[med-svn] [SCM] clustalx branch, meta, updated. dae5baa41d93c88b4a5bbd3559bec550f7b2b460

[Charles Plessy]

The following commit has been merged in the meta branch:
commit dae5baa41d93c88b4a5bbd3559bec550f7b2b460
Author: Charles Plessy <plessy at debian.org>
Date:   Wed Nov 16 14:48:34 2011 +0900

    Build logs for clustalx_2.1+lgpl-2_amd64.changes.

diff --git a/amd64.log b/amd64.log
index 99ff2d7..7bc7d43 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,23 +1,26 @@
-sbuild (Debian sbuild) 0.60.8 (12 Dec 2010) on aqwa.igloo
+sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on anx191
 
 ╔══════════════════════════════════════════════════════════════════════════════╗
-║ clustalx 2.1+lgpl-1 (amd64)                             27 févr. 2011 22:48 ║
+║ clustalx 2.1+lgpl-2 (amd64)                                16 Nov 2011 14:38 ║
 ╚══════════════════════════════════════════════════════════════════════════════╝
 
 Package: clustalx
-Version: 2.1+lgpl-1
-Source Version: 2.1+lgpl-1
+Version: 2.1+lgpl-2
+Source Version: 2.1+lgpl-2
+Distribution: unstable
 Architecture: amd64
-Get:1 ftp://ftp.jaist.ac.jp sid InRelease [147 kB]
-Get:2 ftp://ftp.jaist.ac.jp sid/main Sources/DiffIndex [2038 B]
-Get:3 ftp://ftp.jaist.ac.jp sid/main amd64 Packages/DiffIndex [2038 B]
-Get:4 ftp://ftp.jaist.ac.jp sid/main TranslationIndex [2232 B]
-Get:5 ftp://ftp.jaist.ac.jp sid/main 2011-02-27-0808.29.pdiff [4073 B]
-Get:6 ftp://ftp.jaist.ac.jp sid/main 2011-02-27-0808.29.pdiff [4073 B]
-Get:7 ftp://ftp.jaist.ac.jp sid/main amd64 2011-02-27-0808.29.pdiff [5573 B]
-Hit ftp://ftp.jaist.ac.jp sid/main Translation-fr
-Get:8 ftp://ftp.jaist.ac.jp sid/main amd64 2011-02-27-0808.29.pdiff [5573 B]
-Fetched 163 kB in 4s (37.9 kB/s)
+
+I: NOTICE: Log filtering will replace 'build/clustalx-1epgPr/clustalx-2.1+lgpl' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/clustalx-1epgPr' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-0602563e-c31d-45b0-b59b-1201327322d7' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot                                                                │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Hit http://ftp.jp.debian.org sid InRelease
+Hit http://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex
+Hit http://ftp.jp.debian.org sid/main TranslationIndex
 Reading package lists...
 Reading package lists...
 Building dependency tree...
@@ -32,433 +35,277 @@ Reading state information...
 Local sources
 ─────────────
 
-clustalx_2.1+lgpl-1.dsc exists in .; copying to chroot
+clustalx_2.1+lgpl-2.dsc exists in .; copying to chroot
 
 Check arch
 ──────────
 
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-9yaGQ0/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Reading package lists...
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver)                          │
+│ Install core build dependencies (apt-based resolver)                         │
 └──────────────────────────────────────────────────────────────────────────────┘
 
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
-Checking for dependency conflicts...
-Installing positive dependencies: 
+Installing build dependencies
 Reading package lists...
 Building dependency tree...
 Reading state information...
+sbuild-build-depends-core-dummy is already the newest version.
 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Removing negative dependencies: 
+Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), libqt4-dev
+Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), libqt4-dev
+dpkg-deb: building package `sbuild-build-depends-clustalx-dummy' in `/«BUILDDIR»/resolver-i9uyAh/apt_archive/sbuild-build-depends-clustalx-dummy.deb'.
+OK
 Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Checking correctness of dependencies...
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install clustalx build dependencies (internal resolver)                      │
+│ Install clustalx build dependencies (apt-based resolver)                     │
 └──────────────────────────────────────────────────────────────────────────────┘
 
