dpkg-buildpackage: source package muscle dpkg-buildpackage: source version 3.70+fix1-1 dpkg-buildpackage: source changed by Charles Plessy fakeroot debian/rules clean test -x debian/rules dh_testroot dh_clean dh_clean: Compatibility levels before 4 are deprecated. LDLIBS=-lm /usr/bin/make -C . CFLAGS="-g -Wall -O2" CXXFLAGS="-g -Wall -O2" CPPFLAGS="" LDFLAGS="" -e -k clean make[1]: Entering directory `/tmp/a/muscle-3.70+fix1' make[1]: *** No rule to make target `clean'. make[1]: Leaving directory `/tmp/a/muscle-3.70+fix1' make: [makefile-clean] Error 2 (ignored) rm -f debian/stamp-makefile-build rm -f *.o make.err make.out rm -f muscle dpkg-source -b muscle-3.70+fix1 dpkg-source: building muscle using existing muscle_3.70+fix1.orig.tar.gz dpkg-source: building muscle in muscle_3.70+fix1-1.diff.gz dpkg-source: building muscle in muscle_3.70+fix1-1.dsc dpkg-genchanges -S >../muscle_3.70+fix1-1_source.changes dpkg-genchanges: including full source code in upload dpkg-buildpackage: source only upload (original source is included) -> Running in no-targz mode I: using fakeroot in build. Current time: Mon Feb 11 09:53:44 BRST 2008 pbuilder-time-stamp: 1202730824 -> copying local configuration -> mounting /proc filesystem -> mounting /dev/pts filesystem -> policy-rc.d already exists Obtaining the cached apt archive contents Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder and should Depends: cdbs, debhelper (>= 5.0.0) dpkg-deb: building package `pbuilder-satisfydepends-dummy' in `/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Reading package lists... Building dependency tree... Reading state information... aptitude is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Selecting previously deselected package pbuilder-satisfydepends-dummy. (Reading database ... 10123 files and directories currently installed.) Unpacking pbuilder-satisfydepends-dummy (from .../pbuilder-satisfydepends-dummy.deb) ... dpkg: dependency problems prevent configuration of pbuilder-satisfydepends-dummy: pbuilder-satisfydepends-dummy depends on cdbs; however: Package cdbs is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>= 5.0.0); however: Package debhelper is not installed. dpkg: error processing pbuilder-satisfydepends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: pbuilder-satisfydepends-dummy Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Building tag database... The following NEW packages will be installed: bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a} groff-base{a} html2text{a} intltool-debian{a} libgomp1{a} libmagic1{a} man-db{a} po-debconf{a} The following partially installed packages will be configured: pbuilder-satisfydepends-dummy 0 packages upgraded, 13 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/7015kB of archives. After unpacking 20.0MB will be used. Writing extended state information... Preconfiguring packages ... Selecting previously deselected package libmagic1. (Reading database ... 10123 files and directories currently installed.) Unpacking libmagic1 (from .../libmagic1_4.23-1_i386.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_4.23-1_i386.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-3_i386.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_6.1.10_i386.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.18.1.1-16_i386.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.5.1-2_i386.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.17-2_i386.deb) ... Selecting previously deselected package libgomp1. Unpacking libgomp1 (from .../libgomp1_4.3-20080202-1_i386.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.17-2_i386.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.11_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_6.0.5_all.deb) ... Selecting previously deselected package cdbs. Unpacking cdbs (from .../archives/cdbs_0.4.51_all.deb) ... Setting up libmagic1 (4.23-1) ... Setting up file (4.23-1) ... Setting up html2text (1.3.2a-3) ... Setting up bsdmainutils (6.1.10) ... Setting up groff-base (1.18.1.1-16) ... Setting up man-db (2.5.1-2) ... Building database of manual pages ... Setting up gettext-base (0.17-2) ... Setting up libgomp1 (4.3-20080202-1) ... Setting up gettext (0.17-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.11) ... Setting up debhelper (6.0.5) ... Setting up cdbs (0.4.51) ... Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Copying back the cached apt archive contents Copying source file -> copying [/tmp/a/muscle_3.70+fix1-1.dsc] -> copying [/tmp/a/muscle_3.70+fix1.orig.tar.gz] -> copying [/tmp/a/muscle_3.70+fix1-1.diff.gz] Extracting source dpkg-source: warning: extracting unsigned source package (./muscle_3.70+fix1-1.dsc) dpkg-source: extracting muscle in muscle-3.70+fix1 dpkg-source: unpacking muscle_3.70+fix1.orig.tar.gz dpkg-source: applying ./muscle_3.70+fix1-1.diff.gz -> Building the package dpkg-buildpackage: source package muscle dpkg-buildpackage: source version 3.70+fix1-1 dpkg-buildpackage: source changed by Charles Plessy dpkg-buildpackage: host architecture i386 fakeroot debian/rules clean test -x debian/rules dh_testroot dh_clean dh_clean: Compatibility levels before 4 are deprecated. LDLIBS=-lm /usr/bin/make -C . CFLAGS="-g -Wall -O2" CXXFLAGS="-g -Wall -O2" CPPFLAGS="" LDFLAGS="" -e -k clean make[1]: Entering directory `/tmp/buildd/muscle-3.70+fix1' make[1]: *** No rule to make target `clean'. make[1]: Leaving directory `/tmp/buildd/muscle-3.70+fix1' make: [makefile-clean] Error 2 (ignored) rm -f debian/stamp-makefile-build rm -f *.o make.err make.out rm -f muscle dpkg-source -b muscle-3.70+fix1 dpkg-source: building muscle using existing muscle_3.70+fix1.orig.tar.gz dpkg-source: building muscle in muscle_3.70+fix1-1.diff.gz dpkg-source: building muscle in muscle_3.70+fix1-1.dsc debian/rules build test -x debian/rules mkdir -p "." echo 5 >debian/compat LDLIBS=-lm /usr/bin/make -C . CFLAGS="-g -Wall -O2" CXXFLAGS="-g -Wall -O2" CPPFLAGS="" LDFLAGS="" -e all make[1]: Entering directory `/tmp/buildd/muscle-3.70+fix1' g++ -c -g -Wall -O2 aligngivenpath.cpp -o aligngivenpath.o aligngivenpath.cpp: In function 'void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)': aligngivenpath.cpp:186: warning: unused variable 'uLengthA' aligngivenpath.cpp:187: warning: unused variable 'uLengthB' aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpath.cpp:335: warning: unused variable 'uColA' aligngivenpath.cpp:336: warning: unused variable 'uColB' aligngivenpath.cpp:346: warning: unused variable 'uColA' aligngivenpath.cpp:354: warning: unused variable 'uColB' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 aligngivenpathsw.cpp -o aligngivenpathsw.o aligngivenpathsw.cpp: In function 'void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)': aligngivenpathsw.cpp:58: warning: unused variable 'uLengthA' aligngivenpathsw.cpp:59: warning: unused variable 'uLengthB' aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpathsw.cpp:204: warning: unused variable 'uColA' aligngivenpathsw.cpp:205: warning: unused variable 'uColB' aligngivenpathsw.cpp:215: warning: unused variable 'uColA' aligngivenpathsw.cpp:223: warning: unused variable 'uColB' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 aligntwomsas.cpp -o aligntwomsas.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 aligntwoprofs.cpp -o aligntwoprofs.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 aln.cpp -o aln.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 alpha.cpp -o alpha.o alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)': alpha.cpp:84: warning: enumeration value 'ALPHA_Undefined' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 anchors.cpp -o anchors.o anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)': anchors.cpp:162: warning: unused variable 'uWindowCenter' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used anchors.cpp:54: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used anchors.cpp:106: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used g++ -c -g -Wall -O2 bittraceback.cpp -o bittraceback.o bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)': bittraceback.cpp:146: warning: unused variable 'Bits' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used bittraceback.cpp:15: warning: 'const char* BitsToStr(char)' defined but not used g++ -c -g -Wall -O2 blosum62.cpp -o blosum62.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 blosumla.cpp -o blosumla.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used blosumla.cpp:7: warning: 'Blosum62LA' defined but not used g++ -c -g -Wall -O2 clust.cpp -o clust.o clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)': clust.cpp:167: warning: enumeration value 'JOIN_Undefined' not handled in switch clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)': clust.cpp:184: warning: unused variable 'uClusterCount' clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)': clust.cpp:204: warning: unused variable 'uClusterCount' clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)': clust.cpp:295: warning: enumeration value 'LINKAGE_Undefined' not handled in switch clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)': clust.cpp:360: warning: unused variable 'dDistLR' clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const': clust.cpp:611: warning: enumeration value 'JOIN_Undefined' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 cluster.cpp -o cluster.o cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)': cluster.cpp:267: warning: unused variable 'dMaxDist' cluster.cpp:283: warning: 'uIndexClosest2' may be used uninitialized in this function cluster.cpp:282: warning: 'uIndexClosest1' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 clwwt.cpp -o clwwt.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 color.cpp -o color.o color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used color.cpp:72: warning: 'int BlosumScore(char, char)' defined but not used g++ -c -g -Wall -O2 cons.cpp -o cons.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 diaglist.cpp -o diaglist.o diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)': diaglist.cpp:52: warning: 'uStartPosB' may be used uninitialized in this function diaglist.cpp:51: warning: 'uStartPosA' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 diffobjscore.cpp -o diffobjscore.o diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)': diffobjscore.cpp:76: warning: unused variable 'uSeqCount' diffobjscore.cpp:77: warning: unused variable 'uColCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 diffpaths.cpp -o diffpaths.