From owner-freebsd-pkg-fallout@FreeBSD.ORG Fri Mar 28 19:47:17 2014 Return-Path: Delivered-To: pkg-fallout@FreeBSD.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 495F1CB3 for ; Fri, 28 Mar 2014 19:47:16 +0000 (UTC) Received: from beefy2.isc.freebsd.org (beefy2.isc.freebsd.org [IPv6:2001:4f8:3:ffe0:4072:0:16:39]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id D5015AD8; Fri, 28 Mar 2014 19:47:16 +0000 (UTC) Received: from beefy2.isc.freebsd.org (localhost [127.0.0.1]) by beefy2.isc.freebsd.org (8.14.8/8.14.8) with ESMTP id s2SJlGoq060050; Fri, 28 Mar 2014 19:47:16 GMT (envelope-from pkg-fallout-builder@FreeBSD.org) Received: (from root@localhost) by beefy2.isc.freebsd.org (8.14.8/8.14.8/Submit) id s2SJlFg5058614; Fri, 28 Mar 2014 19:47:15 GMT (envelope-from pkg-fallout-builder@FreeBSD.org) Date: Fri, 28 Mar 2014 19:47:15 GMT From: pkg-fallout-builder@FreeBSD.org Message-Id: <201403281947.s2SJlFg5058614@beefy2.isc.freebsd.org> To: mzaki@m.u-tokyo.ac.jp Subject: [REL - head-amd64-default][biology/muscle] Failed for muscle-3.6 in build Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.17 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 28 Mar 2014 19:47:17 -0000 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: miwi@FreeBSD.org Ident: $FreeBSD: head/biology/muscle/Makefile 348042 2014-03-13 07:41:34Z miwi $ Log URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-03-28_07h44m43s/logs/muscle-3.6.log Build URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-03-28_07h44m43s Log: ====>> Building biology/muscle build started at Fri Mar 28 19:46:42 UTC 2014 port directory: /usr/ports/biology/muscle building for: FreeBSD head-amd64-default-job-23 11.0-CURRENT FreeBSD 11.0-CURRENT r263175 amd64 maintained by: mzaki@m.u-tokyo.ac.jp Makefile ident: $FreeBSD: head/biology/muscle/Makefile 348042 2014-03-13 07:41:34Z miwi $ Poudriere version: 3.1-pre ---Begin Environment--- OSVERSION=1100013 UNAME_v=FreeBSD 11.0-CURRENT r263175 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 MASTERMNT=/usr/local/poudriere/data/build/head-amd64-default/ref PKG_EXT=txz tpid=11129 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-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" 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--- 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 =================================================== =========================================================================== =================================================== ===> 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.txz Installing pkg-1.2.7... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of muscle-3.6 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by muscle-3.6 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for muscle-3.6 ===> Converting DOS text files to UNIX text files ===> Applying FreeBSD patches for muscle-3.6 =========================================================================== =================================================== ===> 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 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for muscle-3.6 =========================================================================== =================================================== ===> 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 [-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