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), libqt4-dev, quilt
-Checking for already installed dependencies...
-base-files: already installed (6.1)
-base-passwd: already installed (3.5.22)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
-e2fsprogs: already installed (1.41.12-2)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
-gzip: already installed (1.3.12-9)
-hostname: already installed (3.05)
-ncurses-base: already installed (5.7+20100313-5)
-ncurses-bin: already installed (5.7+20100313-5)
-perl-base: already installed (5.10.1-17)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 8.1.2
-libqt4-dev: missing
-quilt: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper libqt4-dev quilt
+Installing build dependencies
 Reading package lists...
 Building dependency tree...
 Reading state information...
 The following extra packages will be installed:
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-  po-debconf qt4-qmake ttf-dejavu-core ucf x11-common
+  debhelper file fontconfig fontconfig-config gettext gettext-base groff-base
+  html2text intltool-debian libaudio2 libcroco3 libdbus-1-3 libexpat1
+  libfontconfig1 libfreetype6 libglib2.0-0 libice6 libjpeg8 liblcms1 libmagic1
+  libmng1 libpcre3 libpipeline1 libqt4-dbus libqt4-declarative libqt4-designer
+  libqt4-dev libqt4-help libqt4-network libqt4-qt3support libqt4-script
+  libqt4-scripttools libqt4-sql libqt4-svg libqt4-test libqt4-xml
+  libqt4-xmlpatterns libqtcore4 libqtgui4 libsm6 libtiff4 libunistring0
+  libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1
+  libxt6 man-db po-debconf qt4-linguist-tools qt4-qmake ttf-dejavu-core ucf
+  x11-common
 Suggested packages:
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-  libasound2-plugins nas liblcms-utils pulseaudio qt4-dev-tools qt4-doc
-  libmysqlclient-dev libsqlite0-dev libsqlite3-dev libpq-dev unixodbc-dev
-  firebird2.1-dev less www-browser libmail-box-perl procmail graphviz
+  dh-make defoma gettext-doc groff nas liblcms-utils
+  libqt4-declarative-folderlistmodel libqt4-declarative-gestures
+  libqt4-declarative-particles qt4-qmlviewer firebird2.1-dev
+  libmysqlclient-dev libpq-dev libsqlite0-dev libsqlite3-dev qt4-dev-tools
+  qt4-doc unixodbc-dev qt4-qtconfig less www-browser libmail-box-perl
 Recommended packages:
   curl wget lynx-cur autopoint dbus libglib2.0-data shared-mime-info
-  libqt4-opengl-dev libqt4-sql-mysql libqt4-sql-odbc libqt4-sql-psql
-  libqt4-sql-sqlite libqt4-sql-sqlite2 libqt4-sql-ibase libcups2 qt4-qtconfig
-  tcpd xml-core libmail-sendmail-perl
+  libqt4-opengl-dev libqtwebkit-dev libqt4-sql-mysql libqt4-sql-odbc
+  libqt4-sql-psql libqt4-sql-sqlite libqt4-sql-sqlite2 libqt4-sql-ibase
+  libcups2 xml-core libmail-sendmail-perl
 The following NEW packages will be installed:
-  bsdmainutils debhelper diffstat file fontconfig fontconfig-config gettext
-  gettext-base groff-base html2text intltool-debian libasound2 libasyncns0
-  libaudio2 libcap2 libcroco3 libdbus-1-3 libexpat1 libflac8 libfontconfig1
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-  libxrender1 libxt6 libxtst6 man-db po-debconf qt4-qmake quilt
-  ttf-dejavu-core ucf x11-common
-0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded.
-Need to get 38.1 MB/50.1 MB of archives.
-After this operation, 141 MB of additional disk space will be used.
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+  debhelper file fontconfig fontconfig-config gettext gettext-base groff-base
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 Moving old data out of the way
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 Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
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 Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
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 Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
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+Setting up x11-common (1:7.6+9) ...
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+invoke-rc.d: policy-rc.d denied execution of start.
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+Setting up libaudio2 (1.9.3-1) ...
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+No schema files found: doing nothing.
+Setting up libxml2 (2.7.8.dfsg-5) ...
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+Setting up libdbus-1-3 (1.4.16-1) ...
+Setting up libexpat1 (2.0.1-7.2) ...
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+Setting up ucf (3.0025+nmu2) ...
+Setting up ttf-dejavu-core (2.33-2) ...
+Setting up fontconfig-config (2.8.0-3) ...
+Setting up libfontconfig1 (2.8.0-3) ...
+Setting up libjpeg8 (8c-2) ...
+Setting up liblcms1 (1.19.dfsg-1+b1) ...
+Setting up libmng1 (1.0.10-3) ...
+Setting up libtiff4 (3.9.5-2) ...
+Setting up libunistring0 (0.9.3-5) ...
+Setting up libxext6 (2:1.3.0-3) ...
+Setting up libxrender1 (1:0.9.6-2) ...
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.0.2-3) ...
 Building database of manual pages ...
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-Setting up ucf (3.0025+nmu1) ...
-debconf: unable to initialize frontend: Dialog
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+Setting up libmagic1 (5.09-2) ...
+Setting up file (5.09-2) ...
+Setting up gettext-base (0.18.1.1-5) ...
 Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
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-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-5) ...
 Setting up intltool-debian (0.35.0+20060710.1) ...
 Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
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-Setting up ttf-dejavu-core (2.32-1) ...
-Setting up fontconfig-config (2.8.0-2.1) ...
-debconf: unable to initialize frontend: Dialog
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-Setting up libfontconfig1 (2.8.0-2.1) ...
-Setting up fontconfig (2.8.0-2.1) ...
+Setting up debhelper (8.9.9) ...
+Setting up fontconfig (2.8.0-3) ...
 Cleaning up old fontconfig caches... done.
 Regenerating fonts cache... done.
-Setting up libasound2 (1.0.23-2.1) ...
-Setting up libasyncns0 (0.3-1.1) ...
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-Setting up x11-common (1:7.6+4) ...
-debconf: unable to initialize frontend: Dialog
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-All runlevel operations denied by policy
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-Setting up libice6 (2:1.0.7-1) ...
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-Setting up libqt4-help (4:4.6.3-4) ...
-Setting up libqt4-test (4:4.6.3-4) ...
-Setting up libqt4-multimedia (4:4.6.3-4) ...
-Setting up qt4-qmake (4:4.6.3-4) ...
+Setting up libqtcore4 (4:4.7.3-8) ...
+Setting up libqt4-xml (4:4.7.3-8) ...
+Setting up libqt4-dbus (4:4.7.3-8) ...
+Setting up libqt4-network (4:4.7.3-8) ...
+Setting up libqt4-script (4:4.7.3-8) ...
+Setting up libqt4-sql (4:4.7.3-8) ...
+Setting up libqt4-xmlpatterns (4:4.7.3-8) ...
+Setting up libqtgui4 (4:4.7.3-8) ...
+Setting up libqt4-declarative (4:4.7.3-8) ...
+Setting up libqt4-designer (4:4.7.3-8) ...
+Setting up libqt4-help (4:4.7.3-8) ...
+Setting up libqt4-qt3support (4:4.7.3-8) ...
+Setting up libqt4-scripttools (4:4.7.3-8) ...
+Setting up libqt4-svg (4:4.7.3-8) ...
+Setting up libqt4-test (4:4.7.3-8) ...
+Setting up qt4-linguist-tools (4:4.7.3-8) ...
+update-alternatives: using /usr/bin/lupdate-qt4 to provide /usr/bin/lupdate (lupdate) in auto mode.
+update-alternatives: using /usr/bin/lrelease-qt4 to provide /usr/bin/lrelease (lrelease) in auto mode.
+Setting up qt4-qmake (4:4.7.3-8) ...
 update-alternatives: using /usr/bin/qmake-qt4 to provide /usr/bin/qmake (qmake) in auto mode.
-Setting up libqt4-dev (4:4.6.3-4) ...
+Setting up libqt4-dev (4:4.7.3-8) ...
 update-alternatives: using /usr/bin/moc-qt4 to provide /usr/bin/moc (moc) in auto mode.
 update-alternatives: using /usr/bin/uic-qt4 to provide /usr/bin/uic (uic) in auto mode.
 update-alternatives: warning: skip creation of /usr/share/man/man1/uic.1.gz because associated file /usr/share/man/man1/uic-qt4.1.gz (of link group uic) doesn't exist.
-update-alternatives: using /usr/bin/lupdate-qt4 to provide /usr/bin/lupdate (lupdate) in auto mode.
-update-alternatives: using /usr/bin/lrelease-qt4 to provide /usr/bin/lrelease (lrelease) in auto mode.
-Setting up quilt (0.48-7) ...
-Removing negative dependencies: 
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.21.0.20110216-2 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-12 gcc-4.4_4.4.5-12 libc6-dev_2.11.2-11 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-12 linux-libc-dev_2.6.37-1
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-12 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 g++_4:4.4.5-2 g++-4.4_4.4.5-12 gcc_4:4.4.5-2 gcc-4.4_4.4.5-12 gcc-4.4-base_4.4.5-12 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libasound2_1.0.23-2.1 libasyncns0_0.3-1.1 libattr1_1:2.4.44-2 libaudio2_1.9.2-4 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcap2_1:2.20-1 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdbus-1-3_1.4.6-1 libdpkg-perl_1.15.8.10 libexpat1_2.0.1-7 libflac8_1.2.1-3 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.4-1 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 libice6_2:1.0.7-1 libjpeg62_6b1-1 liblcms1_1.18.dfsg-1.2+b3 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmng1_1.0.10-1+b1 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libogg0_1.2.0~dfsg-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libphonon4_4:4.6.0really4.4.2-1 libpipeline1_1.1.0-1 libpng12-0_1.2.44-1 libpulse-mainloop-glib0_0.9.21-4 libpulse0_0.9.21-4 libqt4-assistant_4:4.6.3-4 libqt4-dbus_4:4.6.3-4 libqt4-designer_4:4.6.3-4 libqt4-dev_4:4.6.3-4 libqt4-help_4:4.6.3-4 libqt4-multimedia_4:4.6.3-4 libqt4-network_4:4.6.3-4 libqt4-qt3support_4:4.6.3-4 libqt4-script_4:4.6.3-4 libqt4-scripttools_4:4.6.3-4 libqt4-sql_4:4.6.3-4 libqt4-svg_4:4.6.3-4 libqt4-test_4:4.6.3-4 libqt4-webkit_4:4.6.3-4 libqt4-xml_4:4.6.3-4 libqt4-xmlpatterns_4:4.6.3-4 libqtcore4_4:4.6.3-4 libqtgui4_4:4.6.3-4 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libsm6_2:1.2.0-1 libsndfile1_1.0.23-1 libsqlite3-0_3.7.5-1 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-12 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtiff4_3.9.4-5 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libvorbis0a_1.3.2-1 libvorbisenc2_1.3.2-1 libwrap0_7.6.q-19 libx11-6_2:1.4.1-5 libx11-data_2:1.4.1-5 libxau6_1:1.0.6-1 libxcb1_1.7-2 libxdmcp6_1:1.1.0-1 libxext6_2:1.2.0-2 libxi6_2:1.4.1-1 libxml2_2.7.8.dfsg-2 libxrender1_1:0.9.6-1 libxt6_1:1.0.9-2 libxtst6_2:1.2.0-1 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 qt4-qmake_4:4.6.3-4 quilt_0.48-7 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 ttf-dejavu-core_2.32-1 tzdata_2011b-2 ucf_3.0025+nmu1 util-linux_2.17.2-9.1 x11-common_1:7.6+4 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3
+Setting up sbuild-build-depends-clustalx-dummy (0.invalid.0) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment                                                            │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 2.6.39-bpo.2-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.1.1-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libaudio2_1.9.3-1 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 libgpm2_1.20.4-4 libice6_2:1.0.7-2 libjpeg8_8c-2 liblcms1_1.19.dfsg-1+b1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmng1_1.0.10-3 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libpod-plainer-perl_1.03-1 libqt4-dbus_4:4.7.3-8 libqt4-declarative_4:4.7.3-8 libqt4-designer_4:4.7.3-8 libqt4-dev_4:4.7.3-8 libqt4-help_4:4.7.3-8 libqt4-network_4:4.7.3-8 libqt4-qt3support_4:4.7.3-8 libqt4-script_4:4.7.3-8 libqt4-scripttools_4:4.7.3-8 libqt4-sql_4:4.7.3-8 libqt4-svg_4:4.7.3-8 libqt4-test_4:4.7.3-8 libqt4-xml_4:4.7.3-8 libqt4-xmlpatterns_4:4.7.3-8 libqtcore4_4:4.7.3-8 libqtgui4_4:4.7.3-8 libquadmath0_4.6.2-4 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsm6_2:1.2.0-2 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libx11-6_2:1.4.4-4 libx11-data_2:1.4.4-4 libxau6_1:1.0.6-4 libxcb1_1.7-4 libxdmcp6_1:1.1.0-4 libxext6_2:1.3.0-3 libxml2_2.7.8.dfsg-5 libxrender1_1:0.9.6-2 libxt6_1:1.1.1-2 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 po-debconf_1.0.16+nmu1 qt4-linguist-tools_4:4.7.3-8 qt4-qmake_4:4.7.3-8 readline-common_6.2-7 sbuild-build-depends-clustalx-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 ttf-dejavu-core_2.33-2 tzdata_2011n-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 x11-common_1:7.6+9 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
 │ Build                                                                        │
@@ -468,317 +315,337 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
 Unpack source
 ─────────────
 
-dpkg-source: warning: extracting unsigned source package (clustalx_2.1+lgpl-1.dsc)
+dpkg-source: warning: extracting unsigned source package (clustalx_2.1+lgpl-2.dsc)
 dpkg-source: info: extracting clustalx in clustalx-2.1+lgpl
 dpkg-source: info: unpacking clustalx_2.1+lgpl.orig.tar.gz
-dpkg-source: info: unpacking clustalx_2.1+lgpl-1.debian.tar.gz
+dpkg-source: info: unpacking clustalx_2.1+lgpl-2.debian.tar.gz
 dpkg-source: info: applying hardcode-accessory-file-locations.patch
 