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 difftrees.cpp -o difftrees.o difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)': difftrees.cpp:161: warning: unused variable 'uLeafCount2' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 difftreese.cpp -o difftreese.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 distcalc.cpp -o distcalc.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 distfunc.cpp -o distfunc.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 distpwkimura.cpp -o distpwkimura.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 domuscle.cpp -o domuscle.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 dosp.cpp -o dosp.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 dpreglist.cpp -o dpreglist.o dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)': dpreglist.cpp:82: warning: unused variable 'uDiagLengthMinusCaps' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 drawtree.cpp -o drawtree.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 edgelist.cpp -o edgelist.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 enumopts.cpp -o enumopts.o In file included from enumopts.cpp:8: enums.h:15: warning: missing braces around initializer for 'EnumOpt' enums.h:15: warning: missing braces around initializer for 'EnumOpt' enums.h:15: warning: missing braces around initializer for 'EnumOpt' enums.h:15: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:28: warning: missing braces around initializer for 'EnumOpt' enums.h:28: warning: missing braces around initializer for 'EnumOpt' enums.h:28: warning: missing braces around initializer for 'EnumOpt' enums.h:28: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:41: warning: missing braces around initializer for 'EnumOpt' enums.h:41: warning: missing braces around initializer for 'EnumOpt' enums.h:41: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:94: warning: missing braces around initializer for 'EnumOpt' enums.h:94: warning: missing braces around initializer for 'EnumOpt' enums.h:94: warning: missing braces around initializer for 'EnumOpt' enums.h:94: warning: missing braces around initializer for 'EnumOpt' intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 enumtostr.cpp -o enumtostr.o In file included from enumtostr.cpp:16: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 estring.cpp -o estring.o estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)': estring.cpp:377: warning: 'cType' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used estring.cpp:464: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used g++ -c -g -Wall -O2 fasta.cpp -o fasta.o fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)': fasta.cpp:15: warning: unused variable 'uSeqCount' fasta.cpp:16: warning: unused variable 'uColCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 fasta2.cpp -o fasta2.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 fastclust.cpp -o fastclust.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 fastdist.cpp -o fastdist.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 fastdistjones.cpp -o fastdistjones.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 fastdistkbit.cpp -o fastdistkbit.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 fastdistkmer.cpp -o fastdistkmer.o fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)': fastdistkmer.cpp:235: warning: unused variable 'KD' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 fastdistmafft.cpp -o fastdistmafft.o fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)': fastdistmafft.cpp:238: warning: unused variable 'pName1' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used fastdistmafft.cpp:104: warning: 'void ListCount(const unsigned char*)' defined but not used g++ -c -g -Wall -O2 fastdistnuc.cpp -o fastdistnuc.o fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)': fastdistnuc.cpp:223: warning: unused variable 'pName1' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used fastdistnuc.cpp:33: warning: 'uResidueGroupCount' defined but not used fastdistnuc.cpp:85: warning: 'void ListCount(const unsigned char*)' defined but not used g++ -c -g -Wall -O2 fastscorepath2.cpp -o fastscorepath2.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 finddiags.cpp -o finddiags.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used finddiags.cpp:11: warning: 'char* TupleToStr(int)' defined but not used g++ -c -g -Wall -O2 finddiagsn.cpp -o finddiagsn.o finddiagsn.cpp: In function 'char* TupleToStr(int)': finddiagsn.cpp:16: warning: comparison between signed and unsigned integer expressions intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used finddiagsn.cpp:12: warning: 'char* TupleToStr(int)' defined but not used g++ -c -g -Wall -O2 glbalign.cpp -o glbalign.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 glbalign352.cpp -o glbalign352.o In file included from glbalign352.cpp:6: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 glbaligndiag.cpp -o glbaligndiag.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 glbalignle.cpp -o glbalignle.o glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignle.cpp:400: warning: 'uInsertPos' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 glbalignsimple.cpp -o glbalignsimple.