Date: Sun, 5 Jan 2014 20:09:45 GMT From: pkg-fallout@FreeBSD.org To: mzaki@m.u-tokyo.ac.jp Cc: pkg-fallout@FreeBSD.org Subject: [REL - head-i386-default][biology/muscle] Failed for muscle-3.6 in build Message-ID: <201401052009.s05K9jLe032791@beefy1.isc.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: mzaki@m.u-tokyo.ac.jp Last committer: bapt@FreeBSD.org Ident: $FreeBSD: head/biology/muscle/Makefile 327709 2013-09-20 15:55:44Z bapt $ Log URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2014-01-05_13h19m02s/logs/muscle-3.6.log Build URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2014-01-05_13h19m02s Log: ====>> Building biology/muscle build started at Sun Jan 5 20:09:14 UTC 2014 port directory: /usr/ports/biology/muscle building for: FreeBSD head-i386-default-job-03 11.0-CURRENT FreeBSD 11.0-CURRENT r256430 i386 maintained by: mzaki@m.u-tokyo.ac.jp Makefile ident: $FreeBSD: head/biology/muscle/Makefile 327709 2013-09-20 15:55:44Z bapt $ Poudriere version: 3.1-pre ---Begin Environment--- UNAME_m=i386 UNAME_p=i386 OSVERSION=1100000 UNAME_v=FreeBSD 11.0-CURRENT r256430 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 MASTERMNT=/usr/local/poudriere/data/build/head-i386-default/ref PKG_EXT=txz tpid=17506 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNG=1 PKGNAME=muscle-3.6 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add PWD=/root MASTERNAME=head-i386-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/poudriere/pkg-static version PKG_BIN=/usr/local/sbin/pkg-static ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- TMPDIR="/tmp" MAKE=gmake SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- TMPDIR="/tmp" SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --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--- ARCH=i386 MACHINE=i386 MACHINE_ARCH=i386 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes NO_RESTRICTED=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ===> Cleaning for muscle-3.6 =======================<phase: check-config >============================ =========================================================================== =======================<phase: pkg-depends >============================ ===> muscle-3.6 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.2.4_1.txz Installing pkg-1.2.4_1... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of muscle-3.6 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> Fetching all distfiles required by muscle-3.6 for building =========================================================================== =======================<phase: checksum >============================ ===> Fetching all distfiles required by muscle-3.6 for building => SHA256 Checksum OK for muscle3.6_src.tar.gz. => SHA256 Checksum OK for muscle.pdf. => SHA256 Checksum OK for muscle.html. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> Fetching all distfiles required by muscle-3.6 for building ===> Extracting for muscle-3.6 => SHA256 Checksum OK for muscle3.6_src.tar.gz. => SHA256 Checksum OK for muscle.pdf. => SHA256 Checksum OK for muscle.html. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for muscle-3.6 ===> Converting DOS text files to UNIX text files ===> Applying FreeBSD patches for muscle-3.6 =========================================================================== =======================<phase: build-depends >============================ ===> muscle-3.6 depends on executable: gmake - not found ===> Verifying install for gmake in /usr/ports/devel/gmake ===> Installing existing package /packages/All/gmake-3.82_1.txz Installing gmake-3.82_1...Installing gettext-0.18.3.1... done done ===> Returning to build of muscle-3.6 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for muscle-3.6 =========================================================================== =======================<phase: build >============================ ===> Building for muscle-3.6 gmake[1]: Entering directory `/wrkdirs/usr/ports/biology/muscle/work/muscle3.6_src' c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o aligngivenpath.o aligngivenpath.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o aligngivenpathsw.o aligngivenpathsw.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o aligntwomsas.o aligntwomsas.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o aligntwoprofs.o aligntwoprofs.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o aln.o aln.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o alpha.o alpha.cpp alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (Alpha) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o anchors.o anchors.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o bittraceback.o bittraceback.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o blosumla.o blosumla.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o clust.o clust.cpp clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] switch (m_CentroidStyle) ^ clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ 3 warnings generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o cluster.o cluster.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o clwwt.o clwwt.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o color.o color.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o cons.o cons.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o diaglist.o diaglist.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o diffobjscore.o diffobjscore.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o diffpaths.o diffpaths.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o difftrees.o difftrees.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o difftreese.o difftreese.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o distcalc.o distcalc.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o distfunc.o distfunc.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o distpwkimura.o distpwkimura.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o domuscle.o domuscle.cpp domuscle.cpp:123:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf(stderr, g_strUseTreeWarning); ^~~~~~~~~~~~~~~~~~~ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o dosp.o dosp.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o dpreglist.o dpreglist.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o drawtree.o drawtree.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o edgelist.o edgelist.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o enumopts.o enumopts.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o enumtostr.o enumtostr.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o estring.o estring.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fasta.o fasta.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fasta2.o fasta2.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fastclust.o fastclust.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fastdist.o fastdist.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fastdistjones.o fastdistjones.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fastdistkbit.o fastdistkbit.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fastdistkmer.o fastdistkmer.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fastdistmafft.o fastdistmafft.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fastdistnuc.o fastdistnuc.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o fastscorepath2.o fastscorepath2.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o finddiags.o finddiags.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o finddiagsn.o finddiagsn.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o glbalign.o glbalign.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o glbalign352.o glbalign352.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o glbaligndiag.o glbaligndiag.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o glbalignle.o glbalignle.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o glbalignsimple.o glbalignsimple.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o glbalignsp.o glbalignsp.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o glbalignspn.o glbalignspn.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o glbalignss.o glbalignss.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o glbalndimer.o glbalndimer.cpp glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch] switch (g_PPScore) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o globals.o globals.cpp globals.cpp:50:10: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] mode = "a"; ^ globals.cpp:52:10: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] mode = "w"; ^ 2 warnings generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o globalslinux.o globalslinux.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o globalswin32.o globalswin32.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o gonnet.o gonnet.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o gotowt.o gotowt.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o henikoffweight.o henikoffweight.