 Check disc space
 ────────────────
 
+Sufficient free space for build
+
+User Environment
+────────────────
+
+HOME=/sbuild-nonexistent
+LOGNAME=charles
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_CHROOT_NAME=sid-amd64-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1000
+SCHROOT_GROUP=charles
+SCHROOT_SESSION_ID=sid-amd64-sbuild-0602563e-c31d-45b0-b59b-1201327322d7
+SCHROOT_UID=31051
+SCHROOT_USER=charles
+SHELL=/bin/sh
+TERM=xterm
+USER=charles
+USERNAME=charles
 
 dpkg-buildpackage
 ─────────────────
 
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): 
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): 
 dpkg-buildpackage: source package clustalx
-dpkg-buildpackage: source version 2.1+lgpl-1
+dpkg-buildpackage: source version 2.1+lgpl-2
 dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
  dpkg-source --before-build clustalx-2.1+lgpl
 dpkg-buildpackage: host architecture amd64
  fakeroot debian/rules clean
-QUILT_PATCHES=debian/patches \
-		quilt --quiltrc /dev/null pop -a -R || test $? = 2
-Removing patch hardcode-accessory-file-locations.patch
-Restoring HelpDisplayWidget.cpp
-Restoring ClustalQtParams.h
-
-No patches applied
-rm -rf .pc debian/stamp-patched
-rm -f moc_*
 dh clean
    dh_testdir
    dh_auto_clean
-   dh_clean
+   debian/rules override_dh_clean
+make[1]: Entering directory `/«BUILDDIR»/clustalx-2.1+lgpl'
+rm -f moc_*
+dh_clean
+make[1]: Leaving directory `/«BUILDDIR»/clustalx-2.1+lgpl'
  dpkg-source -b clustalx-2.1+lgpl
 dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: warning: patches have not been applied, applying them now (use --no-preparation to override)
-dpkg-source: info: applying hardcode-accessory-file-locations.patch
 dpkg-source: info: building clustalx using existing ./clustalx_2.1+lgpl.orig.tar.gz
-dpkg-source: info: building clustalx in clustalx_2.1+lgpl-1.debian.tar.gz
-dpkg-source: info: building clustalx in clustalx_2.1+lgpl-1.dsc
+dpkg-source: info: building clustalx in clustalx_2.1+lgpl-2.debian.tar.gz
+dpkg-source: info: building clustalx in clustalx_2.1+lgpl-2.dsc
  debian/rules build
-QUILT_PATCHES=debian/patches \
-		quilt --quiltrc /dev/null push -a || test $? = 2
-File series fully applied, ends at patch hardcode-accessory-file-locations.patch
-touch debian/stamp-patched
-dh_testdir
-qmake-qt4
 dh build
    dh_testdir
-   dh_auto_configure
+   debian/rules override_dh_auto_configure
+make[1]: Entering directory `/«BUILDDIR»/clustalx-2.1+lgpl'
+qmake-qt4
+make[1]: Leaving directory `/«BUILDDIR»/clustalx-2.1+lgpl'
    dh_auto_build
-make[1]: Entering directory `/build/charles-clustalx_2.1+lgpl-1-amd64-UL4EU4/clustalx-2.1+lgpl'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentParameters.o AlignmentParameters.cpp
-AlignmentParameters.cpp:48: warning: unused parameter 'event'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp
+make[1]: Entering directory `/«BUILDDIR»/clustalx-2.1+lgpl'
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentParameters.o AlignmentParameters.cpp
+AlignmentParameters.cpp:48:6: warning: unused parameter 'event' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp
 AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()':
-AlignmentViewerWidget.cpp:588: warning: comparison between signed and unsigned integer expressions
+AlignmentViewerWidget.cpp:588:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()':
-AlignmentViewerWidget.cpp:645: warning: comparison between signed and unsigned integer expressions
-AlignmentViewerWidget.cpp:652: warning: comparison between signed and unsigned integer expressions
+AlignmentViewerWidget.cpp:645:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentViewerWidget.cpp:652:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 AlignmentViewerWidget.cpp: At global scope:
-AlignmentViewerWidget.cpp:781: warning: unused parameter 'event'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentWidget.o AlignmentWidget.cpp
+AlignmentViewerWidget.cpp:781:6: warning: unused parameter 'event' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentWidget.o AlignmentWidget.cpp
 AlignmentWidget.h: In constructor 'AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)':
-AlignmentWidget.h:170: warning: 'AlignmentWidget::blackAndWhite' will be initialized after
-AlignmentWidget.h:161: warning:   'std::vector<QPixmap, std::allocator<QPixmap> >* AlignmentWidget::selectedColoredRes'
-AlignmentWidget.cpp:65: warning:   when initialized here
+AlignmentWidget.h:170:10: warning: 'AlignmentWidget::blackAndWhite' will be initialized after [-Wreorder]
+AlignmentWidget.h:161:27: warning:   'std::vector<QPixmap, std::allocator<QPixmap> >* AlignmentWidget::selectedColoredRes' [-Wreorder]
+AlignmentWidget.cpp:65:1: warning:   when initialized here [-Wreorder]
 AlignmentWidget.cpp: In member function 'void AlignmentWidget::calculatePixMaps()':
-AlignmentWidget.cpp:225: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:235: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:268: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:280: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:291: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:215: warning: unused variable 'codeForSpace'
+AlignmentWidget.cpp:225:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:235:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:268:78: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:280:81: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:291:88: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable]
 AlignmentWidget.cpp: In member function 'void AlignmentWidget::generateSecStructurePixmaps()':
-AlignmentWidget.cpp:333: warning: comparison between signed and unsigned integer expressions
+AlignmentWidget.cpp:333:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 AlignmentWidget.cpp: In member function 'void AlignmentWidget::drawContents(QPainter*, int, int, int, int)':
-AlignmentWidget.cpp:569: warning: comparison between signed and unsigned integer expressions
+AlignmentWidget.cpp:569:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()':
-AlignmentWidget.cpp:689: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:693: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:700: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:701: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:725: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:737: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:760: warning: comparison between signed and unsigned integer expressions
-AlignmentWidget.cpp:771: warning: comparison between signed and unsigned integer expressions
+AlignmentWidget.cpp:689:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:693:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:700:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:701:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:725:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:737:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:760:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+AlignmentWidget.cpp:771:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 AlignmentWidget.cpp: In member function 'void AlignmentWidget::makeColorMask(clustalw::Array2D<int>*, ColorParameters*)':
-AlignmentWidget.cpp:878: warning: comparison between signed and unsigned integer expressions
+AlignmentWidget.cpp:878:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()':
-AlignmentWidget.cpp:927: warning: comparison between signed and unsigned integer expressions
+AlignmentWidget.cpp:927:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()':
-AlignmentWidget.cpp:1039: warning: comparison between signed and unsigned integer expressions
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignOutputFileNames.o AlignOutputFileNames.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ColorFileXmlParser.o ColorFileXmlParser.cpp
-ColorFileXmlParser.cpp:74:13: warning: multi-line comment
-ColorFileXmlParser.cpp:84: warning: unused parameter 'parentItem'
-ColorFileXmlParser.cpp:138: warning: unused parameter 'parentItem'
-ColorFileXmlParser.cpp:175: warning: unused parameter 'parentItem'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ColorParameters.o ColorParameters.cpp
+AlignmentWidget.cpp:1039:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignOutputFileNames.o AlignOutputFileNames.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ColorFileXmlParser.o ColorFileXmlParser.cpp
+ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment]
+ColorFileXmlParser.cpp:84:5: warning: unused parameter 'parentItem' [-Wunused-parameter]
+ColorFileXmlParser.cpp:138:6: warning: unused parameter 'parentItem' [-Wunused-parameter]
+ColorFileXmlParser.cpp:175:5: warning: unused parameter 'parentItem' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ColorParameters.o ColorParameters.cpp
 ColorParameters.cpp: In member function 'QColor ColorParameters::getResidueColor(QChar, QChar)':
-ColorParameters.cpp:160: warning: comparison between signed and unsigned integer expressions
-ColorParameters.cpp:174: warning: unused variable 'temp'
-ColorParameters.cpp:157: warning: unused variable 'showRes'
-ColorParameters.cpp:158: warning: unused variable 'showCon'
+ColorParameters.cpp:160:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ColorParameters.cpp:174:26: warning: unused variable 'temp' [-Wunused-variable]
+ColorParameters.cpp:157:10: warning: unused variable 'showRes' [-Wunused-variable]
+ColorParameters.cpp:158:10: warning: unused variable 'showCon' [-Wunused-variable]
 ColorParameters.cpp: In member function 'int ColorParameters::getResidueColorNum(QChar, QChar)':
-ColorParameters.cpp:197: warning: comparison between signed and unsigned integer expressions
-ColorParameters.cpp:211: warning: unused variable 'temp'
-ColorParameters.cpp:194: warning: unused variable 'showRes'
-ColorParameters.cpp:195: warning: unused variable 'showCon'
+ColorParameters.cpp:197:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ColorParameters.cpp:211:26: warning: unused variable 'temp' [-Wunused-variable]
+ColorParameters.cpp:194:10: warning: unused variable 'showRes' [-Wunused-variable]
+ColorParameters.cpp:195:10: warning: unused variable 'showCon' [-Wunused-variable]
 ColorParameters.cpp: In member function 'void ColorParameters::printColorInfo()':
-ColorParameters.cpp:229: warning: comparison between signed and unsigned integer expressions
+ColorParameters.cpp:229:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 ColorParameters.cpp: In member function 'int ColorParameters::getIndexOfColor(QColor)':
-ColorParameters.cpp:238: warning: comparison between signed and unsigned integer expressions
+ColorParameters.cpp:238:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 ColorParameters.cpp: In member function 'QColor ColorParameters::getColorFromNum(int)':
-ColorParameters.cpp:251: warning: comparison between signed and unsigned integer expressions
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ColumnScoreParams.o ColumnScoreParams.cpp
-ColumnScoreParams.cpp:51: warning: unused parameter 'event'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FileDialog.o FileDialog.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o HardCodedColorScheme.o HardCodedColorScheme.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o HelpDisplayWidget.o HelpDisplayWidget.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o HistogramWidget.o HistogramWidget.cpp
+ColorParameters.cpp:251:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ColumnScoreParams.o ColumnScoreParams.cpp
+ColumnScoreParams.cpp:51:6: warning: unused parameter 'event' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FileDialog.o FileDialog.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o HardCodedColorScheme.o HardCodedColorScheme.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o HelpDisplayWidget.o HelpDisplayWidget.cpp
+HelpDisplayWidget.cpp: In member function 'std::string* HelpDisplayWidget::loadHelpInformation(char)':
+HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o HistogramWidget.o HistogramWidget.cpp
 HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)':
-HistogramWidget.cpp:180: warning: comparison between signed and unsigned integer expressions
-HistogramWidget.cpp:198: warning: comparison between signed and unsigned integer expressions
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o KeyController.o KeyController.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o LowScoringSegParams.o LowScoringSegParams.cpp
-LowScoringSegParams.cpp:51: warning: unused parameter 'event'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o main.o main.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o mainwindow.o mainwindow.cpp
-mainwindow.cpp:198: warning: unused parameter 'event'
-mainwindow.cpp:1454: warning: unused parameter 'type'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PairwiseParams.o PairwiseParams.cpp
-PairwiseParams.cpp:74: warning: unused parameter 'event'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PostscriptFileParams.o PostscriptFileParams.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProteinGapParameters.o ProteinGapParameters.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PSPrinter.o PSPrinter.cpp
+HistogramWidget.cpp:180:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+HistogramWidget.cpp:198:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o KeyController.o KeyController.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o LowScoringSegParams.o LowScoringSegParams.cpp
+LowScoringSegParams.cpp:51:6: warning: unused parameter 'event' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o main.o main.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o mainwindow.o mainwindow.cpp
+mainwindow.cpp:198:6: warning: unused parameter 'event' [-Wunused-parameter]
+mainwindow.cpp:1454:6: warning: unused parameter 'type' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PairwiseParams.o PairwiseParams.cpp
+PairwiseParams.cpp:74:6: warning: unused parameter 'event' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PostscriptFileParams.o PostscriptFileParams.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProteinGapParameters.o ProteinGapParameters.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PSPrinter.o PSPrinter.cpp
 PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)':
-PSPrinter.cpp:207: warning: comparison between signed and unsigned integer expressions
-PSPrinter.cpp:307: warning: comparison between signed and unsigned integer expressions
-PSPrinter.cpp:421: warning: comparison between signed and unsigned integer expressions
-PSPrinter.cpp:55: warning: unused variable 'err'
-PSPrinter.cpp:73: warning: unused variable 'gapPos1'
-PSPrinter.cpp:74: warning: unused variable 'gapPos2'
+PSPrinter.cpp:207:67: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+PSPrinter.cpp:307:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+PSPrinter.cpp:421:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable]
+PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable]
+PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable]
 PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)':
-PSPrinter.cpp:587: warning: comparison between signed and unsigned integer expressions
+PSPrinter.cpp:587:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)':
-PSPrinter.cpp:730: warning: comparison between signed and unsigned integer expressions
+PSPrinter.cpp:730:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)':
-PSPrinter.cpp:789: warning: comparison between signed and unsigned integer expressions
-PSPrinter.cpp:781: warning: unused variable 'psY'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o QTUtility.o QTUtility.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Resources.o Resources.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SaveSeqFile.o SaveSeqFile.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SearchForString.o SearchForString.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SecStructOptions.o SecStructOptions.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SeqNameWidget.o SeqNameWidget.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o TreeFormatOptions.o TreeFormatOptions.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o TreeOutputFileNames.o TreeOutputFileNames.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o WritePostscriptFile.o WritePostscriptFile.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Clustal.o clustalW/Clustal.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Help.o clustalW/Help.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Alignment.o clustalW/alignment/Alignment.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Sequence.o clustalW/alignment/Sequence.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FileParser.o clustalW/fileInput/FileParser.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FileReader.o clustalW/fileInput/FileReader.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o InFileStream.o clustalW/fileInput/InFileStream.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp
-clustalW/fileInput/MSFFileParser.cpp:34: warning: unused parameter 'offendingSeq'
-clustalW/fileInput/MSFFileParser.cpp:246: warning: unused parameter 'gapPenaltyMask'
-clustalW/fileInput/MSFFileParser.cpp:246: warning: unused parameter 'secStructMask'
-clustalW/fileInput/MSFFileParser.cpp:246: warning: unused parameter 'secStructName'
-clustalW/fileInput/MSFFileParser.cpp:246: warning: unused parameter 'length'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp
-clustalW/fileInput/PearsonFileParser.cpp:199: warning: unused parameter 'offendingSeq'
-clustalW/fileInput/PearsonFileParser.cpp:444: warning: unused parameter 'gapPenaltyMask'
-clustalW/fileInput/PearsonFileParser.cpp:444: warning: unused parameter 'secStructMask'
-clustalW/fileInput/PearsonFileParser.cpp:444: warning: unused parameter 'secStructName'
-clustalW/fileInput/PearsonFileParser.cpp:444: warning: unused parameter 'length'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp
-clustalW/fileInput/PIRFileParser.cpp:292: warning: unused parameter 'gapPenaltyMask'
-clustalW/fileInput/PIRFileParser.cpp:292: warning: unused parameter 'secStructMask'
-clustalW/fileInput/PIRFileParser.cpp:292: warning: unused parameter 'secStructName'
