[Debian-med-packaging] Bug#437599: muscle: not handling nostrip build option (policy 10.1)
Julien Danjou
acid at debian.org
Mon Aug 13 08:37:04 UTC 2007
Package: muscle
Version: 3.60-1
Severity: wishlist
User: buildd at naquadah.org
Usertags: nostrip
Hello,
There was a problem while autobuilding your package with DEB_BUILD_OPTIONS=nostrip.
Final binaries are still stripped.
If you call dh_strip correctly in debian/rules, this may mean that upstream
is stripping anyway.
You should look for call to strip, ld -s or install -s which may strip binaries.
> Automatic build of muscle_3.60-1 on octave for sid/i386 by rebuildd 0.2.2-r136
> Build started at 2007-08-13 07:14:04.881967
> ******************************************************************************
> Reading package lists...
> Building dependency tree...
> Reading state information...
> Need to get 206kB of source archives.
> Get:1 http://ftp.fr.debian.org sid/main muscle 3.60-1 (dsc) [732B]
> Get:2 http://ftp.fr.debian.org sid/main muscle 3.60-1 (tar) [185kB]
> Get:3 http://ftp.fr.debian.org sid/main muscle 3.60-1 (diff) [20.2kB]
> Fetched 206kB in 0s (739kB/s)
> Download complete and in download only mode
> W: /home/staff/jd/.pbuilderrc does not exist
> I: using fakeroot in build.
> Current time: Mon Aug 13 07:14:08 UTC 2007
> pbuilder-time-stamp: 1186989248
> Building the build Environment
> -> extracting base tarball [/var/cache/pbuilder/sid.tgz]
> -> creating local configuration
> -> 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 parse the build-deps
> -> Considering build-dep debhelper (>= 4.0.0)
> -> Trying debhelper
> -> Considering build-dep xsltproc
> -> Trying xsltproc
> -> Considering build-dep docbook-xsl
> -> Trying docbook-xsl
> -> Installing debhelper xsltproc docbook-xsl
> Reading package lists...
> Building dependency tree...
> Reading state information...
> The following extra packages will be installed:
> file gettext gettext-base html2text intltool-debian libmagic1 libxml2
> libxslt1.1 po-debconf sgml-base xml-core
> Suggested packages:
> dh-make xalan fop libsaxon-java libxalan2-java cvs gettext-doc sgml-base-doc
> Recommended packages:
> docbook-xml docbook-xsl-doc-html docbook-xsl-doc-pdf docbook-xsl-doc-text
> docbook-xsl-doc curl wget lynx libmail-sendmail-perl libcompress-zlib-perl
> The following NEW packages will be installed:
> debhelper docbook-xsl file gettext gettext-base html2text intltool-debian
> libmagic1 libxml2 libxslt1.1 po-debconf sgml-base xml-core xsltproc
> debconf: delaying package configuration, since apt-utils is not installed
> 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded.
> Need to get 0B/5724kB of archives.
> After unpacking 24.1MB of additional disk space will be used.
> Selecting previously deselected package libmagic1.
> (Reading database ... 8969 files and directories currently installed.)
> Unpacking libmagic1 (from .../libmagic1_4.21-2_i386.deb) ...
> Selecting previously deselected package file.
> Unpacking file (from .../archives/file_4.21-2_i386.deb) ...
> Selecting previously deselected package gettext-base.
> Unpacking gettext-base (from .../gettext-base_0.16.1-2_i386.deb) ...
> Selecting previously deselected package html2text.
> Unpacking html2text (from .../html2text_1.3.2a-3_i386.deb) ...
> Selecting previously deselected package gettext.
> Unpacking gettext (from .../gettext_0.16.1-2_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_1.0.9_all.deb) ...
> Selecting previously deselected package debhelper.
> Unpacking debhelper (from .../debhelper_5.0.53_all.deb) ...
> Selecting previously deselected package sgml-base.
> Unpacking sgml-base (from .../sgml-base_1.26_all.deb) ...
