=>> Building biology/clustal-omega build started at Fri Mar 29 22:48:23 GMT 2024 port directory: /usr/ports/biology/clustal-omega package name: clustal-omega-1.2.4 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 410 Mar 8 2023 /usr/ports/biology/clustal-omega/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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--End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work/.cache HOME=/wrkdirs/usr/ports/biology/clustal-omega/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/clustal-omega/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/clustal-omega/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" CCACHE_DIR="/root/.ccache" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work/.cache 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BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/clustal-omega" EXAMPLESDIR="share/examples/clustal-omega" DATADIR="share/clustal-omega" WWWDIR="www/clustal-omega" ETCDIR="etc/clustal-omega" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/clustal-omega DOCSDIR=/usr/local/share/doc/clustal-omega EXAMPLESDIR=/usr/local/share/examples/clustal-omega WWWDIR=/usr/local/www/clustal-omega ETCDIR=/usr/local/etc/clustal-omega --End SUB_LIST-- ---Begin make.conf--- 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 #### #### CCACHE_CPP2=1 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 ===> clustal-omega-1.2.4 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 ===> clustal-omega-1.2.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of clustal-omega-1.2.4 =========================================================================== =================================================== ===== 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 clustal-omega-1.2.4 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by clustal-omega-1.2.4 for building => SHA256 Checksum OK for clustal-omega-1.2.4.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 clustal-omega-1.2.4 for building ===> Extracting for clustal-omega-1.2.4 => SHA256 Checksum OK for clustal-omega-1.2.4.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 clustal-omega-1.2.4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> clustal-omega-1.2.4 depends on shared library: libargtable2.so - not found ===> Installing existing package /packages/All/argtable-2.13_3.pkg [pkg-builder.dan.net.uk] Installing argtable-2.13_3... [pkg-builder.dan.net.uk] Extracting argtable-2.13_3: .......... done ===== Message from argtable-2.13_3: -- ===> NOTICE: The argtable port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> clustal-omega-1.2.4 depends on shared library: libargtable2.so - found (/usr/local/lib/libargtable2.so) ===> Returning to build of clustal-omega-1.2.4 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for clustal-omega-1.2.4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/clustal-omega/work/clustal-omega-1.2.4/m4/libtool.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/clustal-omega/work/clustal-omega-1.2.4/configure configure: loading site script /usr/ports/Templates/config.site configure: Welcome to Clustal Omega - version 1.2.4 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... 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(cached) 524288 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking for /usr/bin/ld option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from cc object... ok checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd13.2 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... (cached) cc checking whether we are using the GNU C compiler... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to accept ISO C89... (cached) none needed checking dependency style of cc... (cached) gcc3 checking how to run the C preprocessor... cpp checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether c++ accepts -g... (cached) yes checking dependency style of c++... (cached) gcc3 checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd13.2 ld.so checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... c++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking for ctype.h... (cached) yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for math.h... (cached) yes checking for memory.h... (cached) yes checking for stdarg.h... (cached) yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for time.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking argtable2.h usability... yes checking argtable2.h presence... yes checking for argtable2.h... yes checking for arg_parse in -largtable2... yes checking for OpenMP flag of C compiler... -fopenmp checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 8 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... (cached) yes checking for ftello... yes checking for fseeko... yes checking for ftello64... no checking for fseeko64... no checking for ftell64... no checking for fseek64... no checking for off_t... (cached) yes checking size of fpos_t... 8 checking if malloc debugging is wanted... no checking whether to build with debug information... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: executing depfiles commands config.status: executing libtool commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for clustal-omega-1.2.4 Making all in src /usr/bin/make all-recursive Making all in hhalign /bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../src -isystem /usr/local/include -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT hhalign.lo -MD -MP -MF .deps/hhalign.Tpo -c -o hhalign.lo hhalign.cpp libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../src -isystem /usr/local/include -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT hhalign.lo -MD -MP -MF .deps/hhalign.Tpo -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o In file included from hhalign.cpp:70: ./hhhmm-C.h:344:60: warning: while loop has empty body [-Wempty-body] {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); break;} ^ ./hhhmm-C.h:344:60: note: put the semicolon on a separate line to silence this warning ./hhhmm-C.h:355:57: warning: while loop has empty body [-Wempty-body] {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); k--; break;} ^ ./hhhmm-C.h:355:57: note: put the semicolon on a separate line to silence this warning In file included from hhalign.cpp:71: ./hhalignment-C.h:1986:23: warning: add explicit braces to avoid dangling else [-Wdangling-else] else wi[k]=0.0; ^ ./hhalignment-C.h:2251:69: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment-C.h:2490:25: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhalign.cpp:72: ./hhhit-C.h:397:9: warning: implicit conversion from 'int' to 'float' changes value from -2147483647 to -2147483648 [-Wimplicit-const-int-float-conversion] score=-INT_MAX; i2=j2=0; bMM[0][0]=STOP; ~^~~~~~~~ In file included from hhalign.cpp:75: ./hhhitlist-C.h:661:9: warning: address of array 'q.fam' will always evaluate to 'true' [-Wpointer-bool-conversion] if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.') ~~^~~ ~~ ./hhhitlist-C.h:838:9: warning: address of array 'q.fam' will always evaluate to 'true' [-Wpointer-bool-conversion] if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.') ~~^~~ ~~ 8 warnings generated. libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../src -isystem /usr/local/include -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT hhalign.lo -MD -MP -MF .deps/hhalign.Tpo -c hhalign.cpp -o hhalign.o >/dev/null 2>&1 mv -f .deps/hhalign.Tpo .deps/hhalign.Plo /bin/sh ../../libtool --tag=CXX --mode=link c++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -o libhhalign.la hhalign.lo -largtable2 -lm -L/usr/local/lib libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o libtool: link: ranlib .libs/libhhalign.a libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" ) Making all in squid /bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../src -isystem /usr/local/include -DCLUSTALO -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT a2m.lo -MD -MP -MF .deps/a2m.Tpo -c -o a2m.lo a2m.