-clustalW/fileInput/PIRFileParser.cpp:292: warning: unused parameter 'length'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp
-clustalW/fileInput/RSFFileParser.cpp:240: warning: unused parameter 'gapPenaltyMask'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClustalWResources.o clustalW/general/ClustalWResources.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o DebugLog.o clustalW/general/DebugLog.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o OutputFile.o clustalW/general/OutputFile.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Stats.o clustalW/general/Stats.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SymMatrix.o clustalW/general/SymMatrix.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o UserParameters.o clustalW/general/UserParameters.cpp
-clustalW/general/UserParameters.cpp:33: warning: unused parameter 'log'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Utility.o clustalW/general/Utility.cpp
-clustalW/general/Utility.cpp:519: warning: unused parameter 'ptrToLabelObj'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Iteration.o clustalW/multipleAlign/Iteration.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o MSA.o clustalW/multipleAlign/MSA.cpp
-clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int, std::allocator<int> >*, clustalw::AlignmentSteps*, int)':
-clustalW/multipleAlign/MSA.cpp:340: warning: unused variable 'alignmentScore'
+PSPrinter.cpp:789:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o QTUtility.o QTUtility.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Resources.o Resources.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SaveSeqFile.o SaveSeqFile.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SearchForString.o SearchForString.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SecStructOptions.o SecStructOptions.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SeqNameWidget.o SeqNameWidget.cpp
+SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)':
+SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o TreeFormatOptions.o TreeFormatOptions.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o TreeOutputFileNames.o TreeOutputFileNames.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o WritePostscriptFile.o WritePostscriptFile.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Clustal.o clustalW/Clustal.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Help.o clustalW/Help.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Alignment.o clustalW/alignment/Alignment.cpp
+clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
+clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Sequence.o clustalW/alignment/Sequence.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FileParser.o clustalW/fileInput/FileParser.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FileReader.o clustalW/fileInput/FileReader.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o InFileStream.o clustalW/fileInput/InFileStream.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp
+clustalW/fileInput/MSFFileParser.cpp:34:22: warning: unused parameter 'offendingSeq' [-Wunused-parameter]
+clustalW/fileInput/MSFFileParser.cpp:246:6: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
+clustalW/fileInput/MSFFileParser.cpp:246:6: warning: unused parameter 'secStructMask' [-Wunused-parameter]
+clustalW/fileInput/MSFFileParser.cpp:246:6: warning: unused parameter 'secStructName' [-Wunused-parameter]
+clustalW/fileInput/MSFFileParser.cpp:246:6: warning: unused parameter 'length' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp
+clustalW/fileInput/PearsonFileParser.cpp:199:14: warning: unused parameter 'offendingSeq' [-Wunused-parameter]
+clustalW/fileInput/PearsonFileParser.cpp:444:6: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
+clustalW/fileInput/PearsonFileParser.cpp:444:6: warning: unused parameter 'secStructMask' [-Wunused-parameter]
+clustalW/fileInput/PearsonFileParser.cpp:444:6: warning: unused parameter 'secStructName' [-Wunused-parameter]
+clustalW/fileInput/PearsonFileParser.cpp:444:6: warning: unused parameter 'length' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp
+clustalW/fileInput/PIRFileParser.cpp:292:6: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
+clustalW/fileInput/PIRFileParser.cpp:292:6: warning: unused parameter 'secStructMask' [-Wunused-parameter]
+clustalW/fileInput/PIRFileParser.cpp:292:6: warning: unused parameter 'secStructName' [-Wunused-parameter]
+clustalW/fileInput/PIRFileParser.cpp:292:6: warning: unused parameter 'length' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp
+clustalW/fileInput/RSFFileParser.cpp:240:6: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClustalWResources.o clustalW/general/ClustalWResources.cpp
+clustalW/general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const':
+clustalW/general/ClustalWResources.cpp:106:12: warning: array subscript is above array bounds [-Warray-bounds]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o DebugLog.o clustalW/general/DebugLog.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o OutputFile.o clustalW/general/OutputFile.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Stats.o clustalW/general/Stats.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SymMatrix.o clustalW/general/SymMatrix.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o UserParameters.o clustalW/general/UserParameters.cpp
+clustalW/general/UserParameters.cpp:33:1: warning: unused parameter 'log' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Utility.o clustalW/general/Utility.cpp
+clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
+clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
+clustalW/general/Utility.cpp: At global scope:
+clustalW/general/Utility.cpp:519:6: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Iteration.o clustalW/multipleAlign/Iteration.cpp
+clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
+clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o MSA.o clustalW/multipleAlign/MSA.cpp
+clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, clustalw::AlignmentSteps*, int)':
+clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
 clustalW/multipleAlign/MSA.cpp: At global scope:
-clustalW/multipleAlign/MSA.cpp:358: warning: unused parameter 'phylipName'
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp
-clustalW/substitutionMatrix/SubMatrix.cpp:1613: warning: unused parameter 'alignResidueType'
-clustalW/substitutionMatrix/SubMatrix.cpp:1613: warning: unused parameter 'alignType'
+clustalW/multipleAlign/MSA.cpp:358:5: warning: unused parameter 'phylipName' [-Wunused-parameter]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp
+clustalW/substitutionMatrix/SubMatrix.cpp:1613:6: warning: unused parameter 'alignResidueType' [-Wunused-parameter]
+clustalW/substitutionMatrix/SubMatrix.cpp:1613:6: warning: unused parameter 'alignType' [-Wunused-parameter]
+clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])':
+clustalW/substitutionMatrix/SubMatrix.cpp:1657:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
+clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])':
+clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
 clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
-clustalW/substitutionMatrix/SubMatrix.cpp:998: warning: 'n' may be used uninitialized in this function
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClusterTree.o clustalW/tree/ClusterTree.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp
-clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printPhylipTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int, std::allocator<int> >*)':
-clustalW/tree/../alignment/../general/SymMatrix.h:183: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false
-clustalW/tree/../alignment/../general/SymMatrix.h:183: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false
-clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printNexusTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int, std::allocator<int> >*)':
-clustalW/tree/../alignment/../general/SymMatrix.h:183: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o NJTree.o clustalW/tree/NJTree.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Tree.o clustalW/tree/Tree.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o TreeInterface.o clustalW/tree/TreeInterface.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp
+clustalW/substitutionMatrix/SubMatrix.cpp:998:9: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClusterTree.o clustalW/tree/ClusterTree.cpp
+clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
+clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
+clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp
+clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printPhylipTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*)':
+clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
+clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
+clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printNexusTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*)':
+clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
+clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o NJTree.o clustalW/tree/NJTree.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Tree.o clustalW/tree/Tree.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o TreeInterface.o clustalW/tree/TreeInterface.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp
 clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::UnRootedClusterTree::treeFromDistMatrix(clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)':
-clustalW/tree/../alignment/../general/SymMatrix.h:183: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Node.o clustalW/tree/UPGMA/Node.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp
+clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o Node.o clustalW/tree/UPGMA/Node.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp
 clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)':
-clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp
+clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp
 clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printPhylipTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)':
-clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false
-clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false
+clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
+clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
 clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printNexusTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)':
-clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false
-clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentParameters.h -o moc_AlignmentParameters.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentWidget.h -o moc_AlignmentWidget.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ColumnScoreParams.h -o moc_ColumnScoreParams.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. FileDialog.h -o moc_FileDialog.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_FileDialog.o moc_FileDialog.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. HistogramWidget.h -o moc_HistogramWidget.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_HistogramWidget.o moc_HistogramWidget.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. LowScoringSegParams.h -o moc_LowScoringSegParams.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. mainwindow.h -o moc_mainwindow.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_mainwindow.o moc_mainwindow.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. PairwiseParams.h -o moc_PairwiseParams.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PairwiseParams.o moc_PairwiseParams.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ProteinGapParameters.h -o moc_ProteinGapParameters.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. PSPrinter.h -o moc_PSPrinter.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PSPrinter.o moc_PSPrinter.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SaveSeqFile.h -o moc_SaveSeqFile.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SearchForString.h -o moc_SearchForString.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SearchForString.o moc_SearchForString.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SecStructOptions.h -o moc_SecStructOptions.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SecStructOptions.o moc_SecStructOptions.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SeqNameWidget.h -o moc_SeqNameWidget.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. TreeFormatOptions.h -o moc_TreeFormatOptions.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. TreeOutputFileNames.h -o moc_TreeOutputFileNames.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp
-/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. WritePostscriptFile.h -o moc_WritePostscriptFile.cpp
-g++ -c -pipe -g -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp
-g++ -Wl,-O1 -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o    -L/usr/lib -lQtXml -lQtGui -lQtCore -lpthread 
-Iteration.o: In function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
-/build/charles-clustalx_2.1+lgpl-1-amd64-UL4EU4/clustalx-2.1+lgpl/clustalW/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
-make[1]: Leaving directory `/build/charles-clustalx_2.1+lgpl-1-amd64-UL4EU4/clustalx-2.1+lgpl'
+clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
+clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentParameters.h -o moc_AlignmentParameters.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignmentWidget.h -o moc_AlignmentWidget.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ColumnScoreParams.h -o moc_ColumnScoreParams.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. FileDialog.h -o moc_FileDialog.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_FileDialog.o moc_FileDialog.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. HistogramWidget.h -o moc_HistogramWidget.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_HistogramWidget.o moc_HistogramWidget.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. LowScoringSegParams.h -o moc_LowScoringSegParams.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. mainwindow.h -o moc_mainwindow.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_mainwindow.o moc_mainwindow.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. PairwiseParams.h -o moc_PairwiseParams.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PairwiseParams.o moc_PairwiseParams.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ProteinGapParameters.h -o moc_ProteinGapParameters.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. PSPrinter.h -o moc_PSPrinter.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PSPrinter.o moc_PSPrinter.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SaveSeqFile.h -o moc_SaveSeqFile.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SearchForString.h -o moc_SearchForString.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SearchForString.o moc_SearchForString.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SecStructOptions.h -o moc_SecStructOptions.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SecStructOptions.o moc_SecStructOptions.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SeqNameWidget.h -o moc_SeqNameWidget.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. TreeFormatOptions.h -o moc_TreeFormatOptions.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. TreeOutputFileNames.h -o moc_TreeOutputFileNames.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp
+/usr/bin/moc-qt4 -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. WritePostscriptFile.h -o moc_WritePostscriptFile.cpp
+g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++-64 -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp
+g++ -m64 -Wl,-O1 -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o    -L/usr/lib -lQtXml -lQtGui -lQtCore -lpthread 
+make[1]: Leaving directory `/«BUILDDIR»/clustalx-2.1+lgpl'
    dh_auto_test
  fakeroot debian/rules binary
-dh_testdir
-qmake-qt4
-dh build
-dh install
+dh binary
    dh_testroot
    dh_prep
    dh_installdirs
@@ -786,9 +653,9 @@ dh install
    dh_install
    dh_installdocs
    debian/rules override_dh_installchangelogs
-make[1]: Entering directory `/build/charles-clustalx_2.1+lgpl-1-amd64-UL4EU4/clustalx-2.1+lgpl'
+make[1]: Entering directory `/«BUILDDIR»/clustalx-2.1+lgpl'
 dh_installchangelogs debian/CHANGELOG.upstream
-make[1]: Leaving directory `/build/charles-clustalx_2.1+lgpl-1-amd64-UL4EU4/clustalx-2.1+lgpl'
+make[1]: Leaving directory `/«BUILDDIR»/clustalx-2.1+lgpl'
    dh_installexamples
    dh_installman
    dh_installcatalogs
@@ -808,7 +675,9 @@ make[1]: Leaving directory `/build/charles-clustalx_2.1+lgpl-1-amd64-UL4EU4/clus
    dh_installudev
    dh_installwm
    dh_installxfonts
+   dh_installgsettings
    dh_bugfiles
+   dh_ucf
    dh_lintian
    dh_gconf
    dh_icons
@@ -817,88 +686,94 @@ make[1]: Leaving directory `/build/charles-clustalx_2.1+lgpl-1-amd64-UL4EU4/clus
    dh_link
    dh_compress
    dh_fixperms
-dh binary-arch
-   dh_strip -a
-   dh_makeshlibs -a
-   dh_shlibdeps -a
-   dh_installdeb -a
-   dh_gencontrol -a
-   dh_md5sums -a
-   dh_builddeb -a
-dpkg-deb: building package `clustalx' in `../clustalx_2.1+lgpl-1_amd64.deb'.
- dpkg-genchanges  >../clustalx_2.1+lgpl-1_amd64.changes
-dpkg-genchanges: including full source code in upload
+   dh_strip
+   dh_makeshlibs
+   dh_shlibdeps
+   dh_installdeb
+   dh_gencontrol
+   dh_md5sums
+   dh_builddeb
+dpkg-deb: building package `clustalx' in `../clustalx_2.1+lgpl-2_amd64.deb'.
+ dpkg-genchanges  >../clustalx_2.1+lgpl-2_amd64.changes
+dpkg-genchanges: not including original source code in upload
  dpkg-source --after-build clustalx-2.1+lgpl
-dpkg-buildpackage: full upload (original source is included)
+dpkg-buildpackage: binary and diff upload (original source NOT included)
 ────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110227-2252
+Build finished at 20111116-1440
+
+Finished
+────────
+
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes                                                                      │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+clustalx_2.1+lgpl-2_amd64.changes:
+──────────────────────────────────
 
