origdir = ../tarballs /home/sw/bin/buildPackage: line 17: .svn/deb-layout: No such file or directory Complete layout information: buildArea=/sw/debian-med/trunk/packages/muscle/build-area origDir=/sw/debian-med/trunk/packages/muscle/tarballs tagsDir=/sw/debian-med/trunk/packages/muscle/tags tagsUrl=svn://svn.debian.org/svn/debian-med/trunk/packages/muscle/tags trunkDir=/sw/debian-med/trunk/packages/muscle/trunk trunkUrl=svn://svn.debian.org/svn/debian-med/trunk/packages/muscle/trunk UNRELEASED tag found - you don't want to release with it, do you? mergeWithUpstream mode detected, looking for /sw/debian-med/trunk/packages/muscle/tarballs/muscle_3.8.31.orig.tar.gz I: mergeWithUpstream property set, looking for upstream source tarball... tar --no-same-owner --no-same-permissions --extract --gzip --file /sw/debian-med/trunk/packages/muscle/tarballs/muscle_3.8.31.orig.tar.gz --directory <1 more argument> mv /sw/debian-med/trunk/packages/muscle/build-area/tmp-0.446153100420819/muscle-3.8.31.orig /sw/debian-med/trunk/packages/muscle/build-area/muscle-3.8.31 mkdir -p /sw/debian-med/trunk/packages/muscle/build-area/muscle-3.8.31/debian/patches /sw/debian-med/trunk/packages/muscle/build-area/muscle-3.8.31/debian cp --parents -laf debian/muscle.1.xml debian/muscle.html debian/muscle.docs debian/copyright debian/dirs debian/muscle.manpages debian/README.Debian debian/muscle.install <10 more arguments> rm -rf /sw/debian-med/trunk/packages/muscle/build-area/tmp-0.446153100420819 chmod -R u+r+w+X,g+r-w+X,o+r-w+X -- /sw/debian-med/trunk/packages/muscle/build-area/muscle-3.8.31 /bin/sh -c pdebuild --buildresult /sw/packages/build-area -- --basetgz /var/cache/pbuilder/base-sid-amd64.tgz --architecture amd64 --distribution sid W: /home/sw/.pbuilderrc does not exist dpkg-buildpackage: source package muscle dpkg-buildpackage: source version 1:3.8.31-2 dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build muscle-3.8.31 fakeroot debian/rules clean test -x debian/rules dh_testroot dh_clean rm -f *.o make.err make.out muscle dpkg-source -b muscle-3.8.31 dpkg-source: warning: no source format specified in debian/source/format, see dpkg-source(1) dpkg-source: info: using source format `1.0' dpkg-source: info: building muscle using existing muscle_3.8.31.orig.tar.gz dpkg-source: info: building muscle in muscle_3.8.31-2.diff.gz dpkg-source: warning: ignoring deletion of file make.out dpkg-source: warning: ignoring deletion of file make.err dpkg-source: info: building muscle in muscle_3.8.31-2.dsc dpkg-genchanges -S >../muscle_3.8.31-2_source.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build muscle-3.8.31 dpkg-buildpackage: source only, diff-only upload (original source NOT included) W: /home/sw/.pbuilderrc does not exist I: using fakeroot in build. I: Current time: Wed Mar 27 08:44:10 CET 2013 I: pbuilder-time-stamp: 1364370250 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/base-sid-amd64.tgz] I: creating local configuration I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /run/shm filesystem I: mounting /dev/pts filesystem I: policy-rc.d already exists I: Obtaining the cached apt archive contents I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 8), cdbs dpkg-deb: building package `pbuilder-satisfydepends-dummy' in `/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 12010 files and directories currently installed.) Unpacking pbuilder-satisfydepends-dummy (from .../pbuilder-satisfydepends-dummy.deb) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 8); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on cdbs; however: Package cdbs is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... 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} libasprintf-dev{a} libasprintf0c2{a} libcroco3{a} libffi5{a} libgettextpo-dev{a} libgettextpo0{a} libglib2.0-0{a} libmagic1{a} libpcre3{a} libpipeline1{a} libunistring0{a} libxml2{a} man-db{a} po-debconf{a} 0 packages upgraded, 23 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/9223 kB of archives. After unpacking 26.3 MB will be used. Writing extended state information... debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:amd64. (Reading database ... 12010 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.2-2_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.2-1_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.3-3_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_1%3a5.11-2.1_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.31-2_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-7+nmu1_amd64.deb) ... Selecting previously unselected package libffi5:amd64. Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-5_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.6-2_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0:amd64. Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../file_1%3a5.11-2.1_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package cdbs. Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package libasprintf-dev:amd64. Unpacking libasprintf-dev:amd64 (from .../libasprintf-dev_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libgettextpo-dev:amd64. Unpacking libgettextpo-dev:amd64 (from .../libgettextpo-dev_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ... Setting up libpipeline1:amd64 (1.2.2-2) ... Setting up groff-base (1.22.2-1) ... Setting up bsdmainutils (9.0.4) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.3-3) ... Building database of manual pages ... Setting up libasprintf0c2:amd64 (0.18.1.1-10) ... Setting up libmagic1:amd64 (1:5.11-2.1) ... Setting up libpcre3:amd64 (1:8.31-2) ... Setting up libxml2:amd64 (2.8.0+dfsg1-7+nmu1) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-5) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.6-2) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-10) ... Setting up file (1:5.11-2.1) ... Setting up gettext-base (0.18.1.1-10) ... Setting up cdbs (0.4.120) ... Setting up html2text (1.3.2a-15) ... Setting up libasprintf-dev:amd64 (0.18.1.1-10) ... Setting up libgettextpo-dev:amd64 (0.18.1.1-10) ... Setting up gettext (0.18.1.1-10) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120909) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: fakeroot debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/109 kB of archives. After this operation, 325 kB of additional disk space will be used. Selecting previously unselected package fakeroot. (Reading database ... 