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used glbalignsimple.cpp:29: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used glbalignsimple.cpp:53: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used g++ -c -g -Wall -O2 glbalignsp.cpp -o glbalignsp.o glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignsp.cpp:272: warning: 'uInsertPos' may be used uninitialized in this function glbalignsp.cpp:339: warning: 'uInsertPos' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 glbalignspn.cpp -o glbalignspn.o glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignspn.cpp:307: warning: 'uInsertPos' may be used uninitialized in this function glbalignspn.cpp:374: warning: 'uInsertPos' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 glbalignss.cpp -o glbalignss.o glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)': glbalignss.cpp:177: warning: unused variable 'ptrRowA' glbalignss.cpp:119: warning: unused variable 'uPrefixCountA' glbalignss.cpp:120: warning: unused variable 'uPrefixCountB' glbalignss.cpp:221: warning: 'uInsertPos' may be used uninitialized in this function glbalignss.cpp:283: warning: 'uInsertPos' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used glbalignss.cpp:11: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used g++ -c -g -Wall -O2 glbalndimer.cpp -o glbalndimer.o glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)': glbalndimer.cpp:123: warning: enumeration value 'PPSCORE_Undefined' not handled in switch glbalndimer.cpp:123: warning: enumeration value 'PPSCORE_SPN' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used glbalndimer.cpp:14: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used g++ -c -g -Wall -O2 globals.cpp -o globals.o globals.cpp: In function 'void Log(const char*, ...)': globals.cpp:50: warning: deprecated conversion from string constant to 'char*' globals.cpp:52: warning: deprecated conversion from string constant to 'char*' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 globalslinux.cpp -o globalslinux.o globalslinux.cpp: In function 'double GetNAN()': globalslinux.cpp:17: warning: dereferencing type-punned pointer will break strict-aliasing rules intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 globalsother.cpp -o globalsother.o In file included from globalsother.cpp:1: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 globalswin32.cpp -o globalswin32.o In file included from globalswin32.cpp:1: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 gonnet.cpp -o gonnet.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used gonnet.cpp:137: warning: 'Gonnet160' defined but not used g++ -c -g -Wall -O2 gotowt.cpp -o gotowt.o g++ -c -g -Wall -O2 henikoffweight.cpp -o henikoffweight.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 henikoffweightpb.cpp -o henikoffweightpb.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 html.cpp -o html.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 hydro.cpp -o hydro.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 intmath.cpp -o intmath.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 local.cpp -o local.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 main.cpp -o main.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 makerootmsa.cpp -o makerootmsa.o makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)': makerootmsa.cpp:18: warning: unused variable 'uSeqLength' makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)': makerootmsa.cpp:93: warning: unused variable 'Path' makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)': makerootmsa.cpp:167: warning: unused variable 'uTreeNodeCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used makerootmsa.cpp:12: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used g++ -c -g -Wall -O2 makerootmsab.cpp -o makerootmsab.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 maketree.cpp -o maketree.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 mhack.cpp -o mhack.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 mpam200.cpp -o mpam200.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 msa.cpp -o msa.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used msa.cpp:385: warning: 'void FmtChar(char, unsigned int)' defined but not used msa.cpp:392: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used msa.cpp:407: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used msa.cpp:419: warning: 'void FmtPad(unsigned int)' defined but not used g++ -c -g -Wall -O2 msa2.cpp -o msa2.o msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)': msa2.cpp:357: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)': msa2.cpp:476: warning: unused variable 'uColCountCat' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 msadistkimura.cpp -o msadistkimura.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 msf.cpp -o msf.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used msf.cpp:24: warning: 'const char* strfind(const char*, const char*)' defined but not used g++ -c -g -Wall -O2 muscle.cpp -o muscle.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 muscleout.cpp -o muscleout.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 nucmx.cpp -o nucmx.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 nwdasimple.cpp -o nwdasimple.