> Selecting previously deselected package xml-core.
> Unpacking xml-core (from .../archives/xml-core_0.11_all.deb) ...
> Selecting previously deselected package docbook-xsl.
> Unpacking docbook-xsl (from .../docbook-xsl_1.72.0.dfsg.1-2_all.deb) ...
> Selecting previously deselected package libxml2.
> Unpacking libxml2 (from .../libxml2_2.6.29.dfsg-1_i386.deb) ...
> Selecting previously deselected package libxslt1.1.
> Unpacking libxslt1.1 (from .../libxslt1.1_1.1.21-2_i386.deb) ...
> Selecting previously deselected package xsltproc.
> Unpacking xsltproc (from .../xsltproc_1.1.21-2_i386.deb) ...
> Setting up libmagic1 (4.21-2) ...
>
> Setting up file (4.21-2) ...
> Setting up gettext-base (0.16.1-2) ...
>
> Setting up html2text (1.3.2a-3) ...
>
> Setting up gettext (0.16.1-2) ...
>
> Setting up intltool-debian (0.35.0+20060710.1) ...
> Setting up po-debconf (1.0.9) ...
> Setting up debhelper (5.0.53) ...
> Setting up sgml-base (1.26) ...
>
> Setting up xml-core (0.11) ...
>
> Setting up docbook-xsl (1.72.0.dfsg.1-2) ...
>
> Setting up libxml2 (2.6.29.dfsg-1) ...
>
> Setting up libxslt1.1 (1.1.21-2) ...
>
> Setting up xsltproc (1.1.21-2) ...
> -> 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 [muscle_3.60-1.dsc]
> -> copying [./muscle_3.60.orig.tar.gz]
> -> copying [./muscle_3.60-1.diff.gz]
> Extracting source
> gpg: can't open `/gnupg/options.skel': No such file or directory
> gpg: Signature made Mon Aug 7 00:03:41 2006 UTC using DSA key ID 1880283C
> gpg: Can't check signature: public key not found
> dpkg-source: extracting muscle in muscle-3.60
> dpkg-source: unpacking muscle_3.60.orig.tar.gz
> dpkg-source: applying ./muscle_3.60-1.diff.gz
> -> Building the package
> Setting DEB_BUILD_OPTIONS=nostrip
> dpkg-buildpackage: source package is muscle
> dpkg-buildpackage: source version is 3.60-1
> dpkg-buildpackage: source changed by Charles Plessy <charles-debian-nospam at plessy.org>
> dpkg-buildpackage: host architecture i386
> dpkg-buildpackage: source version without epoch 3.60-1
> fakeroot debian/rules clean
> dh_testdir
> dh_testroot
> rm -f build-stamp configure-stamp
> # Add here commands to clean up after the build process.
> /usr/bin/make clean
> make[1]: Entering directory `/tmp/buildd/muscle-3.60'
> rm -f *.o make.err make.out
> rm -f muscle
> make[1]: Leaving directory `/tmp/buildd/muscle-3.60'
> dh_clean muscle.1
> dpkg-source -b muscle-3.60
> dpkg-source: building muscle using existing muscle_3.60.orig.tar.gz
> dpkg-source: building muscle in muscle_3.60-1.diff.gz
> dpkg-source: building muscle in muscle_3.60-1.dsc
> debian/rules build
> dh_testdir
> # Add here commands to configure the package.
> touch configure-stamp
> dh_testdir
> # Add here commands to compile the package.