13467 files and directories currently installed.) Unpacking fakeroot (from .../fakeroot_1.18.4-2_amd64.deb) ... Processing triggers for man-db ... Setting up fakeroot (1.18.4-2) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode I: Copying back the cached apt archive contents I: Copying source file I: copying [../muscle_3.8.31-2.dsc] I: copying [../muscle_3.8.31.orig.tar.gz] I: copying [../muscle_3.8.31-2.diff.gz] I: Extracting source dpkg-source: warning: extracting unsigned source package (muscle_3.8.31-2.dsc) dpkg-source: info: extracting muscle in muscle-3.8.31 dpkg-source: info: unpacking muscle_3.8.31.orig.tar.gz dpkg-source: info: applying muscle_3.8.31-2.diff.gz I: Building the package I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" dpkg-buildpackage -us -uc -rfakeroot dpkg-buildpackage: source package muscle dpkg-buildpackage: source version 1:3.8.31-2 dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build muscle-3.8.31 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean test -x debian/rules dh_testroot dh_clean rm -f *.o make.err make.out muscle dpkg-source -b muscle-3.8.31 dpkg-source: warning: no source format specified in debian/source/format, see dpkg-source(1) dpkg-source: info: using source format `1.0' dpkg-source: info: building muscle using existing muscle_3.8.31.orig.tar.gz dpkg-source: info: building muscle in muscle_3.8.31-2.diff.gz dpkg-source: warning: ignoring deletion of file make.err dpkg-source: warning: ignoring deletion of file make.out dpkg-source: info: building muscle in muscle_3.8.31-2.dsc debian/rules build test -x debian/rules mkdir -p "." g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aligngivenpath.o aligngivenpath.cpp 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:186:17: warning: unused variable 'uLengthA' [-Wunused-variable] aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable] aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable] aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable] aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable] aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable] In file included from muscle.h:34:0, from aligngivenpath.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aligngivenpathsw.o aligngivenpathsw.cpp 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:58:17: warning: unused variable 'uLengthA' [-Wunused-variable] aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable] aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable] aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable] aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable] aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable] In file included from muscle.h:34:0, from aligngivenpathsw.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aligntwomsas.o aligntwomsas.cpp In file included from muscle.h:34:0, from aligntwomsas.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aligntwoprofs.o aligntwoprofs.cpp In file included from muscle.h:34:0, from aligntwoprofs.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aln.o aln.cpp In file included from muscle.h:34:0, from aln.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o alpha.o alpha.cpp alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)': alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from alpha.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o anchors.o anchors.cpp anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)': anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable] In file included from muscle.h:34:0, from anchors.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function] anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o bittraceback.o bittraceback.cpp bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)': bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable] In file included from muscle.h:34:0, from bittraceback.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o blosum62.o blosum62.cpp In file included from muscle.h:34:0, from blosum62.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o blosumla.o blosumla.cpp In file included from muscle.h:34:0, from blosumla.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o clust.o clust.cpp clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)': clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)': clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable] clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)': clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable] clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)': clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)': clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable] clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const': clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from clust.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o cluster.o cluster.cpp cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)': cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable] cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable] cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wmaybe-uninitialized] cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from cluster.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o clwwt.o clwwt.cpp In file included from muscle.h:34:0, from clwwt.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o color.o color.cpp color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] color.cpp:34:2: warning: missing braces around initializer for 'int [23]' [-Wmissing-braces] In file included from muscle.h:34:0, from color.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o cons.o cons.cpp In file included from muscle.h:34:0, from cons.cpp:7: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o diaglist.o diaglist.cpp diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)': diaglist.cpp:77:39: warning: 'uStartPosB' may be used uninitialized in this function [-Wmaybe-uninitialized] diaglist.cpp:77:39: warning: 'uStartPosA' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from diaglist.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o diffobjscore.o diffobjscore.cpp diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)': diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable] diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable] In file included from muscle.h:34:0, from diffobjscore.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o diffpaths.o diffpaths.cpp In file included from muscle.h:34:0, from diffpaths.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o difftrees.o difftrees.cpp difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)': difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable] In file included from muscle.h:34:0, from difftrees.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o difftreese.o difftreese.cpp In file included from muscle.h:34:0, from difftreese.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o distcalc.o distcalc.cpp In file included from muscle.h:34:0, from distcalc.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o distfunc.o distfunc.cpp In file included from muscle.h:34:0, from distfunc.