-clustalx_2.1+lgpl-1_amd64.changes:
 Format: 1.8
-Date: Sun, 27 Feb 2011 22:36:51 +0900
+Date: Wed, 16 Nov 2011 14:37:03 +0900
 Source: clustalx
 Binary: clustalx
 Architecture: source amd64
-Version: 2.1+lgpl-1
+Version: 2.1+lgpl-2
 Distribution: unstable
 Urgency: low
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Changed-By: Charles Plessy <plessy at debian.org>
 Description: 
  clustalx   - Multiple alignment of nucleic acid and protein sequences (graphic
+Closes: 648812
 Changes: 
- clustalx (2.1+lgpl-1) unstable; urgency=low
+ clustalx (2.1+lgpl-2) unstable; urgency=low
  .
-   * New upstream archive, that makes clear the relicensing to LGPL-3+.
-     - Mangled debian version name in debian/watch.
-     - Explained why ‘+lgpl’ in debian/README.Debian.
-     - Removed XS-Autobuild field from debian/control.
-     - Changed archive area in debian/control.
-     - Updated license in debian/copyright.
-     - Removed Commercial field in debian/upstream-metadata.yaml.
-   * Removed un-needed documentation (debian/clustalx.docs).
-   * Source package hosted in a Git repository (debian/control).
-   * Use debhelper 8 (debian/control, debian/compat).
+   [8b9662e] Update providing upgrade path to backports (Closes: #648812).
+   [727f540] Corrected and normalised copyright file with config-edit.
+   [fa455a0] Conforms to Policy version 3.9.2 (no changes needed).
+   [9cd039b] Updated Homepage.
+   [a36daf1] Rely on dpkg-dev for patching and removed build-dependancy on quilt.
+   [51bde59] Support build-arch and build-indep targets through dh.
+   [c3b9f16] Signal and configure the use of git-buildpackage.
 Checksums-Sha1: 
- adcbc2f88fb947075462fcf410732d1233b85526 1103 clustalx_2.1+lgpl-1.dsc
- 63196a4e113a22e5e575f223d76b7406f4f70795 341649 clustalx_2.1+lgpl.orig.tar.gz
- c92222d36c291cce607dbe40c3539dd44b8e23bf 11667 clustalx_2.1+lgpl-1.debian.tar.gz
- 9d6a70bd7292b5e895bc1983e7bf82407cf23e5f 561624 clustalx_2.1+lgpl-1_amd64.deb
+ b412cf7b42a7585915846e6870442457ba161af6 1151 clustalx_2.1+lgpl-2.dsc
+ 4cc5778da200071be4d231d274d16f6c1e3fa627 11934 clustalx_2.1+lgpl-2.debian.tar.gz
+ 514d598dbef7f65c1b2aa0175574cad3bb008397 569184 clustalx_2.1+lgpl-2_amd64.deb
 Checksums-Sha256: 
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 Files: 
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- 5b1f2f1cc8e939411ab0f934cafa072a 341649 science optional clustalx_2.1+lgpl.orig.tar.gz
- 05b819560ffa9ed8b7b8d24c9049d5f4 11667 science optional clustalx_2.1+lgpl-1.debian.tar.gz
- afc8a9139121cafa899fecdb787467b7 561624 science optional clustalx_2.1+lgpl-1_amd64.deb
+ 448f753d37f80f24ac5a987ffa1d494d 1151 science optional clustalx_2.1+lgpl-2.dsc
+ 770b022f2e09559de22d79a63457a1a1 11934 science optional clustalx_2.1+lgpl-2.debian.tar.gz
+ 78f02c1141ae855ab65e52f4ae32827b 569184 science optional clustalx_2.1+lgpl-2_amd64.deb
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
 │ Package contents                                                             │
 └──────────────────────────────────────────────────────────────────────────────┘
 
