RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '587248-1518481', '/home/buildd/filecache-default/8ad0092cb75d28342a75c20f8fdcef2fec398cb6'] Synching the system clock with the buildd NTP service... 9 May 23:10:22 ntpdate[27360]: adjust time server 10.211.37.1 offset 0.000046 sec Unpacking chroot for build 587248-1518481 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '587248-1518481'] Mounting chroot for build 587248-1518481 RUN: /usr/share/launchpad-buildd/slavebin/apply-ogre-model ['apply-ogre-model', '587248-1518481', 'universe'] Attempting OGRE for universe in build-587248-1518481 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '587248-1518481', 'deb http://ftpmaster.internal/ubuntu intrepid main restricted universe'] Overriding sources.list in build-587248-1518481 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '587248-1518481'] Updating debian chroot for build 587248-1518481 Get:1 http://ftpmaster.internal intrepid Release.gpg [191B] Get:2 http://ftpmaster.internal intrepid Release [65.9kB] Get:3 http://ftpmaster.internal intrepid/main Packages [1176kB] Get:4 http://ftpmaster.internal intrepid/restricted Packages [1974B] Get:5 http://ftpmaster.internal intrepid/universe Packages [4290kB] Fetched 5533kB in 3s (1779kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: cpp-4.3 g++-4.3 gcc-4.3 gcc-4.3-base libgmp3c2 libmpfr1ldbl libstdc++6-4.3-dev The following packages will be upgraded: apt base-files base-passwd bash binutils bsdutils ccache cpio cpp cpp-4.2 debconf debconf-english findutils g++ g++-4.2 gcc gcc-4.2 gcc-4.2-base grep gzip hostname libacl1 libattr1 libgcc1 libgomp1 libslang2 libstdc++6 libstdc++6-4.2-dev make makedev mawk mount patch perl perl-base perl-modules python2.5-minimal sed tar util-linux zlib1g Extracting templates from packages: 62% Extracting templates from packages: 100% Preconfiguring packages ... 41 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/35.1MB of archives. After this operation, 38.2MB of additional disk space will be used. dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9166 files and directories currently installed.) Preparing to replace mawk 1.3.3-11ubuntu2 (using .../mawk_1.3.3-11.1ubuntu1_lpia.deb) ... Unpacking replacement mawk ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace base-passwd 3.5.16 (using .../base-passwd_3.5.17_lpia.deb) ... Unpacking replacement base-passwd ... Setting up base-passwd (3.5.17) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9167 files and directories currently installed.) Preparing to replace base-files 4.0.1ubuntu5 (using .../base-files_4.0.1ubuntu6_lpia.deb) ... Unpacking replacement base-files ... Setting up mawk (1.3.3-11.1ubuntu1) ... Setting up base-files (4.0.1ubuntu6) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9167 files and directories currently installed.) Preparing to replace bash 3.2-0ubuntu16 (using .../bash_3.2-2ubuntu1_lpia.deb) ... Unpacking replacement bash ... Setting up bash (3.2-2ubuntu1) ... Installing new version of config file /etc/skel/.bashrc ... Installing new version of config file /etc/skel/.profile ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9167 files and directories currently installed.) Preparing to replace findutils 4.2.32-1ubuntu2 (using .../findutils_4.4.0-2ubuntu1_lpia.deb) ... Unpacking replacement findutils ... Setting up findutils (4.4.0-2ubuntu1) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9168 files and directories currently installed.) Preparing to replace grep 2.5.3~dfsg-3 (using .../grep_2.5.3~dfsg-5_lpia.deb) ... Unpacking replacement grep ... Setting up grep (2.5.3~dfsg-5) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9168 files and directories currently installed.) Preparing to replace gzip 1.3.12-3.2 (using .../gzip_1.3.12-6_lpia.deb) ... Unpacking replacement gzip ... Setting up gzip (1.3.12-6) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9168 files and directories currently installed.) Preparing to replace hostname 2.94 (using .../hostname_2.95_lpia.deb) ... Unpacking replacement hostname ... Setting up hostname (2.95) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9169 files and directories currently installed.) Preparing to replace mount 2.13.1-5ubuntu1 (using .../mount_2.14~rc2-0ubuntu1_lpia.deb) ... Unpacking replacement mount ... Setting up mount (2.14~rc2-0ubuntu1) ... (Reading database ... 9169 files and directories currently installed.) Preparing to replace perl-modules 5.8.8-12 (using .../perl-modules_5.10.0-10_all.deb) ... Unpacking replacement perl-modules ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace perl 5.8.8-12 (using .../perl_5.10.0-10_lpia.deb) ... Unpacking replacement perl ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace perl-base 5.8.8-12 (using .../perl-base_5.10.0-10_lpia.