> /usr/bin/make CFLAGS="-Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1"
> make[1]: Entering directory `/tmp/buildd/muscle-3.60'
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 aligntwomsas.cpp -o aligntwomsas.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 aligntwoprofs.cpp -o aligntwoprofs.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 aln.cpp -o aln.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 clust.cpp -o clust.o
> clustset.h:9: warning: 'class ClustSet' has virtual functions but non-virtual destructor
> 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 cons.cpp -o cons.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 distcalc.cpp -o distcalc.o
> distcalc.h:10: warning: 'class DistCalc' has virtual functions but non-virtual destructor
> distcalc.h:19: warning: 'class DistCalcDF' has virtual functions but non-virtual destructor
> distcalc.h:32: warning: 'class DistCalcMSA' has virtual functions but non-virtual destructor
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o
> 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:60: warning: missing braces around initializer for 'EnumOpt'
> enums.h:60: warning: missing braces around initializer for 'EnumOpt'
> enums.h:60: warning: missing braces around initializer for 'EnumOpt'
> enums.h:60: warning: missing braces around initializer for 'EnumOpt'
> enums.h:60: warning: missing braces around initializer for 'EnumOpt'
> enums.h:60: warning: missing braces around initializer for 'EnumOpt'
> enums.h:60: warning: missing braces around initializer for 'EnumOpt'
> enums.h:60: warning: missing braces around initializer for 'EnumOpt'
> enums.h:60: warning: missing braces around initializer for 'EnumOpt'
> enums.h:67: warning: missing braces around initializer for 'EnumOpt'
> enums.h:67: warning: missing braces around initializer for 'EnumOpt'
> enums.h:67: warning: missing braces around initializer for 'EnumOpt'
> enums.h:67: warning: missing braces around initializer for 'EnumOpt'
> enums.h:67: warning: missing braces around initializer for 'EnumOpt'
> enums.h:76: warning: missing braces around initializer for 'EnumOpt'
> enums.h:76: warning: missing braces around initializer for 'EnumOpt'
> enums.h:76: warning: missing braces around initializer for 'EnumOpt'
> enums.h:76: warning: missing braces around initializer for 'EnumOpt'
> enums.h:76: warning: missing braces around initializer for 'EnumOpt'
> enums.h:76: warning: missing braces around initializer for 'EnumOpt'
> enums.h:76: warning: missing braces around initializer for 'EnumOpt'
> enums.h:85: warning: missing braces around initializer for 'EnumOpt'
> enums.h:85: warning: missing braces around initializer for 'EnumOpt'
> enums.h:85: warning: missing braces around initializer for 'EnumOpt'
> enums.h:85: warning: missing braces around initializer for 'EnumOpt'
> enums.h:85: warning: missing braces around initializer for 'EnumOpt'
> enums.h:85: warning: missing braces around initializer for 'EnumOpt'
> enums.h:85: warning: missing braces around initializer for 'EnumOpt'
> enums.h:91: warning: missing braces around initializer for 'EnumOpt'
> enums.h:91: warning: missing braces around initializer for 'EnumOpt'
> enums.h:91: warning: missing braces around initializer for 'EnumOpt'
> enums.h:91: warning: missing braces around initializer for 'EnumOpt'
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.o
> clustset.h:9: warning: 'class ClustSet' has virtual functions but non-virtual destructor
> clustsetdf.h:12: warning: 'class ClustSetDF' has virtual functions but non-virtual destructor
> distcalc.h:10: warning: 'class DistCalc' has virtual functions but non-virtual destructor
> distcalc.h:19: warning: 'class DistCalcDF' has virtual functions but non-virtual destructor
> distcalc.h:32: warning: 'class DistCalcMSA' has virtual functions but non-virtual destructor
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 globals.cpp -o globals.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 gotowt.cpp -o gotowt.o
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 html.cpp -o html.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 local.cpp -o local.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 mhack.cpp -o mhack.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 msadistkimura.cpp -o msadistkimura.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 muscle.cpp -o muscle.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 nwdasmall.cpp -o nwdasmall.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 nwrec.cpp -o nwrec.o