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o distpwkimura.o distpwkimura.cpp In file included from muscle.h:34:0, from distpwkimura.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o domuscle.o domuscle.cpp In file included from muscle.h:34:0, from domuscle.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dosp.o dosp.cpp In file included from muscle.h:34:0, from dosp.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dpreglist.o dpreglist.cpp dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)': dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable] In file included from muscle.h:34:0, from dpreglist.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o drawtree.o drawtree.cpp In file included from muscle.h:34:0, from drawtree.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o edgelist.o edgelist.cpp In file included from muscle.h:34:0, from edgelist.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o enumopts.o enumopts.cpp In file included from enumopts.cpp:8:0: enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:15:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:22:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:28:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:36:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:41:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:49:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:63:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:70:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:79:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:88:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] enums.h:94:1: warning: missing braces around initializer for 'EnumOpt' [-Wmissing-braces] In file included from muscle.h:34:0, from enumopts.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o enumtostr.o enumtostr.cpp In file included from muscle.h:34:0, from enumtostr.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o estring.o estring.cpp estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)': estring.cpp:409:3: warning: 'cType' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from estring.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fasta.o fasta.cpp fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)': fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable] fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable] In file included from muscle.h:34:0, from fasta.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fasta2.o fasta2.cpp In file included from muscle.h:34:0, from fasta2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastclust.o fastclust.cpp In file included from muscle.h:34:0, from fastclust.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdist.o fastdist.cpp In file included from muscle.h:34:0, from fastdist.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistjones.o fastdistjones.cpp In file included from muscle.h:34:0, from fastdistjones.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistkbit.o fastdistkbit.cpp In file included from muscle.h:34:0, from fastdistkbit.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistkmer.o fastdistkmer.cpp fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)': fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable] In file included from muscle.h:34:0, from fastdistkmer.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistmafft.o fastdistmafft.cpp fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)': fastdistmafft.cpp:238:15: warning: unused variable 'pName1' [-Wunused-variable] In file included from muscle.h:34:0, from fastdistmafft.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistnuc.o fastdistnuc.cpp fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)': fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable] In file included from muscle.h:34:0, from fastdistnuc.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable] fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastscorepath2.o fastscorepath2.cpp In file included from muscle.h:34:0, from fastscorepath2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o finddiags.o finddiags.cpp In file included from muscle.h:34:0, from finddiags.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o finddiagsn.o finddiagsn.cpp finddiagsn.cpp: In function 'char* TupleToStr(int)': finddiagsn.cpp:16:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from muscle.h:34:0, from finddiagsn.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalign.o glbalign.cpp In file included from muscle.h:34:0, from glbalign.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalign352.o glbalign352.cpp In file included from muscle.h:34:0, from glbalign352.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbaligndiag.o glbaligndiag.cpp In file included from muscle.h:34:0, from glbaligndiag.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignle.o glbalignle.cpp glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignle.cpp:427:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from glbalignle.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignsimple.o glbalignsimple.cpp In file included from muscle.h:34:0, from glbalignsimple.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function] glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignsp.o glbalignsp.cpp glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignsp.cpp:366:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] glbalignsp.cpp:305:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from glbalignsp.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignspn.o glbalignspn.cpp glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignspn.cpp:401:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] glbalignspn.cpp:340:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from glbalignspn.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignss.o glbalignss.cpp glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)': glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable] glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable] glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] glbalignss.cpp:310:49: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] glbalignss.cpp:252:50: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from glbalignss.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalndimer.o glbalndimer.cpp glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)': glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from glbalndimer.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globals.o globals.cpp In file included from muscle.h:34:0, from globals.cpp:6: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globalslinux.o globalslinux.cpp globalslinux.cpp: In function 'double GetNAN()': globalslinux.cpp:17:28: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] In file included from muscle.h:34:0, from globalslinux.