac.o src/iupac.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/msf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/msf.o -MD -MP -MF $depbase.Tpo -c -o src/msf.o src/msf.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/revcomp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/revcomp.o -MD -MP -MF $depbase.Tpo -c -o src/revcomp.o src/revcomp.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/selex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/selex.o -MD -MP -MF $depbase.Tpo -c -o src/selex.o src/selex.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sre_ctype.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/sre_ctype.o -MD -MP -MF $depbase.Tpo -c -o src/sre_ctype.o src/sre_ctype.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sre_math.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/sre_math.o -MD -MP -MF $depbase.Tpo -c -o src/sre_math.o src/sre_math.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sre_string.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/sre_string.o -MD -MP -MF $depbase.Tpo -c -o src/sre_string.o src/sre_string.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/stack.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/stack.o -MD -MP -MF $depbase.Tpo -c -o src/stack.o src/stack.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/types.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/types.o -MD -MP -MF $depbase.Tpo -c -o src/types.o src/types.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/gnuregex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/gnuregex.o -MD -MP -MF $depbase.Tpo -c -o src/gnuregex.o src/gnuregex.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/interleaved.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/interleaved.o -MD -MP -MF $depbase.Tpo -c -o src/interleaved.o src/interleaved.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/getopt.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/getopt.o -MD -MP -MF $depbase.Tpo -c -o src/getopt.o src/getopt.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/eufind_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/eufind_main.o -MD -MP -MF $depbase.Tpo -c -o src/eufind_main.o src/eufind_main.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/pavesi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/pavesi.o -MD -MP -MF $depbase.Tpo -c -o src/pavesi.o src/pavesi.c && mv -f $depbase.Tpo $depbase.Po cc -O3 -fstack-protector-strong -o bin/eufindtRNA src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/eufind_main.o src/pavesi.o -lm cc -DHAVE_CONFIG_H -I. -DTSCANDIR=\"/usr/local/share\/tRNAscan-SE\/models\" -O3 -MT src/bin_trnascan_1_4-trnascan.o -MD -MP -MF src/.deps/bin_trnascan_1_4-trnascan.Tpo -c -o src/bin_trnascan_1_4-trnascan.o `test -f 'src/trnascan.c' || echo './'`src/trnascan.c mv -f src/.deps/bin_trnascan_1_4-trnascan.Tpo src/.deps/bin_trnascan_1_4-trnascan.Po cc -DTSCANDIR=\"/usr/local/share\/tRNAscan-SE\/models\" -O3 -fstack-protector-strong -o bin/trnascan-1.4 src/bin_trnascan_1_4-trnascan.o -lm depbase=`echo src/align.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/align.o -MD -MP -MF $depbase.Tpo -c -o src/align.o src/align.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/dbviterbi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/dbviterbi.o -MD -MP -MF $depbase.Tpo -c -o src/dbviterbi.o src/dbviterbi.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/debug.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/debug.o -MD -MP -MF $depbase.Tpo -c -o src/debug.o src/debug.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/emit.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/emit.o -MD -MP -MF $depbase.Tpo -c -o src/emit.o src/emit.