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 objscoreda.cpp -o objscoreda.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 options.cpp -o options.o
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:78: warning: missing braces around initializer for 'VALUE_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> options.cpp:116: warning: missing braces around initializer for 'FLAG_OPT'
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o
> params.cpp: In function 'void SetPPCommandLineParams()':
> params.cpp:416: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp:417: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp: In function 'void SetPPScore(bool)':
> params.cpp:434: warning: enumeration value 'PPSCORE_Undefined' not handled in switch
> params.cpp: In function 'void SetParams()':
> params.cpp:585: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp:586: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp:588: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp:589: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp:591: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp:592: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp:594: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp:595: warning: dereferencing type-punned pointer will break strict-aliasing rules
> params.cpp:597: 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.o
> phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)':
> phy.cpp:604: warning: unused variable 'dEdgeLength'
> intmath.h: At global scope:
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 phy4.cpp -o phy4.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 phyfromfile.cpp -o phyfromfile.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 phytofile.cpp -o phytofile.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 posgap.cpp -o posgap.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.o
> clustset.h:9: warning: 'class ClustSet' has virtual functions but non-virtual destructor
> msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
> msadist.h:17: warning: enumeration value 'DISTANCE_Undefined' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch
> clustsetmsa.h: At global scope:
> clustsetmsa.h:14: warning: 'class ClustSetMSA' has virtual functions but non-virtual destructor
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 profile.cpp -o profile.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o
> clustset.h:9: warning: 'class ClustSet' has virtual functions but non-virtual destructor
> msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
> msadist.h:17: warning: enumeration value 'DISTANCE_Undefined' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch
> clustsetmsa.h: At global scope:
> clustsetmsa.h:14: warning: 'class ClustSetMSA' has virtual functions but non-virtual destructor
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o
> 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 termgaps.cpp -o termgaps.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 threewaywt.cpp -o threewaywt.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 tracebackopt.cpp -o tracebackopt.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 treefrommsa.cpp -o treefrommsa.o
> clustset.h:9: warning: 'class ClustSet' has virtual functions but non-virtual destructor
> msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
> msadist.h:17: warning: enumeration value 'DISTANCE_Undefined' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch
> msadist.h:17: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch
> clustsetmsa.h: At global scope:
> clustsetmsa.h:14: warning: 'class ClustSetMSA' has virtual functions but non-virtual destructor
> distcalc.h:10: warning: 'class DistCalc' has virtual functions but non-virtual destructor
> distcalc.h:19: warning: 'class DistCalcDF' has virtual functions but non-virtual destructor
> distcalc.h:32: warning: 'class DistCalcMSA' has virtual functions but non-virtual destructor
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 upgma2.cpp -o upgma2.o
> distcalc.h:10: warning: 'class DistCalc' has virtual functions but non-virtual destructor
> distcalc.h:19: warning: 'class DistCalcDF' has virtual functions but non-virtual destructor
> distcalc.h:32: warning: 'class DistCalcMSA' has virtual functions but non-virtual destructor
> upgma2.cpp:361: warning: 'class DistCalcTest' has virtual functions but non-virtual destructor
> 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 -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 validateids.cpp -o validateids.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.o