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.10.0-10) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9410 files and directories currently installed.) Preparing to replace sed 4.1.5-5 (using .../archives/sed_4.1.5-8_lpia.deb) ... Unpacking replacement sed ... Setting up sed (4.1.5-8) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9410 files and directories currently installed.) Preparing to replace tar 1.19-3 (using .../archives/tar_1.20-1_lpia.deb) ... Unpacking replacement tar ... Setting up tar (1.20-1) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9410 files and directories currently installed.) Preparing to replace util-linux 2.13.1-5ubuntu1 (using .../util-linux_2.14~rc2-0ubuntu1_lpia.deb) ... Unpacking replacement util-linux ... Setting up util-linux (2.14~rc2-0ubuntu1) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9412 files and directories currently installed.) Preparing to replace bsdutils 1:2.13.1-5ubuntu1 (using .../bsdutils_1%3a2.14~rc2-0ubuntu1_lpia.deb) ... Unpacking replacement bsdutils ... Setting up bsdutils (1:2.14~rc2-0ubuntu1) ... (Reading database ... 9412 files and directories currently installed.) Preparing to replace debconf-english 1.5.20 (using .../debconf-english_1.5.21_all.deb) ... Unpacking replacement debconf-english ... Setting up debconf-english (1.5.21) ... (Reading database ... 9412 files and directories currently installed.) Preparing to replace debconf 1.5.20 (using .../debconf_1.5.21_all.deb) ... Unpacking replacement debconf ... Setting up debconf (1.5.21) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package gcc-4.3-base. (Reading database ... 9412 files and directories currently installed.) Unpacking gcc-4.3-base (from .../gcc-4.3-base_4.3.0-3ubuntu5_lpia.deb) ... Setting up gcc-4.3-base (4.3.0-3ubuntu5) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9417 files and directories currently installed.) Preparing to replace libgcc1 1:4.2.3-2ubuntu7 (using .../libgcc1_1%3a4.3.0-3ubuntu5_lpia.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.3.0-3ubuntu5) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9417 files and directories currently installed.) Preparing to replace libstdc++6 4.2.3-2ubuntu7 (using .../libstdc++6_4.3.0-3ubuntu5_lpia.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.3.0-3ubuntu5) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9417 files and directories currently installed.) Preparing to replace apt 0.7.9ubuntu17 (using .../apt_0.7.14ubuntu2_lpia.deb) ... Unpacking replacement apt ... Setting up apt (0.7.14ubuntu2) ... Installing new version of config file /etc/apt/apt.conf.d/01ubuntu ... Installing new version of config file /etc/cron.daily/apt ... Processing triggers for libc6 ... ldconfig deferred processing now taking place dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9417 files and directories currently installed.) Preparing to replace libattr1 1:2.4.39-1 (using .../libattr1_1%3a2.4.41-1_lpia.deb) ... Unpacking replacement libattr1 ... Setting up libattr1 (1:2.4.41-1) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9416 files and directories currently installed.) Preparing to replace libacl1 2.2.45-1 (using .../libacl1_2.2.47-2_lpia.deb) ... Unpacking replacement libacl1 ... Setting up libacl1 (2.2.47-2) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9415 files and directories currently installed.) Preparing to replace libslang2 2.1.3-2 (using .../libslang2_2.1.3-3_lpia.deb) ... Unpacking replacement libslang2 ... Setting up libslang2 (2.1.3-3) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9415 files and directories currently installed.) Preparing to replace zlib1g 1:1.2.3.3.dfsg-7ubuntu1 (using .../zlib1g_1%3a1.2.3.3.dfsg-12ubuntu1_lpia.deb) ... Unpacking replacement zlib1g ... Setting up zlib1g (1:1.2.3.3.dfsg-12ubuntu1) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9415 files and directories currently installed.) Preparing to replace python2.5-minimal 2.5.2-2ubuntu4 (using .../python2.5-minimal_2.5.2-4ubuntu1_lpia.deb) ... Unpacking replacement python2.5-minimal ... Setting up python2.5-minimal (2.5.2-4ubuntu1) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) (Reading database ... 