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 nwdasimple2.cpp -o nwdasimple2.o In file included from nwdasimple2.cpp:3: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 nwdasmall.cpp -o nwdasmall.o In file included from nwdasmall.cpp:4: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 nwrec.cpp -o nwrec.o g++ -c -g -Wall -O2 nwsmall.cpp -o nwsmall.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 objscore.cpp -o objscore.o objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)': objscore.cpp:31: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch objscore.cpp:31: warning: enumeration value 'OBJSCORE_SPM' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 objscore2.cpp -o objscore2.o objscore2.cpp: In function 'SCORE TermGapScore(bool)': objscore2.cpp:22: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)': objscore2.cpp:62: warning: unused variable 'scoreGaps' objscore2.cpp:63: warning: unused variable 'bGapping1' objscore2.cpp:64: warning: unused variable 'bGapping2' objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)': objscore2.cpp:314: warning: unused variable 'uColCount2' objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)': objscore2.cpp:493: warning: unused variable 'w' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 objscoreda.cpp -o objscoreda.o In file included from objscoreda.cpp:4: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 onexception.cpp -o onexception.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 options.cpp -o options.o options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 outweights.cpp -o outweights.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 pam200mafft.cpp -o pam200mafft.o pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used pam200mafft.cpp:6: warning: 'PAM200' defined but not used g++ -c -g -Wall -O2 params.cpp -o params.o params.cpp: In function 'void SetPPCommandLineParams()': params.cpp:420: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:421: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:423: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:424: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp: In function 'void SetPPScore(bool)': params.cpp:441: warning: enumeration value 'PPSCORE_Undefined' not handled in switch params.cpp: In function 'void SetParams()': params.cpp:599: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:600: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:602: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:603: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:605: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:606: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:608: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:609: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:611: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:612: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:614: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:615: warning: dereferencing type-punned pointer will break strict-aliasing rules params.cpp:617: warning: dereferencing type-punned pointer will break strict-aliasing rules intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 phy.cpp -o phy.o phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)': phy.cpp:665: warning: unused variable 'dEdgeLength' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 phy2.cpp -o phy2.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 phy3.cpp -o phy3.o phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)': phy3.cpp:125: warning: unused variable 'dThisDist' phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)': phy3.cpp:167: warning: unused variable 'uLeafCount' phy3.cpp:190: warning: unused variable 'dAllMaxDist' phy3.cpp:191: warning: unused variable 'uMaxFrom' phy3.cpp:192: warning: unused variable 'uMaxTo' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used phy3.cpp:45: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used g++ -c -g -Wall -O2 phy4.cpp -o phy4.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 phyfromclust.cpp -o phyfromclust.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 phyfromfile.cpp -o phyfromfile.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 physeq.cpp -o physeq.o physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const': physeq.cpp:60: warning: comparison between signed and unsigned integer expressions physeq.cpp:71: warning: comparison between signed and unsigned integer expressions physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const': physeq.cpp:112: warning: comparison between signed and unsigned integer expressions physeq.cpp:124: warning: comparison between signed and unsigned integer expressions intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 phytofile.cpp -o phytofile.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 posgap.cpp -o posgap.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 ppscore.cpp -o ppscore.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 profdb.cpp -o profdb.o In file included from clustsetmsa.h:8, from profdb.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22: warning: enumeration value 'DISTANCE_Undefined' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Edit' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 profile.cpp -o profile.