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../src -isystem /usr/local/include -DCLUSTALO -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT a2m.lo -MD -MP -MF .deps/a2m.Tpo -c a2m.c -fPIC -DPIC -o .libs/a2m.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../src -isystem /usr/local/include -DCLUSTALO -O3 -O2 -pipe -fstack-protector-strong 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clustal-omega.c:134:58: warning: implicit conversion from 'double' to 'int' changes value from 0.01 to 0 [-Wliteral-conversion] static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^~~~ 1 warning generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT clustal-omega.lo -MD -MP -MF .deps/clustal-omega.Tpo -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1 mv -f .deps/clustal-omega.Tpo .deps/clustal-omega.Plo /bin/sh ../libtool --tag=CC --mode=link cc -O3 -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -static -fstack-protector-strong -o libclustalo.la -rpath /usr/local/lib clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm -L/usr/local/lib libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x 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.libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.o libtool: link: ranlib .libs/libclustalo.a libtool: link: rm -fr .libs/libclustalo.lax libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" ) c++ -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp mv -f .deps/main.Tpo .deps/main.Po cc -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT mymain.o -MD -MP -MF .deps/mymain.Tpo -c -o mymain.o mymain.c mv -f .deps/mymain.Tpo .deps/mymain.Po /bin/sh ../libtool --tag=CXX --mode=link c++ -O3 -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm -L/usr/local/lib libtool: link: c++ -O3 -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -o clustalo main.o mymain.o ./.libs/libclustalo.a -L/usr/local/lib -largtable2 -lm =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for clustal-omega-1.2.4 ===> Generating temporary packing list Making install in src Making install in hhalign test -z "/usr/local/include/clustalo/hhalign" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/hhalign" install -m 0644 'general.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/hhalign/general.h' install -m 0644 'hhfunc.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/hhalign/hhfunc.h' Making install in squid test -z "/usr/local/include/clustalo/squid" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid" install -m 0644 'gki.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/gki.h' install -m 0644 'gsi64.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/gsi64.h' install -m 0644 'msa.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/msa.h' install -m 0644 'rk.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/rk.h' install -m 0644 'squid.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/squid.h' install -m 0644 'stopwatch.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/stopwatch.h' install -m 0644 'sqfuncs.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/sqfuncs.h' install -m 0644 'sre_random.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/sre_random.h' install -m 0644 'ssi.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/ssi.h' install -m 0644 'stockholm.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/stockholm.h' install -m 0644 'vectorops.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/vectorops.h' install -m 0644 'version.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/squid/version.h' Making install in kmpp Making install in clustal test -z "/usr/local/include/clustalo/clustal" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal" install -m 0644 'hhalign_wrapper.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/hhalign_wrapper.h' install -m 0644 'ktuple_pair.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/ktuple_pair.h' install -m 0644 'log.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/log.h' install -m 0644 'mbed.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/mbed.h' install -m 0644 'muscle_tree.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/muscle_tree.h' install -m 0644 'pair_dist.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/pair_dist.h' install -m 0644 'progress.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/progress.h' install -m 0644 'seq.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/seq.h' install -m 0644 'symmatrix.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/symmatrix.h' install -m 0644 'tree.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/tree.h' install -m 0644 'util.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/util.h' install -m 0644 'weights.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/clustal/weights.h' test -z "/usr/local/lib" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/lib" /bin/sh ../libtool --mode=install /usr/bin/install -c 'libclustalo.la' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/lib/libclustalo.la' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/lib/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/lib/libclustalo.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/lib/libclustalo.a libtool: install: ranlib /wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/lib/libclustalo.a libtool: install: warning: remember to run `libtool --finish /usr/local/lib' test -z "/usr/local/bin" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/bin" /bin/sh ../libtool --mode=install install -s -m 555 'clustalo' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/bin/clustalo' libtool: install: install -m 555 -s clustalo /wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/bin/clustalo test -z "/usr/local/include/clustalo/" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo/" install -m 0644 'clustal-omega-config.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo//clustal-omega-config.h' install -m 0644 'clustal-omega.h' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/include/clustalo//clustal-omega.h' test -z "/usr/local/share/doc/clustal-omega" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/share/doc/clustal-omega" install -m 0644 'README' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/share/doc/clustal-omega/README' test -z "/usr/local/lib/pkgconfig" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/lib/pkgconfig" install -m 0644 'clustalo.pc' '/wrkdirs/usr/ports/biology/clustal-omega/work/stage/usr/local/lib/pkgconfig/clustalo.pc' ====> 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=2024-03-29T22:48:23+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 clustal-omega-1.2.4 ===> Building clustal-omega-1.2.4 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for clustal-omega-1.2.4 build of biology/clustal-omega | clustal-omega-1.2.4 ended at Fri Mar 29 22:49:47 GMT 2024 build time: 00:01:24