9415 files and directories currently installed.) Preparing to replace cpio 2.9-6ubuntu1 (using .../archives/cpio_2.9-13_lpia.deb) ... Unpacking replacement cpio ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace libgomp1 4.2.3-2ubuntu7 (using .../libgomp1_4.3.0-3ubuntu5_lpia.deb) ... Unpacking replacement libgomp1 ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace binutils 2.18.1~cvs20080103-0ubuntu1 (using .../binutils_2.18.50.20080509-0ubuntu1_lpia.deb) ... Unpacking replacement binutils ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace libstdc++6-4.2-dev 4.2.3-2ubuntu7 (using .../libstdc++6-4.2-dev_4.2.3-4ubuntu1_lpia.deb) ... Unpacking replacement libstdc++6-4.2-dev ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace g++-4.2 4.2.3-2ubuntu7 (using .../g++-4.2_4.2.3-4ubuntu1_lpia.deb) ... Unpacking replacement g++-4.2 ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace gcc-4.2 4.2.3-2ubuntu7 (using .../gcc-4.2_4.2.3-4ubuntu1_lpia.deb) ... Unpacking replacement gcc-4.2 ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace cpp-4.2 4.2.3-2ubuntu7 (using .../cpp-4.2_4.2.3-4ubuntu1_lpia.deb) ... Unpacking replacement cpp-4.2 ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace gcc-4.2-base 4.2.3-2ubuntu7 (using .../gcc-4.2-base_4.2.3-4ubuntu1_lpia.deb) ... Unpacking replacement gcc-4.2-base ... Preparing to replace makedev 2.3.1-84ubuntu1 (using .../makedev_2.3.1-88_all.deb) ... Removing obsolete conffile /etc/init.d/makedev ... Removing any system startup links for /etc/init.d/makedev ... /etc/rc1.d/K20makedev /etc/rc2.d/S20makedev /etc/rc3.d/S20makedev /etc/rc4.d/S20makedev /etc/rc5.d/S20makedev Unpacking replacement makedev ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package libgmp3c2. Unpacking libgmp3c2 (from .../libgmp3c2_2%3a4.2.2+dfsg-1ubuntu2_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package libmpfr1ldbl. Unpacking libmpfr1ldbl (from .../libmpfr1ldbl_2.3.1.dfsg.1-2ubuntu1_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package cpp-4.3. Unpacking cpp-4.3 (from .../cpp-4.3_4.3.0-3ubuntu5_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace cpp 4:4.2.3-1ubuntu3 (using .../cpp_4%3a4.3.0-5ubuntu2_lpia.deb) ... Unpacking replacement cpp ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace ccache 2.4-11 (using .../ccache_2.4-15_lpia.deb) ... Unpacking replacement ccache ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package gcc-4.3. Unpacking gcc-4.3 (from .../gcc-4.3_4.3.0-3ubuntu5_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package libstdc++6-4.3-dev. Unpacking libstdc++6-4.3-dev (from .../libstdc++6-4.3-dev_4.3.0-3ubuntu5_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package g++-4.3. Unpacking g++-4.3 (from .../g++-4.3_4.3.0-3ubuntu5_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace gcc 4:4.2.3-1ubuntu3 (using .../gcc_4%3a4.3.0-5ubuntu2_lpia.deb) ... Removing old gcc doc directory. Unpacking replacement gcc ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace g++ 4:4.2.3-1ubuntu3 (using .../g++_4%3a4.3.0-5ubuntu2_lpia.deb) ... Unpacking replacement g++ ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace make 3.81-3build1 (using .../archives/make_3.81-4_lpia.deb) ... Unpacking replacement make ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Preparing to replace patch 2.5.9-4 (using .../patch_2.5.9-5_lpia.deb) ... Unpacking replacement patch ... Setting up cpio (2.9-13) ... Setting up libgomp1 (4.3.0-3ubuntu5) ... Setting up binutils (2.18.50.20080509-0ubuntu1) ... Setting up gcc-4.2-base (4.2.3-4ubuntu1) ... Setting up cpp-4.2 (4.2.3-4ubuntu1) ... Setting up gcc-4.2 (4.2.3-4ubuntu1) ... Setting up makedev (2.3.1-88) ... Setting up libgmp3c2 (2:4.2.2+dfsg-1ubuntu2) ... Setting up libmpfr1ldbl (2.3.1.dfsg.1-2ubuntu1) ... Setting up cpp-4.3 (4.3.0-3ubuntu5) ... Setting up cpp (4:4.3.0-5ubuntu2) ... Setting up ccache (2.4-15) ... Setting up gcc-4.3 (4.3.0-3ubuntu5) ... Setting up gcc (4:4.3.0-5ubuntu2) ... Setting up make (3.81-4) ... Setting up patch (2.5.9-5) ... Setting up libstdc++6-4.3-dev (4.3.0-3ubuntu5) ... Setting up perl-modules (5.10.0-10) ... Setting up libstdc++6-4.2-dev (4.2.3-4ubuntu1) ... Setting up g++-4.3 (4.3.0-3ubuntu5) ... Setting up g++ (4:4.3.0-5ubuntu2) ... Setting up perl (5.10.0-10) ... Setting up g++-4.2 (4.2.3-4ubuntu1) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '587248-1518481', '--nolog', '--batch', '--archive=ubuntu', '--purpose=PRIMARY', '--dist=intrepid', '--comp=universe', 'muscle_3.70+fix1-2.dsc'] Initiating build Automatic build of muscle_3.70+fix1-2 on zirconium by sbuild/lpia 1.170.5 Build started at 20080509-2311 ****************************************************************************** muscle_3.70+fix1-2.