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:     mz...@m.u-tokyo.ac.jp
Last committer: oha...@freebsd.org
Ident:          $FreeBSD: head/biology/muscle/Makefile 356095 2014-06-01 
11:05:43Z ohauer $
Log URL:        
http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-06-13_11h07m42s/logs/muscle-3.6.log
Build URL:      
http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-06-13_11h07m42s
Log:

====>> Building biology/muscle
build started at Sat Jun 14 00:34:14 UTC 2014
port directory: /usr/ports/biology/muscle
building for: FreeBSD head-amd64-default-job-09 11.0-CURRENT FreeBSD 
11.0-CURRENT r267342 amd64
maintained by: mz...@m.u-tokyo.ac.jp
Makefile ident:      $FreeBSD: head/biology/muscle/Makefile 356095 2014-06-01 
11:05:43Z ohauer $
Poudriere version: 3.1-pre
Host OSVERSION: 1100022
Jail OSVERSION: 1100022

---Begin Environment---
OSVERSION=1100022
UNAME_v=FreeBSD 11.0-CURRENT r267342
UNAME_r=11.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/build/head-amd64-default/ref
PKG_EXT=txz
tpid=12750
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
OLDPWD=/usr/local/poudriere/data/build/head-amd64-default/ref/poudriere/rdeps
PWD=/usr/local/poudriere/data/build/head-amd64-default/ref/poudriere/pool
MASTERNAME=head-amd64-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" NO_PIE=yes 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--

--PLIST_SUB--
OSREL=11.0
PREFIX=%D
LOCALBASE=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
PORTDATA=""
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---
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
# clean-restricted ran via poudriere.conf NO_RESTRICTED
#NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
===>  Cleaning for muscle-3.6
=======================<phase: check-sanity   >============================
===========================================================================
=======================<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-1.2.7_2.txz
Installing pkg-1.2.7_2... 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_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
<snip>
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 [-Wc++11-compat-deprecated-writable-strings]
                mode = "a";
                       ^
globals.cpp:52:10: warning: conversion from string literal to 'char *' is 
deprecated [-Wc++11-compat-deprecated-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 [-Wc++11-compat-deprecated-writable-strings]
        case LL: return "LL";
                        ^
spfast.cpp:19:18: warning: conversion from string literal to 'char *' is 
deprecated [-Wc++11-compat-deprecated-writable-strings]
        case LG: return "LG";
                        ^
spfast.cpp:20:18: warning: conversion from string literal to 'char *' is 
deprecated [-Wc++11-compat-deprecated-writable-strings]
        case GL: return "GL";
                        ^
spfast.cpp:21:18: warning: conversion from string literal to 'char *' is 
deprecated [-Wc++11-compat-deprecated-writable-strings]
        case GG: return "GG";
                        ^
spfast.cpp:24:9: warning: conversion from string literal to 'char *' is 
deprecated [-Wc++11-compat-deprecated-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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