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/fast-dbviterbi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/fast-dbviterbi.o -MD -MP -MF $depbase.Tpo -c -o src/fast-dbviterbi.o src/fast-dbviterbi.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/fastmodelmaker.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/fastmodelmaker.o -MD -MP -MF $depbase.Tpo -c -o src/fastmodelmaker.o src/fastmodelmaker.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/konings.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/konings.o -MD -MP -MF $depbase.Tpo -c -o src/konings.o src/konings.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/lengthdist.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/lengthdist.o -MD -MP -MF $depbase.Tpo -c -o src/lengthdist.o src/lengthdist.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/maxmodelmaker.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/maxmodelmaker.o -MD -MP -MF $depbase.Tpo -c -o src/maxmodelmaker.o src/maxmodelmaker.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/misc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/misc.o -MD -MP -MF $depbase.Tpo -c -o src/misc.o src/misc.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/model.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/model.o -MD -MP -MF $depbase.Tpo -c -o src/model.o src/model.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/modelmaking.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/modelmaking.o -MD -MP -MF $depbase.Tpo -c -o src/modelmaking.o src/modelmaking.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/prior.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/prior.o -MD -MP -MF $depbase.Tpo -c -o src/prior.o src/prior.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/probify.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/probify.o -MD -MP -MF $depbase.Tpo -c -o src/probify.o src/probify.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/save.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/save.o -MD -MP -MF $depbase.Tpo -c -o src/save.o src/save.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/smallviterbi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/smallviterbi.o -MD -MP -MF $depbase.Tpo -c -o src/smallviterbi.o src/smallviterbi.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/scorestack.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/scorestack.o -MD -MP -MF $depbase.Tpo -c -o src/scorestack.o src/scorestack.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/structs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/structs.o -MD -MP -MF $depbase.Tpo -c -o src/structs.o src/structs.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/trace.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/trace.o -MD -MP -MF $depbase.Tpo -c -o src/trace.o src/trace.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/viterbi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/viterbi.o -MD -MP -MF $depbase.Tpo -c -o src/viterbi.o src/viterbi.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/scan_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/scan_main.o -MD -MP -MF $depbase.Tpo -c -o src/scan_main.o src/scan_main.c && mv -f $depbase.Tpo $depbase.Po cc -O3 -fstack-protector-strong -o bin/covels-SE src/align.o src/dbviterbi.o src/debug.o src/emit.o src/fast-dbviterbi.o src/fastmodelmaker.o src/konings.o src/lengthdist.o src/maxmodelmaker.o src/misc.o src/model.o src/modelmaking.o src/prior.o src/probify.o src/save.o src/smallviterbi.o src/scorestack.o src/structs.o src/trace.o src/viterbi.o src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/scan_main.o -lm depbase=`echo src/score_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -O3 -MT src/score_main.o -MD -MP -MF $depbase.Tpo -c -o src/score_main.o src/score_main.c && mv -f $depbase.Tpo $depbase.Po cc -O3 -fstack-protector-strong -o bin/coves-SE src/align.o src/dbviterbi.o src/debug.o src/emit.o src/fast-dbviterbi.o src/fastmodelmaker.o src/konings.o src/lengthdist.o src/maxmodelmaker.o src/misc.o src/model.o src/modelmaking.o src/prior.o src/probify.o src/save.o src/smallviterbi.o src/scorestack.o src/structs.o src/trace.o src/viterbi.o src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/score_main.o -lm sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./src/sstofa.in > bin/sstofa chmod +x bin/sstofa sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./src/fasta2gsi.in > bin/fasta2gsi chmod +x bin/fasta2gsi sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter chmod +x bin/EukHighConfidenceFilter sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./MitoHighConfidenceFilter.in > bin/MitoHighConfidenceFilter chmod +x bin/MitoHighConfidenceFilter sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./tRNAscan-SE.src > tRNAscan-SE chmod +x tRNAscan-SE sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./tRNAscan-SE.conf.src > tRNAscan-SE.conf chmod +x tRNAscan-SE.conf =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> tRNAscan-SE-2.0.11 depends on executable: cmsearch - not found ===> Installing existing package /packages/All/infernal-1.1.4_1.pkg [pkg-builder.dan.net.uk] Installing infernal-1.1.4_1... [pkg-builder.dan.net.uk] Extracting infernal-1.1.4_1: .......... done ===> tRNAscan-SE-2.0.11 depends on executable: cmsearch - found ===> Returning to build of tRNAscan-SE-2.0.11 ===> tRNAscan-SE-2.0.11 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for tRNAscan-SE-2.0.11 ===> Generating temporary packing list /bin/mkdir -p '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/bin' install -s -m 555 bin/eufindtRNA bin/trnascan-1.4 bin/covels-SE bin/coves-SE '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/bin' install -m 555 bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/etc' install -m 0644 tRNAscan-SE.conf '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/etc' /bin/mkdir -p '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/share/tRNAscan-SE/gcode' install -m 0644 lib/gcode/gcode.cilnuc lib/gcode/gcode.echdmito lib/gcode/gcode.invmito lib/gcode/gcode.marsumito lib/gcode/gcode.othmito lib/gcode/gcode.vertmito lib/gcode/gcode.ystmito '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/share/tRNAscan-SE/gcode' /bin/mkdir -p '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/share/tRNAscan-SE/models' install -m 0644 lib/models/Cren-eury-BHB-noncan.cm lib/models/Dsignal lib/models/ESELC.cm lib/models/PSELC.cm lib/models/TPCsignal lib/models/TRNA2-arch.cm lib/models/TRNA2-archns.cm lib/models/TRNA2-bact.cm lib/models/TRNA2-bactns.cm lib/models/TRNA2-euk.cm lib/models/TRNA2-eukns.cm lib/models/TRNA2.cm lib/models/TRNA2ns.cm lib/models/TRNAinf-1415-ns.cm lib/models/TRNAinf-1415.cm lib/models/TRNAinf-arch-3h.cm lib/models/TRNAinf-arch-5h.cm lib/models/TRNAinf-arch-SeC.cm lib/models/TRNAinf-arch-iso lib/models/TRNAinf-arch-iso.i1f lib/models/TRNAinf-arch-iso.i1i lib/models/TRNAinf-arch-iso.i1m lib/models/TRNAinf-arch-iso.i1p lib/models/TRNAinf-arch-ns.cm lib/models/TRNAinf-arch.cm lib/models/TRNAinf-bact-SeC.cm lib/models/TRNAinf-bact-iso lib/models/TRNAinf-bact-iso.i1f lib/models/TRNAinf-bact-iso.i1i lib/models/TRNAinf-bact-iso.i1m lib/models/TRNAinf-bact-iso.i1p lib/models/TRNAinf-bact-ns.cm lib/models/TRNAinf-bact.cm lib/models/TRNAinf-euk-SeC.cm lib/models/TRNAinf-euk-iso lib/models/TRNAinf-euk-iso.i1f lib/models/TRNAinf-euk-iso.i1i lib/models/TRNAinf-euk-iso.i1m lib/models/TRNAinf-euk-iso.i1p lib/models/TRNAinf-euk-ns.cm '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/share/tRNAscan-SE/models' install -m 0644 lib/models/TRNAinf-euk.cm lib/models/TRNAinf-mito-mammal lib/models/TRNAinf-mito-mammal-Ala.cm lib/models/TRNAinf-mito-mammal-Arg.cm lib/models/TRNAinf-mito-mammal-Asn.cm lib/models/TRNAinf-mito-mammal-Asp.cm lib/models/TRNAinf-mito-mammal-Cys.cm lib/models/TRNAinf-mito-mammal-Gln.cm lib/models/TRNAinf-mito-mammal-Glu.cm lib/models/TRNAinf-mito-mammal-Gly.cm lib/models/TRNAinf-mito-mammal-His.cm lib/models/TRNAinf-mito-mammal-Ile.cm lib/models/TRNAinf-mito-mammal-LeuTAA.cm lib/models/TRNAinf-mito-mammal-LeuTAG.cm lib/models/TRNAinf-mito-mammal-Lys.cm lib/models/TRNAinf-mito-mammal-Met.cm lib/models/TRNAinf-mito-mammal-Phe.cm lib/models/TRNAinf-mito-mammal-Pro.cm lib/models/TRNAinf-mito-mammal-SerGCT.cm lib/models/TRNAinf-mito-mammal-SerTGA.cm lib/models/TRNAinf-mito-mammal-Thr.cm lib/models/TRNAinf-mito-mammal-Trp.cm lib/models/TRNAinf-mito-mammal-Tyr.cm lib/models/TRNAinf-mito-mammal-Val.cm lib/models/TRNAinf-mito-mammal.i1f lib/models/TRNAinf-mito-mammal.i1i lib/models/TRNAinf-mito-mammal.i1m lib/models/TRNAinf-mito-mammal.i1p lib/models/TRNAinf-mito-vert lib/models/TRNAinf-mito-vert-Ala.cm lib/models/TRNAinf-mito-vert-Arg.cm lib/models/TRNAinf-mito-vert-Asn.cm lib/models/TRNAinf-mito-vert-Asp.cm lib/models/TRNAinf-mito-vert-Cys-no-darm.cm lib/models/TRNAinf-mito-vert-Cys.cm lib/models/TRNAinf-mito-vert-Gln.cm lib/models/TRNAinf-mito-vert-Glu.cm lib/models/TRNAinf-mito-vert-Gly.cm lib/models/TRNAinf-mito-vert-His.cm lib/models/TRNAinf-mito-vert-Ile.cm '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/share/tRNAscan-SE/models' install -m 0644 lib/models/TRNAinf-mito-vert-LeuTAA.cm lib/models/TRNAinf-mito-vert-LeuTAG.cm lib/models/TRNAinf-mito-vert-Lys.cm lib/models/TRNAinf-mito-vert-Met.cm lib/models/TRNAinf-mito-vert-Phe.cm lib/models/TRNAinf-mito-vert-Pro.cm lib/models/TRNAinf-mito-vert-SerGCT.cm lib/models/TRNAinf-mito-vert-SerTGA.cm lib/models/TRNAinf-mito-vert-Thr.cm lib/models/TRNAinf-mito-vert-Trp.cm lib/models/TRNAinf-mito-vert-Tyr.cm lib/models/TRNAinf-mito-vert-Val.cm lib/models/TRNAinf-mito-vert.i1f lib/models/TRNAinf-mito-vert.i1i lib/models/TRNAinf-mito-vert.i1m lib/models/TRNAinf-mito-vert.i1p lib/models/TRNAinf-ns.cm lib/models/TRNAinf.cm lib/models/Thaum-BHB-noncan.cm '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/share/tRNAscan-SE/models' /bin/mkdir -p '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/share/tRNAscan-SE/tRNAscanSE' install -m 0644 lib/tRNAscanSE/ArrayCMscanResults.pm lib/tRNAscanSE/ArraytRNA.pm lib/tRNAscanSE/CM.pm lib/tRNAscanSE/CMscanResultFile.pm lib/tRNAscanSE/Configuration.pm lib/tRNAscanSE/Constants.pm lib/tRNAscanSE/Eufind.pm lib/tRNAscanSE/FpScanResultFile.pm lib/tRNAscanSE/GeneticCode.pm lib/tRNAscanSE/IntResultFile.pm lib/tRNAscanSE/LogFile.pm lib/tRNAscanSE/MultiResultFile.pm lib/tRNAscanSE/Options.pm lib/tRNAscanSE/ResultFileReader.pm lib/tRNAscanSE/SS.pm lib/tRNAscanSE/ScanResult.pm lib/tRNAscanSE/Sequence.pm lib/tRNAscanSE/SprinzlAlign.pm lib/tRNAscanSE/SprinzlAlignResults.pm lib/tRNAscanSE/SprinzlPos.pm lib/tRNAscanSE/Stats.pm lib/tRNAscanSE/Tscan.pm lib/tRNAscanSE/Utils.pm lib/tRNAscanSE/tRNA.pm '/wrkdirs/usr/ports/biology/tRNAscan-SE/work/stage/usr/local/share/tRNAscan-SE/tRNAscanSE' ====> 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=2024-04-02T13:49:08+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' '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 tRNAscan-SE-2.0.11 ===> Building tRNAscan-SE-2.0.11 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for tRNAscan-SE-2.0.11 build of biology/tRNAscan-SE | tRNAscan-SE-2.0.11 ended at Tue Apr 2 14:49:49 BST 2024 build time: 00:00:42