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: cdbs, debhelper (>= 5.0.0) Checking for already installed source dependencies... cdbs: missing debhelper: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install cdbs debhelper Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: g++-4.2 libstdc++6-4.2-dev Use 'apt-get autoremove' to remove them. The following extra packages will be installed: autoconf automake1.7 autotools-dev bsdmainutils fdupes file gettext gettext-base groff-base html2text ifupdown intltool intltool-debian libexpat1 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libmagic1 liburi-perl libwww-perl libxml-parser-perl m4 man-db net-tools netbase po-debconf update-inetd Suggested packages: autobook autoconf-archive autoconf-doc autoconf2.13 gnu-standards libtool vacation wamerican wordlist whois devscripts doc-base dh-make cvs gettext-doc groff iproute dhcp3-client dhcp-client ppp libio-socket-ssl-perl less www-browser Recommended packages: automake automaken curl wget lynx libcompress-zlib-perl libhtml-format-perl libmailtools-perl libmail-box-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake1.7 autotools-dev bsdmainutils cdbs debhelper fdupes file gettext gettext-base groff-base html2text ifupdown intltool intltool-debian libexpat1 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libmagic1 liburi-perl libwww-perl libxml-parser-perl m4 man-db net-tools netbase po-debconf update-inetd dpkg-preconfigure: unable to re-open stdin: 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/8920kB of archives. After this operation, 29.4MB of additional disk space will be used. dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package gettext-base. (Reading database ... 10185 files and directories currently installed.) Unpacking gettext-base (from .../gettext-base_0.17-2ubuntu1_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package net-tools. Unpacking net-tools (from .../net-tools_1.60-19ubuntu1_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package ifupdown. Unpacking ifupdown (from .../ifupdown_0.6.8ubuntu8_lpia.deb) ... Selecting previously deselected package update-inetd. Unpacking update-inetd (from .../update-inetd_4.30_all.deb) ... Selecting previously deselected package netbase. Unpacking netbase (from .../netbase_4.30ubuntu1_all.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_6.1.10ubuntu2_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_4.24-2_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package file. Unpacking file (from .../archives/file_4.24-2_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.18.1.1-20_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-0ubuntu1_lpia.deb) ... Selecting previously deselected package libhtml-tagset-perl. Unpacking libhtml-tagset-perl (from .../libhtml-tagset-perl_3.20-2_all.deb) ... Selecting previously deselected package liburi-perl. Unpacking liburi-perl (from .../liburi-perl_1.35.dfsg.1-1_all.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package libhtml-parser-perl. Unpacking libhtml-parser-perl (from .../libhtml-parser-perl_3.56-1build1_lpia.deb) ... Selecting previously deselected package libhtml-tree-perl. Unpacking libhtml-tree-perl (from .../libhtml-tree-perl_3.23-1_all.deb) ... Selecting previously deselected package libwww-perl. Unpacking libwww-perl (from .../libwww-perl_5.812-1_all.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package libxml-parser-perl. Unpacking libxml-parser-perl (from .../libxml-parser-perl_2.36-1.1build1_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.5.2-1_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package m4. Unpacking m4 (from .../archives/m4_1.4.11-1_lpia.deb) ... Selecting previously deselected package autoconf. Unpacking autoconf (from .../autoconf_2.61-7_all.deb) ... Selecting previously deselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20080123.1_all.deb) ... Selecting previously deselected package automake1.7. Unpacking automake1.7 (from .../automake1.7_1.7.9-9_all.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-3build2_lpia.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.17-2ubuntu1_lpia.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.12.1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_7.0.8ubuntu1_all.deb) ... dpkg - warning, overriding problem because --force enabled: package architecture (lpia) does not match system (i386) Selecting previously deselected package fdupes. Unpacking fdupes (from .../fdupes_1.50-PR2-1_lpia.deb) ... Selecting previously deselected package intltool. Unpacking intltool (from .../intltool_0.37.1-1ubuntu1_all.deb) ... Selecting previously deselected package cdbs. Unpacking cdbs (from .../cdbs_0.4.52ubuntu1_all.deb) ... Setting up gettext-base (0.17-2ubuntu1) ... Setting up net-tools (1.60-19ubuntu1) ... Setting up ifupdown (0.6.8ubuntu8) ... ifupdown.postinst: Warning: No 'iface lo' definition found in /etc/network/interfaces