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o henikoffweightpb.o henikoffweightpb.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o html.o html.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o hydro.o hydro.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o intmath.o intmath.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o local.o local.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o main.o main.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o makerootmsa.o makerootmsa.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o makerootmsab.o makerootmsab.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o mhack.o mhack.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o mpam200.o mpam200.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o msa.o msa.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o msa2.o msa2.cpp msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] switch (Method) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o msadistkimura.o msadistkimura.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o msf.o msf.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o muscle.o muscle.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o muscleout.o muscleout.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o nucmx.o nucmx.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o nwdasimple.o nwdasimple.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o nwdasimple2.o nwdasimple2.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o nwdasmall.o nwdasmall.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o nwrec.o nwrec.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o nwsmall.o nwsmall.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o objscore.o objscore.cpp objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch] switch (OS) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o objscore2.o objscore2.cpp objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] switch (g_TermGaps) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o objscoreda.o objscoreda.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o onexception.o onexception.cpp onexception.cpp:11:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf(stderr, szOnExceptionMessage); ^~~~~~~~~~~~~~~~~~~~ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o options.o options.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o outweights.o outweights.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o pam200mafft.o pam200mafft.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o params.o params.cpp params.cpp:434:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o phy.o phy.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o phy2.o phy2.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o phy3.o phy3.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o phy4.o phy4.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o phyfromclust.o phyfromclust.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o phyfromfile.o phyfromfile.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o physeq.o physeq.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o phytofile.o phytofile.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o posgap.o posgap.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o ppscore.o ppscore.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o profdb.o profdb.cpp In file included from profdb.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:17:10: warning: 7 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o profile.o profile.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o profilefrommsa.o profilefrommsa.cpp profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (g_Alpha) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o progalign.o progalign.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o progress.o progress.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o progressivealign.o progressivealign.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o pwpath.o pwpath.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o readmx.o readmx.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o realigndiffs.o realigndiffs.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o realigndiffse.o realigndiffse.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o refine.o refine.cpp In file included from refine.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:17:10: warning: 7 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o refinehoriz.o refinehoriz.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o refinesubfams.o refinesubfams.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o refinetree.o refinetree.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o refinetreee.o refinetreee.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o refinevert.o refinevert.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o refinew.o refinew.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o savebest.o savebest.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o scoregaps.o scoregaps.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o scorehistory.o scorehistory.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o scorepp.o scorepp.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o seq.o seq.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o seqvect.o seqvect.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o setblosumweights.o setblosumweights.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o setgscweights.o setgscweights.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o setnewhandler.o setnewhandler.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o spfast.o spfast.cpp spfast.cpp:18:18: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] case LL: return "LL"; ^ spfast.cpp:19:18: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] case LG: return "LG"; ^ spfast.cpp:20:18: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] case GL: return "GL"; ^ spfast.cpp:21:18: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] case GG: return "GG"; ^ spfast.cpp:24:9: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] return "?"; ^ 5 warnings generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o sptest.o sptest.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o stabilize.o stabilize.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o subfam.o subfam.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o subfams.o subfams.cpp subfams.cpp:44:25: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] for (unsigned i = 0; i < uNodeCount; ++i) ~ ^ ~~~~~~~~~~ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o sw.o sw.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o termgaps.o termgaps.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o textfile.o textfile.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o threewaywt.o threewaywt.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o traceback.o traceback.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o tracebackopt.o tracebackopt.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o tracebacksw.o tracebacksw.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o treefrommsa.o treefrommsa.cpp In file included from treefrommsa.cpp:5: In file included from ./clustsetmsa.h:8: ./msadist.h:17:10: warning: 7 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ 1 warning generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o typetostr.o typetostr.cpp typetostr.cpp:13:33: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] sprintf(Str, "%02d:%02d:%02d", hh, mm, ss); ~~~~ ^~ %02ld typetostr.cpp:13:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] sprintf(Str, "%02d:%02d:%02d", hh, mm, ss); ~~~~ ^~ %02ld typetostr.cpp:13:41: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] sprintf(Str, "%02d:%02d:%02d", hh, mm, ss); ~~~~ ^~ %02ld 3 warnings generated. c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o upgma2.o upgma2.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o usage.o usage.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o validateids.o validateids.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o vtml2.o vtml2.cpp c++ -O2 -pipe -fno-strict-aliasing -O3 -funroll-loops -Winline -DNDEBUG=1 -c -o writescorefile.o writescorefile.cpp g++ -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.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 globalswin32.o gonnet.o gotowt.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.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 optio ns.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 scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm -lkvm gmake[1]: g++: Command not found gmake[1]: *** [muscle] Error 127 gmake[1]: Leaving directory `/wrkdirs/usr/ports/biology/muscle/work/muscle3.6_src' *** Error code 1 Stop. make: stopped in /usr/ports/biology/muscle ===> Cleaning for muscle-3.6
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