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globalsosx.o globalsosx.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globalsother.o globalsother.cpp In file included from muscle.h:34:0, from globalsother.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globalswin32.o globalswin32.cpp In file included from muscle.h:34:0, from globalswin32.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o gonnet.o gonnet.cpp In file included from muscle.h:34:0, from gonnet.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o henikoffweight.o henikoffweight.cpp In file included from muscle.h:34:0, from henikoffweight.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o henikoffweightpb.o henikoffweightpb.cpp In file included from muscle.h:34:0, from henikoffweightpb.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o html.o html.cpp In file included from muscle.h:34:0, from html.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o hydro.o hydro.cpp In file included from muscle.h:34:0, from hydro.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o intmath.o intmath.cpp In file included from muscle.h:34:0, from intmath.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o local.o local.cpp In file included from muscle.h:34:0, from local.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o main.o main.cpp In file included from muscle.h:34:0, from main.cpp:3: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o makerootmsa.o makerootmsa.cpp makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)': makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable] makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)': makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable] makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)': makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable] In file included from muscle.h:34:0, from makerootmsa.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o makerootmsab.o makerootmsab.cpp In file included from muscle.h:34:0, from makerootmsab.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o maketree.o maketree.cpp In file included from muscle.h:34:0, from maketree.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o mhack.o mhack.cpp In file included from muscle.h:34:0, from mhack.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o mpam200.o mpam200.cpp In file included from muscle.h:34:0, from mpam200.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o msa.o msa.cpp In file included from muscle.h:34:0, from msa.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function] msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function] msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function] msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o msa2.o msa2.cpp msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)': msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)': msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable] In file included from muscle.h:34:0, from msa2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o msadistkimura.o msadistkimura.cpp In file included from muscle.h:34:0, from msadistkimura.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o msf.o msf.cpp In file included from muscle.h:34:0, from msf.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o muscle.o muscle.cpp In file included from muscle.h:34:0, from muscle.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o muscleout.o muscleout.cpp In file included from muscle.h:34:0, from muscleout.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nucmx.o nucmx.cpp In file included from muscle.h:34:0, from nucmx.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwdasimple.o nwdasimple.cpp In file included from muscle.h:34:0, from nwdasimple.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwdasimple2.o nwdasimple2.cpp In file included from muscle.h:34:0, from nwdasimple2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwdasmall.o nwdasmall.cpp In file included from muscle.h:34:0, from nwdasmall.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwrec.o nwrec.cpp g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwsmall.o nwsmall.cpp In file included from muscle.h:34:0, from nwsmall.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o objscore.o objscore.cpp objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)': objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch] objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from objscore.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o objscore2.o objscore2.cpp objscore2.cpp: In function 'SCORE TermGapScore(bool)': objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)': objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable] objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable] objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable] objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)': objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)': objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable] objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)': objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable] In file included from muscle.h:34:0, from objscore2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o objscoreda.o objscoreda.cpp In file included from muscle.h:34:0, from objscoreda.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o onexception.o onexception.cpp In file included from muscle.h:34:0, from onexception.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o options.o options.cpp options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:84:2: warning: missing braces around initializer for 'VALUE_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] options.cpp:124:2: warning: missing braces around initializer for 'FLAG_OPT' [-Wmissing-braces] In file included from muscle.h:34:0, from options.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o outweights.o outweights.cpp In file included from muscle.h:34:0, from outweights.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o pam200mafft.o pam200mafft.cpp pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] pam200mafft.cpp:32:2: warning: missing braces around initializer for 'float [23]' [-Wmissing-braces] In file included from muscle.h:34:0, from pam200mafft.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o params.o params.cpp params.cpp: In function 'void SetPPScore(bool)': params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from params.