ifupdown.postinst: Warning: No 'auto lo' statement found in /etc/network/interfaces Setting up update-inetd (4.30) ... Setting up netbase (4.30ubuntu1) ... Setting up bsdmainutils (6.1.10ubuntu2) ... Setting up libmagic1 (4.24-2) ... Setting up file (4.24-2) ... Setting up groff-base (1.18.1.1-20) ... Setting up libexpat1 (2.0.1-0ubuntu1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up liburi-perl (1.35.dfsg.1-1) ... Setting up libhtml-parser-perl (3.56-1build1) ... Setting up libhtml-tree-perl (3.23-1) ... Setting up libwww-perl (5.812-1) ... Setting up libxml-parser-perl (2.36-1.1build1) ... Setting up man-db (2.5.2-1) ... Building database of manual pages ... Setting up m4 (1.4.11-1) ... Setting up autoconf (2.61-7) ... Setting up autotools-dev (20080123.1) ... Setting up automake1.7 (1.7.9-9) ... Setting up html2text (1.3.2a-3build2) ... Setting up gettext (0.17-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.12.1) ... Setting up debhelper (7.0.8ubuntu1) ... Setting up fdupes (1.50-PR2-1) ... Setting up intltool (0.37.1-1ubuntu1) ... Setting up cdbs (0.4.52ubuntu1) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.7-10ubuntu3 make_3.81-4 dpkg-dev_1.14.16.6ubuntu3 gcc-4.3_4.3.0-3ubuntu5 g++-4.3_4.3.0-3ubuntu5 binutils_2.18.50.20080509-0ubuntu1 libstdc++6_4.3.0-3ubuntu5 libstdc++6-4.3-dev_4.3.0-3ubuntu5 ------------------------------------------------------------------------------ sh: gcc: not found dpkg-source: warning: Couldn't determine gcc system type, falling back to default (native compilation) gpg: Signature made Thu Feb 14 02:55:23 2008 GMT using DSA key ID BAFEC7F2 gpg: Can't check signature: public key not found dpkg-source: extracting muscle in muscle-3.70+fix1 dpkg-source: unpacking muscle_3.70+fix1.orig.tar.gz dpkg-source: applying /home/buildd/build-587248-1518481/muscle_3.70+fix1-2.diff.gz dpkg-buildpackage: set CPPFLAGS to default value: dpkg-buildpackage: set CFLAGS to default value: -g -O2 dpkg-buildpackage: set CXXFLAGS to default value: -g -O2 dpkg-buildpackage: set FFLAGS to default value: -g -O2 dpkg-buildpackage: set LDFLAGS to default value: -Wl,-Bsymbolic-functions dpkg-buildpackage: source package muscle dpkg-buildpackage: source version 3.70+fix1-2 dpkg-buildpackage: host architecture lpia /usr/bin/fakeroot debian/rules clean test -x debian/rules dh_testroot dh_clean LDLIBS=-lm /usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="-Wl,-Bsymbolic-functions" -e -k clean make[1]: Entering directory `/build/buildd/muscle-3.70+fix1' make[1]: *** No rule to make target `clean'. make[1]: Leaving directory `/build/buildd/muscle-3.70+fix1' make: [makefile-clean] Error 2 (ignored) rm -f debian/stamp-makefile-build rm -f *.o make.err make.out rm -f muscle debian/rules build test -x debian/rules mkdir -p "." LDLIBS=-lm /usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="-Wl,-Bsymbolic-functions" -e all make[1]: Entering directory `/build/buildd/muscle-3.70+fix1' g++ -c -g -O2 -g -Wall -O2 aligngivenpath.cpp -o aligngivenpath.o aligngivenpath.cpp: In function 'void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)': aligngivenpath.cpp:186: warning: unused variable 'uLengthA' aligngivenpath.cpp:187: warning: unused variable 'uLengthB' aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpath.cpp:335: warning: unused variable 'uColA' aligngivenpath.cpp:336: warning: unused variable 'uColB' aligngivenpath.cpp:346: warning: unused variable 'uColA' aligngivenpath.cpp:354: warning: unused variable 'uColB' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 aligngivenpathsw.cpp -o aligngivenpathsw.o aligngivenpathsw.cpp: In function 'void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)': aligngivenpathsw.cpp:58: warning: unused variable 'uLengthA' aligngivenpathsw.cpp:59: warning: unused variable 'uLengthB' aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpathsw.cpp:204: warning: unused variable 'uColA' aligngivenpathsw.cpp:205: warning: unused variable 'uColB' aligngivenpathsw.cpp:215: warning: unused variable 'uColA' aligngivenpathsw.cpp:223: warning: unused variable 'uColB' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 aligntwomsas.cpp -o aligntwomsas.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 aligntwoprofs.cpp -o aligntwoprofs.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 aln.cpp -o aln.