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 profilefrommsa.cpp -o profilefrommsa.o profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)': profilefrommsa.cpp:131: warning: comparison between signed and unsigned integer expressions profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)': profilefrommsa.cpp:230: warning: enumeration value 'ALPHA_Undefined' not handled in switch profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)': profilefrommsa.cpp:245: warning: unused variable 'uSeqCount' profilefrommsa.cpp:253: warning: unused variable 'uHydrophobicRunLength' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used profilefrommsa.cpp:15: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used g++ -c -g -Wall -O2 progalign.cpp -o progalign.o progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)': progalign.cpp:41: warning: unused variable 'uIterCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 progress.cpp -o progress.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 progressivealign.cpp -o progressivealign.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 pwpath.cpp -o pwpath.o pwpath.cpp: In member function 'void PWPath::Validate() const': pwpath.cpp:79: warning: unused variable 'LastEdge' pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)': pwpath.cpp:212: warning: unused variable 'uEdgeIndex' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 readmx.cpp -o readmx.o readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]': readmx.cpp:83: warning: comparison between signed and unsigned integer expressions readmx.cpp:84: warning: comparison between signed and unsigned integer expressions intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used readmx.cpp:30: warning: 'unsigned int MxCharToLetter(char)' defined but not used g++ -c -g -Wall -O2 realigndiffs.cpp -o realigndiffs.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 realigndiffse.cpp -o realigndiffse.o realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)': realigndiffse.cpp:72: warning: unused variable 'uNewRight' realigndiffse.cpp:75: warning: unused variable 'uOldRight' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 refine.cpp -o refine.o In file included from clustsetmsa.h:8, from refine.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22: warning: enumeration value 'DISTANCE_Undefined' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Edit' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 refinehoriz.cpp -o refinehoriz.o refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)': refinehoriz.cpp:247: warning: 'bRight' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 refinesubfams.cpp -o refinesubfams.o refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)': refinesubfams.cpp:63: warning: unused variable 'uNodeCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 refinetree.cpp -o refinetree.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 refinetreee.cpp -o refinetreee.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 refinevert.cpp -o refinevert.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 refinew.cpp -o refinew.o refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)': refinew.cpp:22: warning: unused variable 'uColCountCat' refinew.cpp: In function 'void RefineW(const MSA&, MSA&)': refinew.cpp:125: warning: unused variable 'uOutCols' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 savebest.cpp -o savebest.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 scoredist.cpp -o scoredist.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 scoregaps.cpp -o scoregaps.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used scoregaps.cpp:37: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used scoregaps.cpp:80: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used g++ -c -g -Wall -O2 scorehistory.cpp -o scorehistory.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 scorepp.cpp -o scorepp.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 seq.cpp -o seq.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 seqvect.cpp -o seqvect.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 setblosumweights.cpp -o setblosumweights.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 setgscweights.cpp -o setgscweights.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 setnewhandler.cpp -o setnewhandler.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 spfast.cpp -o spfast.o spfast.cpp: In function 'char* GapTypeToStr(int)': spfast.cpp:18: warning: deprecated conversion from string constant to 'char*' spfast.cpp:19: warning: deprecated conversion from string constant to 'char*' spfast.cpp:20: warning: deprecated conversion from string constant to 'char*' spfast.cpp:21: warning: deprecated conversion from string constant to 'char*' spfast.cpp:24: warning: deprecated conversion from string constant to 'char*' spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)': spfast.cpp:252: warning: unused variable 'uSeqCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used spfast.cpp:14: warning: 'char* GapTypeToStr(int)' defined but not used spfast.cpp:59: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used g++ -c -g -Wall -O2 sptest.cpp -o sptest.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 stabilize.cpp -o stabilize.