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -c -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 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
> intmath.h: At global scope:
> intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used
> g++ -Wall -g -O2 -funroll-loops -Winline -DNDEBUG=1 -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 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 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
> strip muscle
> make[1]: Leaving directory `/tmp/buildd/muscle-3.60'
> #/usr/bin/docbook-to-man debian/muscle.sgml > muscle.1
> xsltproc -''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl debian/manpage.xml
> I/O error : Attempt to load network entity http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd
> debian/manpage.xml:45: warning: failed to load external entity "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"
> ]>
> ^
> Note: meta source : No productname or alternative muscle
> Note: meta source : No refmiscinfo at class=source muscle
> Note: meta version: No productnumber or alternative muscle
> Note: meta version: No refmiscinfo at class=version muscle
> Warn: meta source : No valid fallback. Leaving empty muscle
> Note: meta manual : No ancestor with title muscle
> Note: meta manual : No refmiscinfo at class=manual muscle
> Warn: meta manual : No valid fallback. Leaving empty muscle
> Note: Writing muscle.1
> touch build-stamp
> fakeroot debian/rules binary
> dh_testdir
> dh_testroot
> dh_installdirs -i
> /usr/bin/make install-doc DESTDIR=/tmp/buildd/muscle-3.60/debian/muscle-doc
> make[1]: Entering directory `/tmp/buildd/muscle-3.60'
> if [ ! -x /tmp/buildd/muscle-3.60/debian/muscle-doc/usr/share/doc/muscle ]; then mkdir -p /tmp/buildd/muscle-3.60/debian/muscle-doc/usr/share/doc/muscle; fi
> if [ ! -x /tmp/buildd/muscle-3.60/debian/muscle-doc/usr/share/doc/muscle-doc ]; then mkdir -p /tmp/buildd/muscle-3.60/debian/muscle-doc/usr/share/doc/muscle-doc; fi
> cp muscle.html /tmp/buildd/muscle-3.60/debian/muscle-doc/usr/share/doc/muscle/
> (cd /tmp/buildd/muscle-3.60/debian/muscle-doc/usr/share/doc/muscle-doc/ && ln -s ../muscle/muscle.html* . )
> make[1]: Leaving directory `/tmp/buildd/muscle-3.60'
> dh_testdir -i
> dh_testroot -i
> dh_installchangelogs -i
> dh_installdocs -i
> dh_installman -i
> dh_link -i
> dh_strip -i
> dh_compress -i
> dh_fixperms -i
> dh_installdeb -i
> dh_shlibdeps -i
> dh_gencontrol -i
> dh_md5sums -i
> dh_builddeb -i
> dpkg-deb: building package `muscle-doc' in `../muscle-doc_3.60-1_all.deb'.
> dh_testdir
> dh_testroot
> dh_clean -k
> dh_installdirs -a
> # Add here commands to install the package into debian/muscle.
> /usr/bin/make install DESTDIR=/tmp/buildd/muscle-3.60/debian/muscle
> make[1]: Entering directory `/tmp/buildd/muscle-3.60'
> if [ ! -x /tmp/buildd/muscle-3.60/debian/muscle/usr/bin ]; then mkdir -p /tmp/buildd/muscle-3.60/debian/muscle/usr/bin; fi
> cp muscle /tmp/buildd/muscle-3.60/debian/muscle/usr/bin/muscle
> make[1]: Leaving directory `/tmp/buildd/muscle-3.60'
> dh_testdir -a
> dh_testroot -a
> dh_installchangelogs -a
> dh_installdocs -a
> dh_installexamples -a
> dh_installman -a
> dh_link -a
> dh_strip -a
> dh_compress -a
> dh_fixperms -a
> dh_installdeb -a
> dh_shlibdeps -a
> dh_gencontrol -a
> dpkg-gencontrol: warning: unknown substitution variable ${misc:Depends}
> dh_md5sums -a
> dh_builddeb -a
> dpkg-deb: building package `muscle' in `../muscle_3.60-1_i386.deb'.
> dpkg-genchanges
> 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
> -> cleaning the build env
> -> removing directory /var/cache/pbuilder/build//23376 and its subdirectories
> Current time: Mon Aug 13 07:21:56 UTC 2007
> pbuilder-time-stamp: 1186989716
> Checking muscle-doc_3.60-1_all.deb for stripped binaries...
> ---------------------------------------
> Checking muscle_3.60-1_i386.deb for stripped binaries...
> ---------------------------------------
> /tmp/muscle_3.60-1_i386.deb/usr/bin/muscle: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.8, dynamically linked (uses shared libs), stripped
>
> ...done
> Removing result files...
> ...done
> ******************************************************************************
> Finished with status POST_BUILD_FAILED at 2007-08-13 07:22:00.662342
> Build needed 0:07:55.780375
--
Julien Danjou
.''`. Debian Developer
: :' : http://julien.danjou.info
`. `' http://people.debian.org/~acid
`- 9A0D 5FD9 EB42 22F6 8974 C95C A462 B51E C2FE E5CD
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