 
-clustalx_2.1+lgpl-1_amd64.deb
+clustalx_2.1+lgpl-2_amd64.deb
 ─────────────────────────────
 
  new debian package, version 2.0.
- size 561624 bytes: control archive= 1636 bytes.
-    1502 bytes,    27 lines      control              
+ size 569184 bytes: control archive= 1651 bytes.
+    1509 bytes,    27 lines      control              
      932 bytes,    14 lines      md5sums              
      551 bytes,    17 lines   *  postinst             #!/bin/sh
      467 bytes,    13 lines   *  postrm               #!/bin/sh
  Package: clustalx
- Version: 2.1+lgpl-1
+ Version: 2.1+lgpl-2
  Architecture: amd64
  Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1448
- Depends: libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libqt4-xml (>= 4:4.5.3), libqtcore4 (>= 4:4.6.1), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 4.4.0)
+ Installed-Size: 1376
+ Depends: libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libqt4-xml (>= 4:4.5.3), libqtcore4 (>= 4:4.6.1), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 4.6)
  Suggests: clustalw, texshade | texlive-latex-extra, boxshade
  Section: science
  Priority: optional
- Homepage: http://www.clustal.org/
+ Homepage: http://www.clustal.org/clustal2/
  Description: Multiple alignment of nucleic acid and protein sequences (graphical interface)
   This package offers a GUI interface for the Clustal multiple sequence
   alignment program. It provides an integrated environment for performing
@@ -917,50 +792,56 @@ clustalx_2.1+lgpl-1_amd64.deb
   An alignment quality analysis can be performed and low-scoring segments or
   exceptional residues can be highlighted.
 