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 subfam.cpp -o subfam.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 subfams.cpp -o subfams.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used subfams.cpp:10: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used subfams.cpp:40: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used subfams.cpp:52: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used g++ -c -g -Wall -O2 sw.cpp -o sw.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used sw.cpp:21: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used g++ -c -g -Wall -O2 termgaps.cpp -o termgaps.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 textfile.cpp -o textfile.o textfile.cpp: In member function 'void TextFile::PutChar(char)': textfile.cpp:107: warning: unused variable 'i' textfile.cpp: In member function 'void TextFile::PutString(const char*)': textfile.cpp:120: warning: unused variable 'iError' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 threewaywt.cpp -o threewaywt.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 tomhydro.cpp -o tomhydro.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 traceback.cpp -o traceback.o traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)': traceback.cpp:21: warning: unused variable 'uPrefixCountB' traceback.cpp:68: warning: 'cPrevEdgeType' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 tracebackopt.cpp -o tracebackopt.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 tracebacksw.cpp -o tracebacksw.o tracebacksw.cpp: In function 'void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)': tracebacksw.cpp:22: warning: unused variable 'uPrefixCountB' tracebacksw.cpp:29: warning: unused variable 'scoreMax' tracebacksw.cpp:43: warning: 'cPrevEdgeType' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 treefrommsa.cpp -o treefrommsa.o In file included from clustsetmsa.h:8, from treefrommsa.cpp:5: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22: warning: enumeration value 'DISTANCE_Undefined' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Edit' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 typetostr.cpp -o typetostr.o typetostr.cpp: In function 'const char* SecsToStr(long unsigned int)': typetostr.cpp:13: warning: format '%02d' expects type 'int', but argument 3 has type 'long int' typetostr.cpp:13: warning: format '%02d' expects type 'int', but argument 4 has type 'long int' typetostr.cpp:13: warning: format '%02d' expects type 'int', but argument 5 has type 'long int' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 upgma2.cpp -o upgma2.o upgma2.cpp: In member function 'virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const': upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)': upgma2.cpp:252: warning: 'dtNewDist' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used upgma2.cpp:68: warning: 'void ListState()' defined but not used g++ -c -g -Wall -O2 usage.cpp -o usage.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 validateids.cpp -o validateids.o In file included from validateids.cpp:4: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 vtml2.cpp -o vtml2.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -Wall -O2 writescorefile.cpp -o writescorefile.o writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)': writescorefile.cpp:27: warning: 'Score' may be used uninitialized in this function writescorefile.cpp:27: note: 'Score' was declared here intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -g -Wall -O2 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsother.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 maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm strip muscle make[1]: Leaving directory `/tmp/buildd/muscle-3.70+fix1' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks fakeroot debian/rules binary test -x debian/rules dh_testroot dh_clean -k dh_installdirs -A mkdir -p "." DEB_MAKE_CHECK_TARGET unset, not running checks DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target dh_installdirs -pmuscle dh_installdocs -pmuscle dh_installexamples -pmuscle dh_installman -pmuscle dh_installinfo -pmuscle dh_installmenu -pmuscle dh_installcron -pmuscle dh_installinit -pmuscle dh_installdebconf -pmuscle dh_installemacsen -pmuscle dh_installcatalogs -pmuscle dh_installpam -pmuscle dh_installlogrotate -pmuscle dh_installlogcheck -pmuscle dh_installmime -pmuscle dh_installchangelogs -pmuscle dh_installudev -pmuscle dh_install -pmuscle dh_link -pmuscle dh_strip -pmuscle dh_compress -pmuscle dh_fixperms -pmuscle dh_makeshlibs -pmuscle dh_installdeb -pmuscle dh_perl -pmuscle dh_shlibdeps -pmuscle dh_gencontrol -pmuscle dpkg-gencontrol: warning: unknown substitution variable ${misc:Depends} dh_md5sums -pmuscle dh_builddeb -pmuscle dpkg-deb: building package `muscle' in `../muscle_3.70+fix1-1_i386.deb'. dpkg-genchanges >../muscle_3.70+fix1-1_i386.changes dpkg-genchanges: including full source code in upload dpkg-buildpackage: full upload (original source is included) Copying back the cached apt archive contents -> unmounting dev/pts filesystem -> unmounting proc filesystem Current time: Mon Feb 11 09:54:58 BRST 2008 pbuilder-time-stamp: 1202730898 -> Copying COW directory -> Invoking pbuilder -> Cleaning COW directory