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phy.o phy.cpp phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)': phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable] In file included from muscle.h:34:0, from phy.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phy2.o phy2.cpp In file included from muscle.h:34:0, from phy2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phy3.o phy3.cpp phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)': phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable] phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)': phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable] phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable] phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable] phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable] phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)': phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable] In file included from muscle.h:34:0, from phy3.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phy4.o phy4.cpp In file included from muscle.h:34:0, from phy4.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phyfromclust.o phyfromclust.cpp In file included from muscle.h:34:0, from phyfromclust.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phyfromfile.o phyfromfile.cpp In file included from muscle.h:34:0, from phyfromfile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o physeq.o physeq.cpp physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const': physeq.cpp:60:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] physeq.cpp:71:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const': physeq.cpp:112:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] physeq.cpp:124:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from muscle.h:34:0, from physeq.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phytofile.o phytofile.cpp In file included from muscle.h:34:0, from phytofile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o posgap.o posgap.cpp In file included from muscle.h:34:0, from posgap.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o ppscore.o ppscore.cpp In file included from muscle.h:34:0, from ppscore.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o profdb.o profdb.cpp In file included from clustsetmsa.h:8:0, from profdb.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from profdb.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o profile.o profile.cpp In file included from muscle.h:34:0, from profile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o profilefrommsa.o profilefrommsa.cpp profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)': profilefrommsa.cpp:131:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)': profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)': profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable] profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable] In file included from muscle.h:34:0, from profilefrommsa.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o progalign.o progalign.cpp progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)': progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable] In file included from muscle.h:34:0, from progalign.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o progress.o progress.cpp In file included from muscle.h:34:0, from progress.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o progressivealign.o progressivealign.cpp In file included from muscle.h:34:0, from progressivealign.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o pwpath.o pwpath.cpp pwpath.cpp: In member function 'void PWPath::Validate() const': pwpath.cpp:79:16: warning: unused variable 'LastEdge' [-Wunused-variable] pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)': pwpath.cpp:212:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable] In file included from muscle.h:34:0, from pwpath.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o readmx.o readmx.cpp readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]': readmx.cpp:83:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] readmx.cpp:84:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from muscle.h:34:0, from readmx.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o realigndiffs.o realigndiffs.cpp In file included from muscle.h:34:0, from realigndiffs.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o realigndiffse.o realigndiffse.cpp realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)': realigndiffse.cpp:72:13: warning: unused variable 'uNewRight' [-Wunused-variable] realigndiffse.cpp:75:13: warning: unused variable 'uOldRight' [-Wunused-variable] In file included from muscle.h:34:0, from realigndiffse.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refine.o refine.cpp In file included from clustsetmsa.h:8:0, from refine.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from refine.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinehoriz.o refinehoriz.cpp In file included from muscle.h:34:0, from refinehoriz.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinesubfams.o refinesubfams.cpp refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)': refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable] In file included from muscle.h:34:0, from refinesubfams.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinetree.o refinetree.cpp In file included from muscle.h:34:0, from refinetree.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinetreee.o refinetreee.cpp In file included from muscle.h:34:0, from refinetreee.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinevert.o refinevert.cpp In file included from muscle.h:34:0, from refinevert.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinew.o refinew.cpp refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)': refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable] refinew.cpp: In function 'void RefineW(const MSA&, MSA&)': refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable] In file included from muscle.h:34:0, from refinew.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o savebest.o savebest.cpp In file included from muscle.h:34:0, from savebest.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o scoredist.o scoredist.cpp In file included from muscle.h:34:0, from scoredist.cpp:3: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o scoregaps.o scoregaps.cpp In file included from muscle.h:34:0, from scoregaps.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function] scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o scorehistory.o scorehistory.cpp In file included from muscle.h:34:0, from scorehistory.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o scorepp.o scorepp.cpp In file included from muscle.h:34:0, from scorepp.