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/lib/
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/lib/mime/
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/lib/mime/packages/
--rw-r--r-- root/root       114 2011-02-27 18:56 ./usr/lib/mime/packages/clustalx
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/mime/
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/mime/packages/
--rw-r--r-- root/root       513 2011-02-27 18:56 ./usr/share/mime/packages/clustalx.xml
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/clustalx/
--rw-r--r-- root/root     69428 2010-11-17 19:12 ./usr/share/clustalx/clustalx.hlp
--rw-r--r-- root/root      5047 2010-11-17 19:12 ./usr/share/clustalx/colprot.xml
--rw-r--r-- root/root       847 2010-11-17 19:12 ./usr/share/clustalx/coldna.xml
--rw-r--r-- root/root      1276 2010-11-17 19:12 ./usr/share/clustalx/colprint.xml
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/applications/
--rw-r--r-- root/root       873 2011-02-27 18:56 ./usr/share/applications/clustalx.desktop
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/menu/
--rw-r--r-- root/root       163 2011-02-27 18:56 ./usr/share/menu/clustalx
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/doc/
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/doc/clustalx/
--rw-r--r-- root/root       410 2011-02-27 19:39 ./usr/share/doc/clustalx/README.Debian
--rw-r--r-- root/root      1758 2011-02-27 19:45 ./usr/share/doc/clustalx/copyright
--rw-r--r-- root/root      3440 2011-02-27 18:56 ./usr/share/doc/clustalx/changelog.gz
--rw-r--r-- root/root      3738 2011-02-27 22:37 ./usr/share/doc/clustalx/changelog.Debian.gz
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/man/
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/share/man/man1/
--rw-r--r-- root/root       797 2011-02-27 22:52 ./usr/share/man/man1/clustalx.1.gz
-drwxr-xr-x root/root         0 2011-02-27 22:52 ./usr/bin/
--rwxr-xr-x root/root   1269776 2011-02-27 22:52 ./usr/bin/clustalx
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/lib/
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/lib/mime/
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/lib/mime/packages/
+-rw-r--r-- root/root       114 2011-11-15 18:59 ./usr/lib/mime/packages/clustalx
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/bin/
+-rwxr-xr-x root/root   1249656 2011-11-16 14:40 ./usr/bin/clustalx
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/clustalx/
+-rw-r--r-- root/root      1276 2011-02-27 19:27 ./usr/share/clustalx/colprint.xml
+-rw-r--r-- root/root       847 2011-02-27 19:27 ./usr/share/clustalx/coldna.xml
+-rw-r--r-- root/root      5047 2011-02-27 19:27 ./usr/share/clustalx/colprot.xml
+-rw-r--r-- root/root     69428 2011-02-27 19:27 ./usr/share/clustalx/clustalx.hlp
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/menu/
+-rw-r--r-- root/root       163 2011-11-15 18:59 ./usr/share/menu/clustalx
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/man/
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/man/man1/
+-rw-r--r-- root/root       797 2011-11-16 14:40 ./usr/share/man/man1/clustalx.1.gz
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/applications/
+-rw-r--r-- root/root       873 2011-11-15 18:59 ./usr/share/applications/clustalx.desktop
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/mime/
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/mime/packages/
+-rw-r--r-- root/root       513 2011-11-15 18:59 ./usr/share/mime/packages/clustalx.xml
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/doc/
+drwxr-xr-x root/root         0 2011-11-16 14:40 ./usr/share/doc/clustalx/
+-rw-r--r-- root/root      3440 2011-11-15 18:59 ./usr/share/doc/clustalx/changelog.gz
+-rw-r--r-- root/root      1794 2011-11-16 13:14 ./usr/share/doc/clustalx/copyright
+-rw-r--r-- root/root      3969 2011-11-16 14:37 ./usr/share/doc/clustalx/changelog.Debian.gz
+-rw-r--r-- root/root       410 2011-11-15 18:59 ./usr/share/doc/clustalx/README.Debian
 
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished                                                                     │
+│ Post Build                                                                   │
 └──────────────────────────────────────────────────────────────────────────────┘
 
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
+
+lintian
+───────
+
+P: clustalx source: unversioned-copyright-format-uri http://dep.debian.net/deps/dep5/
+I: clustalx: spelling-error-in-binary usr/bin/clustalx preceeded preceded
+
+I: Lintian run was successful.
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build                                                                   │
+│ Cleanup                                                                      │
 └──────────────────────────────────────────────────────────────────────────────┘
 
-Purging /var/lib/schroot/mount/sid-amd64-sbuild-31872989-3665-48fa-b8a8-c266bc84a9eb/build/charles-clustalx_2.1+lgpl-1-amd64-UL4EU4
+Purging /«BUILDDIR»
 Reading package lists...
 Building dependency tree...
 Reading state information...
@@ -969,52 +850,36 @@ Reading package lists...
 Building dependency tree...
 Reading state information...
 The following packages will be REMOVED:
-  bsdmainutils* debhelper* diffstat* file* fontconfig* fontconfig-config*
-  gettext* gettext-base* groff-base* html2text* intltool-debian* libasound2*
-  libasyncns0* libaudio2* libcap2* libcroco3* libdbus-1-3* libexpat1*
-  libflac8* libfontconfig1* libfreetype6* libglib2.0-0* libice6* libjpeg62*
-  liblcms1* libmagic1* libmng1* libogg0* libpcre3* libphonon4* libpipeline1*
-  libpng12-0* libpulse-mainloop-glib0* libpulse0* libqt4-assistant*
-  libqt4-dbus* libqt4-designer* libqt4-dev* libqt4-help* libqt4-multimedia*
+  debhelper* file* fontconfig* fontconfig-config* gettext* gettext-base*
+  groff-base* html2text* intltool-debian* libaudio2* libcroco3* libdbus-1-3*
+  libexpat1* libfontconfig1* libfreetype6* libglib2.0-0* libice6* libjpeg8*
+  liblcms1* libmagic1* libmng1* libpcre3* libpipeline1* libqt4-dbus*
+  libqt4-declarative* libqt4-designer* libqt4-dev* libqt4-help*
   libqt4-network* libqt4-qt3support* libqt4-script* libqt4-scripttools*
-  libqt4-sql* libqt4-svg* libqt4-test* libqt4-webkit* libqt4-xml*
-  libqt4-xmlpatterns* libqtcore4* libqtgui4* libsm6* libsndfile1*
-  libsqlite3-0* libtiff4* libunistring0* libvorbis0a* libvorbisenc2* libwrap0*
-  libx11-6* libx11-data* libxau6* libxcb1* libxdmcp6* libxext6* libxi6*
-  libxml2* libxrender1* libxt6* libxtst6* man-db* po-debconf* qt4-qmake*
-  quilt* ttf-dejavu-core* ucf* x11-common*
-0 upgraded, 0 newly installed, 78 to remove and 0 not upgraded.
-After this operation, 141 MB disk space will be freed.
-(Reading database ... 15914 files and directories currently installed.)
+  libqt4-sql* libqt4-svg* libqt4-test* libqt4-xml* libqt4-xmlpatterns*
+  libqtcore4* libqtgui4* libsm6* libtiff4* libunistring0* libx11-6*
+  libx11-data* libxau6* libxcb1* libxdmcp6* libxext6* libxml2* libxrender1*
+  libxt6* man-db* po-debconf* qt4-linguist-tools* qt4-qmake*
+  sbuild-build-depends-clustalx-dummy* ttf-dejavu-core* ucf* x11-common*
+0 upgraded, 0 newly installed, 59 to remove and 0 not upgraded.
+After this operation, 123 MB disk space will be freed.
+(Reading database ... 16230 files and directories currently installed.)
+Removing sbuild-build-depends-clustalx-dummy ...
 Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-debconf: unable to initialize frontend: Dialog
-debconf: (TERM is not set, so the dialog frontend is not usable.)
-debconf: falling back to frontend: Readline
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
 Removing file ...
 Removing libqt4-dev ...
-Removing libqt4-webkit ...
-Purging configuration files for libqt4-webkit ...
 Removing libqt4-svg ...
 Purging configuration files for libqt4-svg ...
 Removing libqt4-scripttools ...
 Purging configuration files for libqt4-scripttools ...
 Removing libqt4-qt3support ...
 Purging configuration files for libqt4-qt3support ...
-Removing libqt4-multimedia ...
-Purging configuration files for libqt4-multimedia ...
 Removing libqt4-help ...
 Purging configuration files for libqt4-help ...
 Removing libqt4-designer ...
 Purging configuration files for libqt4-designer ...
-Removing libphonon4 ...
-Purging configuration files for libphonon4 ...
+Removing libqt4-declarative ...
+Purging configuration files for libqt4-declarative ...
 Removing libqtgui4 ...
 Purging configuration files for libqtgui4 ...
 Removing fontconfig ...
@@ -1023,56 +888,40 @@ Removing libfontconfig1 ...
 Purging configuration files for libfontconfig1 ...
 Removing fontconfig-config ...
 Purging configuration files for fontconfig-config ...
-debconf: unable to initialize frontend: Dialog
-debconf: (TERM is not set, so the dialog frontend is not usable.)
-debconf: falling back to frontend: Readline
 Removing po-debconf ...
 Removing intltool-debian ...
 Removing gettext ...
 Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
 Removing groff-base ...
 Purging configuration files for groff-base ...
 Removing html2text ...
 Purging configuration files for html2text ...
-Removing libasound2 ...
-Purging configuration files for libasound2 ...
-Removing libpulse-mainloop-glib0 ...
-Purging configuration files for libpulse-mainloop-glib0 ...
-Removing libpulse0 ...
-Purging configuration files for libpulse0 ...
-Removing libasyncns0 ...
-Purging configuration files for libasyncns0 ...
 Removing libaudio2 ...
-Removing libcap2 ...
-Purging configuration files for libcap2 ...
 Removing libcroco3 ...
 Purging configuration files for libcroco3 ...
 Removing libqt4-script ...
 Purging configuration files for libqt4-script ...
+Removing libqt4-xmlpatterns ...
+Purging configuration files for libqt4-xmlpatterns ...
+Removing libqt4-network ...
+Purging configuration files for libqt4-network ...
 Removing libqt4-dbus ...
 Purging configuration files for libqt4-dbus ...
 Removing libdbus-1-3 ...
 Purging configuration files for libdbus-1-3 ...
 Removing libexpat1 ...
 Purging configuration files for libexpat1 ...
-Removing libsndfile1 ...
-Purging configuration files for libsndfile1 ...
-Removing libflac8 ...
-Purging configuration files for libflac8 ...
 Removing libfreetype6 ...
 Purging configuration files for libfreetype6 ...
-Removing libqt4-xmlpatterns ...
-Purging configuration files for libqt4-xmlpatterns ...
+Removing qt4-linguist-tools ...
 Removing libqt4-xml ...
 Purging configuration files for libqt4-xml ...
 Removing libqt4-test ...
 Purging configuration files for libqt4-test ...
 Removing libqt4-sql ...
 Purging configuration files for libqt4-sql ...
-Removing libqt4-assistant ...
-Purging configuration files for libqt4-assistant ...
-Removing libqt4-network ...
-Purging configuration files for libqt4-network ...
 Removing libqtcore4 ...
 Purging configuration files for libqtcore4 ...
 Removing libglib2.0-0 ...
@@ -1087,35 +936,19 @@ Removing libtiff4 ...
 Purging configuration files for libtiff4 ...
 Removing libmng1 ...
 Purging configuration files for libmng1 ...
-Removing libjpeg62 ...
+Removing libjpeg8 ...
 Removing liblcms1 ...
 Purging configuration files for liblcms1 ...
 Removing libmagic1 ...
 Purging configuration files for libmagic1 ...
-Removing libvorbisenc2 ...
-Purging configuration files for libvorbisenc2 ...
-Removing libvorbis0a ...
-Purging configuration files for libvorbis0a ...
-Removing libogg0 ...
-Purging configuration files for libogg0 ...
 Removing libpcre3 ...
 Purging configuration files for libpcre3 ...
 Removing libpipeline1 ...
 Purging configuration files for libpipeline1 ...
-Removing libpng12-0 ...
-Purging configuration files for libpng12-0 ...
-Removing libsqlite3-0 ...
-Purging configuration files for libsqlite3-0 ...
 Removing libunistring0 ...
 Purging configuration files for libunistring0 ...
-Removing libwrap0 ...
-Purging configuration files for libwrap0 ...
-Removing libxtst6 ...
-Purging configuration files for libxtst6 ...
 Removing libxrender1 ...
 Purging configuration files for libxrender1 ...
-Removing libxi6 ...
-Purging configuration files for libxi6 ...
 Removing libxext6 ...
 Purging configuration files for libxext6 ...
 Removing libx11-6 ...
@@ -1133,33 +966,28 @@ Removing qt4-qmake ...
 Removing ttf-dejavu-core ...
 Removing ucf ...
 Purging configuration files for ucf ...
-debconf: unable to initialize frontend: Dialog
-debconf: (TERM is not set, so the dialog frontend is not usable.)
-debconf: falling back to frontend: Readline
 Removing x11-common ...
 All runlevel operations denied by policy
 invoke-rc.d: policy-rc.d denied execution of stop.
 Purging configuration files for x11-common ...
-debconf: unable to initialize frontend: Dialog
-debconf: (TERM is not set, so the dialog frontend is not usable.)
-debconf: falling back to frontend: Readline
 
