[REL - head-i386-default][biology/muscle] Failed for muscle-3.6 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Nov 30 18:22:32 UTC 2013
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 at m.u-tokyo.ac.jp
Last committer: bapt at 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/2013-11-30_07h27m42s/logs/muscle-3.6.log
Build URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-11-30_07h27m42s
Log:
====>> Building biology/muscle
build started at Sat Nov 30 18:22:03 UTC 2013
port directory: /usr/ports/biology/muscle
building for: FreeBSD head-i386-default-job-21 11.0-CURRENT FreeBSD 11.0-CURRENT r256430 i386
maintained by: mzaki at 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
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
STATUS=1
MASTERMNT=/usr/local/poudriere/data/build/head-i386-default/ref
PKG_EXT=txz
tpid=2091
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-1.2.1.txz
Installing pkg-1.2.1... 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
===> 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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