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o seq.o seq.cpp In file included from muscle.h:34:0, from seq.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o seqvect.o seqvect.cpp In file included from muscle.h:34:0, from seqvect.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o setblosumweights.o setblosumweights.cpp In file included from muscle.h:34:0, from setblosumweights.cpp:42: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o setgscweights.o setgscweights.cpp In file included from muscle.h:34:0, from setgscweights.cpp:104: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o setnewhandler.o setnewhandler.cpp In file included from muscle.h:34:0, from setnewhandler.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o spfast.o spfast.cpp spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)': spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable] In file included from muscle.h:34:0, from spfast.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function] spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o sptest.o sptest.cpp In file included from muscle.h:34:0, from sptest.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o stabilize.o stabilize.cpp In file included from muscle.h:34:0, from stabilize.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o subfam.o subfam.cpp subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)': subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable] In file included from muscle.h:34:0, from subfam.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o subfams.o subfams.cpp In file included from muscle.h:34:0, from subfams.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function] subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function] subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o sw.o sw.cpp In file included from muscle.h:34:0, from sw.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o termgaps.o termgaps.cpp In file included from muscle.h:34:0, from termgaps.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o textfile.o textfile.cpp textfile.cpp: In member function 'void TextFile::PutChar(char)': textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable] textfile.cpp: In member function 'void TextFile::PutString(const char*)': textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable] In file included from muscle.h:34:0, from textfile.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o threewaywt.o threewaywt.cpp In file included from muscle.h:34:0, from threewaywt.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o tomhydro.o tomhydro.cpp In file included from muscle.h:34:0, from tomhydro.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o traceback.o traceback.cpp traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)': traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] traceback.cpp:59:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from traceback.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o tracebackopt.o tracebackopt.cpp In file included from muscle.h:34:0, from tracebackopt.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o tracebacksw.o tracebacksw.cpp 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:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable] tracebacksw.cpp:34:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from tracebacksw.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o treefrommsa.o treefrommsa.cpp In file included from clustsetmsa.h:8:0, from treefrommsa.cpp:5: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from treefrommsa.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o typetostr.o typetostr.cpp In file included from muscle.h:34:0, from typetostr.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o upgma2.o upgma2.cpp upgma2.cpp: In member function 'virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const': upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces] upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces] upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces] upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces] upgma2.cpp:371:4: warning: missing braces around initializer for 'dist_t [5] {aka float [5]}' [-Wmissing-braces] upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)': upgma2.cpp:292:26: warning: 'dtNewDist' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from muscle.h:34:0, from upgma2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o usage.o usage.cpp In file included from muscle.h:34:0, from usage.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o validateids.o validateids.cpp In file included from muscle.h:34:0, from validateids.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o vtml2.o vtml2.cpp In file included from muscle.h:34:0, from vtml2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o writescorefile.o writescorefile.cpp writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)': writescorefile.cpp:40:17: warning: 'Score' may be used uninitialized in this function [-Wmaybe-uninitialized] writescorefile.cpp:27:11: note: 'Score' was declared here In file included from muscle.h:34:0, from writescorefile.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -Wl,-z,relro -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 globalsosx.o globalsother.o globalswin32.o gonnet.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 fakeroot debian/rules binary test -x debian/rules dh_testroot dh_prep dh_installdirs -A mkdir -p "." g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -Wl,-z,relro -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 globalsosx.o globalsother.o globalswin32.o gonnet.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 Adding cdbs dependencies to debian/muscle.substvars 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_installchangelogs -pmuscle dh_installudev -pmuscle dh_lintian -pmuscle dh_bugfiles -pmuscle dh_install -pmuscle dh_link -pmuscle dh_installmime -pmuscle dh_installgsettings -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 dh_md5sums -pmuscle dh_builddeb -pmuscle dpkg-deb: building package `muscle' in `../muscle_3.8.31-2_amd64.deb'. dpkg-genchanges >../muscle_3.8.31-2_amd64.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build muscle-3.8.31 dpkg-buildpackage: binary and diff upload (original source NOT included) I: Copying back the cached apt archive contents I: unmounting dev/pts filesystem I: unmounting run/shm filesystem I: unmounting proc filesystem I: cleaning the build env I: removing directory /var/cache/pbuilder/build//9504 and its subdirectories I: Current time: Wed Mar 27 08:46:31 CET 2013 Could not read the .changes file: /sw/debian-med/trunk/packages/muscle/build-area/. rm -rf /sw/debian-med/trunk/packages/muscle/build-area/muscle-3.8.31 I: pbuilder-time-stamp: 1364370391