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 alpha.cpp -o alpha.o alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)': alpha.cpp:84: warning: enumeration value 'ALPHA_Undefined' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 anchors.cpp -o anchors.o anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)': anchors.cpp:162: warning: unused variable 'uWindowCenter' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used anchors.cpp:54: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used anchors.cpp:106: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used g++ -c -g -O2 -g -Wall -O2 bittraceback.cpp -o bittraceback.o bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)': bittraceback.cpp:146: warning: unused variable 'Bits' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used bittraceback.cpp:15: warning: 'const char* BitsToStr(char)' defined but not used g++ -c -g -O2 -g -Wall -O2 blosum62.cpp -o blosum62.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 blosumla.cpp -o blosumla.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used blosumla.cpp:7: warning: 'Blosum62LA' defined but not used g++ -c -g -O2 -g -Wall -O2 clust.cpp -o clust.o clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)': clust.cpp:167: warning: enumeration value 'JOIN_Undefined' not handled in switch clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)': clust.cpp:184: warning: unused variable 'uClusterCount' clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)': clust.cpp:204: warning: unused variable 'uClusterCount' clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)': clust.cpp:295: warning: enumeration value 'LINKAGE_Undefined' not handled in switch clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)': clust.cpp:360: warning: unused variable 'dDistLR' clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const': clust.cpp:611: warning: enumeration value 'JOIN_Undefined' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 cluster.cpp -o cluster.o cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)': cluster.cpp:267: warning: unused variable 'dMaxDist' cluster.cpp:283: warning: 'uIndexClosest2' may be used uninitialized in this function cluster.cpp:282: warning: 'uIndexClosest1' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 clwwt.cpp -o clwwt.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 color.cpp -o color.o color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' color.cpp:34: warning: missing braces around initializer for 'int [23]' intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used color.cpp:72: warning: 'int BlosumScore(char, char)' defined but not used g++ -c -g -O2 -g -Wall -O2 cons.cpp -o cons.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 diaglist.cpp -o diaglist.o diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)': diaglist.cpp:52: warning: 'uStartPosB' may be used uninitialized in this function diaglist.cpp:51: warning: 'uStartPosA' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 diffobjscore.cpp -o diffobjscore.o diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)': diffobjscore.cpp:76: warning: unused variable 'uSeqCount' diffobjscore.cpp:77: warning: unused variable 'uColCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 diffpaths.cpp -o diffpaths.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 difftrees.cpp -o difftrees.o difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)': difftrees.cpp:161: warning: unused variable 'uLeafCount2' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 difftreese.cpp -o difftreese.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 distcalc.cpp -o distcalc.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 distfunc.cpp -o distfunc.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 distpwkimura.cpp -o distpwkimura.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 domuscle.cpp -o domuscle.o domuscle.cpp: In function 'void DoMuscle()': domuscle.cpp:123: warning: format not a string literal and no format arguments intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 dosp.cpp -o dosp.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 dpreglist.cpp -o dpreglist.o dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)': dpreglist.cpp:82: warning: unused variable 'uDiagLengthMinusCaps' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 drawtree.cpp -o drawtree.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 edgelist.cpp -o edgelist.