=>> Building biology/tRNAscan-SE build started at Mon Mar 16 23:42:06 EDT 2026 port directory: /usr/ports/biology/tRNAscan-SE package name: tRNAscan-SE-2.0.11 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 504 Aug 27 2024 /usr/ports/biology/tRNAscan-SE/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: 5a4350de941e Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 10 ---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/10/.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-- mzaki@e-mail.ne.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --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/tRNAscan-SE/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/tRNAscan-SE/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/tRNAscan-SE/work/.cache HOME=/wrkdirs/usr/ports/biology/tRNAscan-SE/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/tRNAscan-SE/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/tRNAscan-SE/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/tRNAscan-SE/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/tRNAscan-SE/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/tRNAscan-SE/work/.cache HOME=/wrkdirs/usr/ports/biology/tRNAscan-SE/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/tRNAscan-SE/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/tRNAscan-SE/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " 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=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/tRNAscan-SE" EXAMPLESDIR="share/examples/tRNAscan-SE" DATADIR="share/tRNAscan-SE" WWWDIR="www/tRNAscan-SE" ETCDIR="etc/tRNAscan-SE" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/tRNAscan-SE DOCSDIR=/usr/local/share/doc/tRNAscan-SE EXAMPLESDIR=/usr/local/share/examples/tRNAscan-SE WWWDIR=/usr/local/www/tRNAscan-SE ETCDIR=/usr/local/etc/tRNAscan-SE --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 ===> tRNAscan-SE-2.0.11 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 ===> 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_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [pkg.DaveG.ca] Installing autoconf-2.72_1... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Installing m4-1.4.21,1... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] `-- Extracting m4-1.4.21,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72_1: .......... done ===> tRNAscan-SE-2.0.11 depends on package: autoconf>=2.72_1 - found ===> Returning to build of tRNAscan-SE-2.0.11 ===> tRNAscan-SE-2.0.11 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [pkg.DaveG.ca] Installing automake-1.18.1... [pkg.DaveG.ca] Extracting automake-1.18.1: .......... done ===> tRNAscan-SE-2.0.11 depends on package: automake>=1.18.1 - found ===> Returning to build of tRNAscan-SE-2.0.11 ===> tRNAscan-SE-2.0.11 depends on package: perl5>=5.42.r<5.43 - found ===> tRNAscan-SE-2.0.11 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. ===> tRNAscan-SE-2.0.11 depends on file: /usr/local/bin/ccache - 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 ===> 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-freebsd15.0 checking host system type... amd64-portbld-freebsd15.0 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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 2 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 $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking whether UID '0' is supported by ustar format... yes checking whether GID '0' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking dependency style of cc... gcc3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for tRNAscan-SE-2.0.11 /usr/bin/make all-am depbase=`echo src/alignio.o | sed 's|[^/]*$|.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 $depbase.Po src/sqio.c:1030:9: warning: comparison of array 'sp' equal to a null pointer is always false [-Wtautological-pointer-compare] 1030 | if (sp==NULL || *sp=='\0') | ^~ ~~~~ 1 warning generated. depbase=`echo src/iupac.o | sed 's|[^/]*$|.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 src/gnuregex.c:795:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 795 | re_set_syntax (syntax) | ^ src/gnuregex.c:1175:37: warning: passing arguments to 'at_begline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1175 | || at_begline_loc_p (pattern, p, syntax)) | ^ src/gnuregex.c:1190:37: warning: passing arguments to 'at_endline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1190 | || at_endline_loc_p (p, pend, syntax)) | ^ src/gnuregex.c:1296:21: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1296 | STORE_JUMP (jump, b, laststart); | ^ src/gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ src/gnuregex.c:1301:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1301 | STORE_JUMP (maybe_pop_jump, b, laststart - 3); | ^ src/gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ src/gnuregex.c:1310:13: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1310 | INSERT_JUMP (keep_string_p ? on_failure_keep_string_jump | ^ src/gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ src/gnuregex.c:1324:17: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1324 | INSERT_JUMP (dummy_failure_jump, laststart, laststart + 6); | ^ src/gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ src/gnuregex.c:1407:39: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1407 | = compile_range (&p, pend, translate, syntax, b); | ^ src/gnuregex.c:1418:41: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1418 | ret = compile_range (&p, pend, translate, syntax, b); | ^ src/gnuregex.c:1631:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1631 | STORE_JUMP (jump_past_alt, fixup_alt_jump, b - 1); | ^ src/gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ src/gnuregex.c:1690:15: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1690 | INSERT_JUMP (on_failure_jump, begalt, b + 6); | ^ src/gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ src/gnuregex.c:1711:17: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1711 | STORE_JUMP (jump_past_alt, fixup_alt_jump, b); | ^ src/gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ src/gnuregex.c:1805:22: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1805 | INSERT_JUMP (jump, laststart, b + 3); | ^ src/gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ src/gnuregex.c:1830:22: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1830 | INSERT_JUMP2 (succeed_n, laststart, | ^ src/gnuregex.c:915:14: note: expanded from macro 'INSERT_JUMP2' 915 | insert_op2 (op, loc, (to) - (loc) - 3, arg, b) | ^ src/gnuregex.c:1839:33: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1839 | insert_op2 (set_number_at, laststart, 5, lower_bound, b); | ^ src/gnuregex.c:1850:26: warning: passing arguments to 'store_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1850 | STORE_JUMP2 (jump_n, b, laststart + 5, | ^ src/gnuregex.c:907:13: note: expanded from macro 'STORE_JUMP2' 907 | store_op2 (op, loc, (to) - (loc) - 3, arg) | ^ src/gnuregex.c:1868:37: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1868 | insert_op2 (set_number_at, laststart, b - laststart, | ^ src/gnuregex.c:1962:42: warning: passing arguments to 'group_in_compile_stack' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1962 | if (group_in_compile_stack (compile_stack, c1)) | ^ src/gnuregex.c:2028:5: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2028 | STORE_JUMP (jump_past_alt, fixup_alt_jump, b); | ^ src/gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ src/gnuregex.c:1049:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1049 | regex_compile (pattern, size, syntax, bufp) | ^ src/gnuregex.c:2054:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2054 | store_op1 (op, loc, arg) | ^ src/gnuregex.c:829:13: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 829 | static void store_op1 (), store_op2 (); | ^ src/gnuregex.c:2067:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2067 | store_op2 (op, loc, arg1, arg2) | ^ src/gnuregex.c:829:27: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 829 | static void store_op1 (), store_op2 (); | ^ src/gnuregex.c:2082:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2082 | insert_op1 (op, loc, arg, end) | ^ src/gnuregex.c:830:13: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 830 | static void insert_op1 (), insert_op2 (); | ^ src/gnuregex.c:2101:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2101 | insert_op2 (op, loc, arg1, arg2, end) | ^ src/gnuregex.c:830:28: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 830 | static void insert_op1 (), insert_op2 (); | ^ src/gnuregex.c:2122:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2122 | at_begline_loc_p (pattern, p, syntax) | ^ src/gnuregex.c:831:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 831 | static boolean at_begline_loc_p (), at_endline_loc_p (); | ^ src/gnuregex.c:2141:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2141 | at_endline_loc_p (p, pend, syntax) | ^ src/gnuregex.c:831:37: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 831 | static boolean at_begline_loc_p (), at_endline_loc_p (); | ^ src/gnuregex.c:2163:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2163 | group_in_compile_stack (compile_stack, regnum) | ^ src/gnuregex.c:832:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 832 | static boolean group_in_compile_stack (); | ^ src/gnuregex.c:2191:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2191 | compile_range (p_ptr, pend, translate, syntax, b) | ^ src/gnuregex.c:833:22: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 833 | static reg_errcode_t compile_range (); | ^ src/gnuregex.c:2523:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2523 | re_compile_fastmap (bufp) | ^ src/gnuregex.c:2808:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2808 | re_set_registers (bufp, regs, num_regs, starts, ends) | ^ src/gnuregex.c:2835:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2835 | re_search (bufp, string, size, startpos, range, regs) | ^ src/gnuregex.c:2868:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2868 | re_search_2 (bufp, string1, size1, string2, size2, startpos, range, regs, stop) | ^ src/gnuregex.c:3127:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3127 | re_match (bufp, string, size, pos, regs) | ^ src/gnuregex.c:3152:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3152 | re_match_2 (bufp, string1, size1, string2, size2, pos, regs, stop) | ^ src/gnuregex.c:3608:43: warning: passing arguments to 'group_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3608 | = group_match_null_string_p (&p1, pend, reg_info); | ^ src/gnuregex.c:3826:38: warning: passing arguments to 'bcmp_translate' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3826 | ? bcmp_translate (d, d2, mcnt, translate) | ^ src/gnuregex.c:4398:48: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4398 | if (!alt_match_null_string_p (p1, p1 + mcnt - 3, | ^ src/gnuregex.c:4428:44: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4428 | if (!alt_match_null_string_p (p1, p1 + mcnt, reg_info)) | ^ src/gnuregex.c:4443:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4443 | if (!common_op_match_null_string_p (&p1, end, reg_info)) | ^ src/gnuregex.c:4348:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4348 | group_match_null_string_p (p, end, reg_info) | ^ src/gnuregex.c:2988:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2988 | group_match_null_string_p (); | ^ src/gnuregex.c:4479:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4479 | if (!common_op_match_null_string_p (&p1, end, reg_info)) | ^ src/gnuregex.c:4457:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4457 | alt_match_null_string_p (p, end, reg_info) | ^ src/gnuregex.c:2986:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2986 | static boolean alt_match_null_string_p (), | ^ src/gnuregex.c:4494:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4494 | common_op_match_null_string_p (p, end, reg_info) | ^ src/gnuregex.c:2987:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2987 | common_op_match_null_string_p (), | ^ src/gnuregex.c:4582:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4582 | bcmp_translate (s1, s2, len, translate) | ^ src/gnuregex.c:2985:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2985 | static int bcmp_translate (); | ^ src/gnuregex.c:4638:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4638 | re_comp (s) | ^ src/gnuregex.c:4676:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4676 | re_exec (s) | ^ src/gnuregex.c:4724:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4724 | regcomp (preg, pattern, cflags) | ^ src/gnuregex.c:4799:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4799 | regexec (preg, string, nmatch, pmatch, eflags) | ^ src/gnuregex.c:4864:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4864 | regerror (errcode, preg, errbuf, errbuf_size) | ^ src/gnuregex.c:4908:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4908 | regfree (preg) | ^ 62 warnings generated. 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 $depbase.Po cc -O3 -o bin/eufindtRNA src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/eufind_main.o src/pavesi.o -lm cc -DHAVE_CONFIG_H -I. -DTSCANDIR=\"/usr/local/share\/tRNAscan-SE\/models\" -O3 -MT src/bin_trnascan_1_4-trnascan.o -MD -MP -MF src/.deps/bin_trnascan_1_4-trnascan.Tpo -c -o src/bin_trnascan_1_4-trnascan.o `test -f 'src/trnascan.c' || echo './'`src/trnascan.c mv -f src/.deps/bin_trnascan_1_4-trnascan.Tpo src/.deps/bin_trnascan_1_4-trnascan.Po cc -DTSCANDIR=\"/usr/local/share\/tRNAscan-SE\/models\" -O3 -o bin/trnascan-1.4 src/bin_trnascan_1_4-trnascan.o -lm depbase=`echo src/align.o | sed 's|[^/]*$|.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 $depbase.Po cc -O3 -o bin/covels-SE src/align.o src/dbviterbi.o src/debug.o src/emit.o src/fast-dbviterbi.o src/fastmodelmaker.o src/konings.o src/lengthdist.o src/maxmodelmaker.o src/misc.o src/model.o src/modelmaking.o src/prior.o src/probify.o src/save.o src/smallviterbi.o src/scorestack.o src/structs.o src/trace.o src/viterbi.o src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/scan_main.o -lm depbase=`echo src/score_main.o | sed 's|[^/]*$|.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 -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-1.1.5.pkg [pkg.DaveG.ca] Installing infernal-1.1.5... [pkg.DaveG.ca] Extracting infernal-1.1.5: .......... 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>=5.42.r<5.43 - 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=2026-03-17T03:42:06+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=5a4350de941e' '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 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 Mon Mar 16 23:42:53 EDT 2026 build time: 00:00:48