 ┌──────────────────────────────────────────────────────────────────────────────┐
 │ Summary                                                                      │
 └──────────────────────────────────────────────────────────────────────────────┘
 
 Architecture: amd64
-Build-Space: 64812
-Build-Time: 164
+Build-Space: 9448
+Build-Time: 82
 Distribution: unstable
-Install-Time: 62
-Job: clustalx_2.1+lgpl-1.dsc
+Install-Time: 69
+Job: clustalx_2.1+lgpl-2.dsc
+Lintian: pass
 Package: clustalx
-Package-Time: 237
-Source-Version: 2.1+lgpl-1
-Space: 64812
+Package-Time: 154
+Source-Version: 2.1+lgpl-2
+Space: 9448
 Status: successful
-Version: 2.1+lgpl-1
+Version: 2.1+lgpl-2
 ────────────────────────────────────────────────────────────────────────────────
-Finished at 20110227-2252
-Build needed 00:03:57, 64812k disc space
+Finished at 20111116-1440
+Build needed 00:02:34, 9448k disc space
diff --git a/changes b/changes
index 4a2592d..ce67ef1 100644
--- a/changes
+++ b/changes
@@ -2,60 +2,55 @@
 Hash: SHA256
 
 Format: 1.8
-Date: Sun, 27 Feb 2011 22:36:51 +0900
+Date: Wed, 16 Nov 2011 14:37:03 +0900
 Source: clustalx
 Binary: clustalx
 Architecture: source amd64
-Version: 2.1+lgpl-1
+Version: 2.1+lgpl-2
 Distribution: unstable
 Urgency: low
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Changed-By: Charles Plessy <plessy at debian.org>
 Description: 
  clustalx   - Multiple alignment of nucleic acid and protein sequences (graphic
+Closes: 648812
 Changes: 
- clustalx (2.1+lgpl-1) unstable; urgency=low
+ clustalx (2.1+lgpl-2) unstable; urgency=low
  .
-   * New upstream archive, that makes clear the relicensing to LGPL-3+.
-     - Mangled debian version name in debian/watch.
-     - Explained why ‘+lgpl’ in debian/README.Debian.
-     - Removed XS-Autobuild field from debian/control.
-     - Changed archive area in debian/control.
-     - Updated license in debian/copyright.
-     - Removed Commercial field in debian/upstream-metadata.yaml.
-   * Removed un-needed documentation (debian/clustalx.docs).
-   * Source package hosted in a Git repository (debian/control).
-   * Use debhelper 8 (debian/control, debian/compat).
+   [8b9662e] Update providing upgrade path to backports (Closes: #648812).
+   [727f540] Corrected and normalised copyright file with config-edit.
+   [fa455a0] Conforms to Policy version 3.9.2 (no changes needed).
+   [9cd039b] Updated Homepage.
+   [a36daf1] Rely on dpkg-dev for patching and removed build-dependancy on quilt.
+   [51bde59] Support build-arch and build-indep targets through dh.
+   [c3b9f16] Signal and configure the use of git-buildpackage.
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- 63196a4e113a22e5e575f223d76b7406f4f70795 341649 clustalx_2.1+lgpl.orig.tar.gz
- c92222d36c291cce607dbe40c3539dd44b8e23bf 11667 clustalx_2.1+lgpl-1.debian.tar.gz
- 9d6a70bd7292b5e895bc1983e7bf82407cf23e5f 561624 clustalx_2.1+lgpl-1_amd64.deb
+ 75ce68516779bcec7f4a6394abdc3006e7d4eb4e 2037 clustalx_2.1+lgpl-2.dsc
+ 4cc5778da200071be4d231d274d16f6c1e3fa627 11934 clustalx_2.1+lgpl-2.debian.tar.gz
+ 514d598dbef7f65c1b2aa0175574cad3bb008397 569184 clustalx_2.1+lgpl-2_amd64.deb
 Checksums-Sha256: 
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- 2c0abcd500a14e3d543fefd4a1f1cc4dc1439b886672cb110b4d57364834e398 561624 clustalx_2.1+lgpl-1_amd64.deb
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 Files: 
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- 5b1f2f1cc8e939411ab0f934cafa072a 341649 science optional clustalx_2.1+lgpl.orig.tar.gz
- 05b819560ffa9ed8b7b8d24c9049d5f4 11667 science optional clustalx_2.1+lgpl-1.debian.tar.gz
- afc8a9139121cafa899fecdb787467b7 561624 science optional clustalx_2.1+lgpl-1_amd64.deb
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diff --git a/dsc b/dsc
index 987f8d0..d7b946b 100644
--- a/dsc
+++ b/dsc
@@ -5,39 +5,41 @@ Format: 3.0 (quilt)
 Source: clustalx
 Binary: clustalx
 Architecture: any
-Version: 2.1+lgpl-1
+Version: 2.1+lgpl-2
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>, Andreas Tille <tille at debian.org>
 Dm-Upload-Allowed: yes
-Homepage: http://www.clustal.org/
-Standards-Version: 3.9.1
+Homepage: http://www.clustal.org/clustal2/
+Standards-Version: 3.9.2
 Vcs-Browser: http://git.debian.org/?p=debian-med/clustalx.git
 Vcs-Git: git://git.debian.org/debian-med/clustalx.git
-Build-Depends: debhelper (>= 8), libqt4-dev, quilt
+Build-Depends: debhelper (>= 8), libqt4-dev
+Package-List: 
+ clustalx deb science optional
 Checksums-Sha1: 
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- c92222d36c291cce607dbe40c3539dd44b8e23bf 11667 clustalx_2.1+lgpl-1.debian.tar.gz
+ d9c700203b37222946e0364a69adb0af52a4975b 338221 clustalx_2.1+lgpl.orig.tar.gz
+ 4cc5778da200071be4d231d274d16f6c1e3fa627 11934 clustalx_2.1+lgpl-2.debian.tar.gz
 Checksums-Sha256: 
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- 36dfb3142ebee39421742ca95c53569189e12d618395a7b2723829c155cb4615 11667 clustalx_2.1+lgpl-1.debian.tar.gz
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- 05b819560ffa9ed8b7b8d24c9049d5f4 11667 clustalx_2.1+lgpl-1.debian.tar.gz
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-- 
Multiple alignment of nucleic acid and protein sequences (graphical interface)