=>> Building biology/muscle build started at Thu Mar 12 23:26:37 EDT 2026 port directory: /usr/ports/biology/muscle package name: muscle-3.8.1551 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: mzaki@e-mail.ne.jp Makefile datestamp: -rw-r--r-- 1 root wheel 552 Aug 27 2024 /usr/ports/biology/muscle/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: fb16dfecae4a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 16 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/16/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- mzaki@e-mail.ne.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/muscle/work/.cache HOME=/wrkdirs/usr/ports/biology/muscle/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/muscle/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/muscle/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/muscle/work/.cache HOME=/wrkdirs/usr/ports/biology/muscle/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/muscle/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/muscle/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/muscle" EXAMPLESDIR="share/examples/muscle" DATADIR="share/muscle" WWWDIR="www/muscle" ETCDIR="etc/muscle" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/muscle DOCSDIR=/usr/local/share/doc/muscle EXAMPLESDIR=/usr/local/share/examples/muscle WWWDIR=/usr/local/www/muscle ETCDIR=/usr/local/etc/muscle --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 ===> muscle-3.8.1551 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 ===> muscle-3.8.1551 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of muscle-3.8.1551 =========================================================================== =================================================== ===== 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 muscle-3.8.1551 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by muscle-3.8.1551 for building => SHA256 Checksum OK for muscle_src_3.8.1551.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 muscle-3.8.1551 for building ===> Extracting for muscle-3.8.1551 => SHA256 Checksum OK for muscle_src_3.8.1551.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 muscle-3.8.1551 ===> Converting DOS text files to UNIX text files ===> Applying FreeBSD patches for muscle-3.8.1551 from /usr/ports/biology/muscle/files /bin/mv /wrkdirs/usr/ports/biology/muscle/work/muscle-3.8.1551/subfams.cpp /wrkdirs/usr/ports/biology/muscle/work/muscle-3.8.1551/subfams.cpp.not_to_be_compiled =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> muscle-3.8.1551 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> muscle-3.8.1551 depends on package: gmake>=4.4.1 - found ===> Returning to build of muscle-3.8.1551 ===> muscle-3.8.1551 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. ===> muscle-3.8.1551 depends on file: /usr/local/bin/ccache - found ===> Returning to build of muscle-3.8.1551 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for muscle-3.8.1551 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for muscle-3.8.1551 c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpath.cpp -o aligngivenpath.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpathsw.cpp -o aligngivenpathsw.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwomsas.cpp -o aligntwomsas.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwoprofs.cpp -o aligntwoprofs.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aln.cpp -o aln.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 alpha.cpp -o alpha.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 anchors.cpp -o anchors.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 bittraceback.cpp -o bittraceback.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 blosum62.cpp -o blosum62.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 blosumla.cpp -o blosumla.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 clust.cpp -o clust.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 cluster.cpp -o cluster.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 color.cpp -o color.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 cons.cpp -o cons.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diaglist.cpp -o diaglist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diffobjscore.cpp -o diffobjscore.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 difftrees.cpp -o difftrees.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distcalc.cpp -o distcalc.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 dpreglist.cpp -o dpreglist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 estring.cpp -o estring.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fasta.cpp -o fasta.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistmafft.cpp -o fastdistmafft.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistnuc.cpp -o fastdistnuc.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 finddiags.cpp -o finddiags.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 finddiagsn.cpp -o finddiagsn.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignle.cpp -o glbalignle.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsimple.cpp -o glbalignsimple.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsp.cpp -o glbalignsp.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignss.cpp -o glbalignss.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalndimer.cpp -o glbalndimer.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globals.cpp -o globals.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalslinux.cpp -o globalslinux.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalsosx.cpp -o globalsosx.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 gonnet.cpp -o gonnet.o alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] 84 | switch (Alpha) | ^~~~~ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 html.cpp -o html.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 local.cpp -o local.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsa.cpp -o makerootmsa.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 maketree.cpp -o maketree.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 mhack.cpp -o mhack.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msa.cpp -o msa.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msadistkimura.cpp -o msadistkimura.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msf.cpp -o msf.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 muscle.cpp -o muscle.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.o glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch] 123 | switch (g_PPScore) | ^~~~~~~~~ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasmall.cpp -o nwdasmall.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwrec.cpp -o nwrec.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscore.cpp -o objscore.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscore2.cpp -o objscore2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscoreda.cpp -o objscoreda.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 options.cpp -o options.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 pam200mafft.cpp -o pam200mafft.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] 167 | switch (m_JoinStyle) | ^~~~~~~~~~~ clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] 295 | switch (m_CentroidStyle) | ^~~~~~~~~~~~~~~ clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] 611 | switch (m_JoinStyle) | ^~~~~~~~~~~ 3 warnings generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy3.cpp -o phy3.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy4.cpp -o phy4.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromfile.cpp -o phyfromfile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 physeq.cpp -o physeq.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phytofile.cpp -o phytofile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 posgap.cpp -o posgap.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profile.cpp -o profile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profilefrommsa.cpp -o profilefrommsa.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progalign.cpp -o progalign.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch] 31 | switch (OS) | ^~ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] 22 | switch (g_TermGaps) | ^~~~~~~~~~ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scoredist.cpp -o scoredist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o params.cpp:441:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] 441 | switch (g_PPScore) | ^~~~~~~~~ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 sw.cpp -o sw.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 termgaps.cpp -o termgaps.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 textfile.cpp -o textfile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 threewaywt.cpp -o threewaywt.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 tomhydro.cpp -o tomhydro.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 traceback.cpp -o traceback.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 tracebackopt.cpp -o tracebackopt.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 tracebacksw.cpp -o tracebacksw.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 treefrommsa.cpp -o treefrommsa.o profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] 230 | switch (g_Alpha) | ^~~~~~~ 1 warning generated. c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 typetostr.cpp -o typetostr.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 upgma2.cpp -o upgma2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 validateids.cpp -o validateids.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 writescorefile.cpp -o writescorefile.o In file included from treefrommsa.cpp:5: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] 22 | switch(m_Distance) | ^~~~~~~~~~ 1 warning generated. msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] 357 | switch (Method) | ^~~~~~ 1 warning generated. In file included from profdb.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] 22 | switch(m_Distance) | ^~~~~~~~~~ 1 warning generated. In file included from refine.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] 22 | switch(m_Distance) | ^~~~~~~~~~ 1 warning generated. seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference] 201 | return (Seq &) *((Seq *) 0); | ^~~~~~~~~~~~ 1 warning generated. c++ -O3 -funroll-loops -Winline -DNDEBUG=1 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -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 muscle-3.8.1551 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/muscle/work/muscle-3.8.1551/muscle /wrkdirs/usr/ports/biology/muscle/work/stage/usr/local/bin ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-03-13T03:26:37+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=fb16dfecae4a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for muscle-3.8.1551 ===> Building muscle-3.8.1551 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for muscle-3.8.1551 build of biology/muscle | muscle-3.8.1551 ended at Thu Mar 12 23:26:48 EDT 2026 build time: 00:00:12