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 enumopts.cpp -o enumopts.o In file included from enumopts.cpp:8: enums.h:15: warning: missing braces around initializer for 'EnumOpt' enums.h:15: warning: missing braces around initializer for 'EnumOpt' enums.h:15: warning: missing braces around initializer for 'EnumOpt' enums.h:15: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:22: warning: missing braces around initializer for 'EnumOpt' enums.h:28: warning: missing braces around initializer for 'EnumOpt' enums.h:28: warning: missing braces around initializer for 'EnumOpt' enums.h:28: warning: missing braces around initializer for 'EnumOpt' enums.h:28: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:36: warning: missing braces around initializer for 'EnumOpt' enums.h:41: warning: missing braces around initializer for 'EnumOpt' enums.h:41: warning: missing braces around initializer for 'EnumOpt' enums.h:41: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:49: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:63: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:70: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:79: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:88: warning: missing braces around initializer for 'EnumOpt' enums.h:94: warning: missing braces around initializer for 'EnumOpt' enums.h:94: warning: missing braces around initializer for 'EnumOpt' enums.h:94: warning: missing braces around initializer for 'EnumOpt' enums.h:94: warning: missing braces around initializer for 'EnumOpt' intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 enumtostr.cpp -o enumtostr.o In file included from enumtostr.cpp:16: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 estring.cpp -o estring.o estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)': estring.cpp:377: warning: 'cType' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used estring.cpp:464: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used g++ -c -g -O2 -g -Wall -O2 fasta.cpp -o fasta.o fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)': fasta.cpp:15: warning: unused variable 'uSeqCount' fasta.cpp:16: warning: unused variable 'uColCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 fasta2.cpp -o fasta2.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 fastclust.cpp -o fastclust.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 fastdist.cpp -o fastdist.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 fastdistjones.cpp -o fastdistjones.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 fastdistkbit.cpp -o fastdistkbit.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 fastdistkmer.cpp -o fastdistkmer.o fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)': fastdistkmer.cpp:235: warning: unused variable 'KD' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 fastdistmafft.cpp -o fastdistmafft.o fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)': fastdistmafft.cpp:238: warning: unused variable 'pName1' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used fastdistmafft.cpp:104: warning: 'void ListCount(const unsigned char*)' defined but not used g++ -c -g -O2 -g -Wall -O2 fastdistnuc.cpp -o fastdistnuc.o fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)': fastdistnuc.cpp:223: warning: unused variable 'pName1' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used fastdistnuc.cpp:33: warning: 'uResidueGroupCount' defined but not used fastdistnuc.cpp:85: warning: 'void ListCount(const unsigned char*)' defined but not used g++ -c -g -O2 -g -Wall -O2 fastscorepath2.cpp -o fastscorepath2.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 finddiags.cpp -o finddiags.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used finddiags.cpp:11: warning: 'char* TupleToStr(int)' defined but not used g++ -c -g -O2 -g -Wall -O2 finddiagsn.cpp -o finddiagsn.o finddiagsn.cpp: In function 'char* TupleToStr(int)': finddiagsn.cpp:16: warning: comparison between signed and unsigned integer expressions intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used finddiagsn.cpp:12: warning: 'char* TupleToStr(int)' defined but not used g++ -c -g -O2 -g -Wall -O2 glbalign.cpp -o glbalign.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 glbalign352.cpp -o glbalign352.o In file included from glbalign352.cpp:6: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 glbaligndiag.cpp -o glbaligndiag.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 glbalignle.cpp -o glbalignle.o glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignle.cpp:400: warning: 'uInsertPos' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 glbalignsimple.cpp -o glbalignsimple.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used glbalignsimple.cpp:29: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used glbalignsimple.cpp:53: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used g++ -c -g -O2 -g -Wall -O2 glbalignsp.cpp -o glbalignsp.o glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignsp.cpp:272: warning: 'uInsertPos' may be used uninitialized in this function glbalignsp.cpp:339: warning: 'uInsertPos' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 glbalignspn.cpp -o glbalignspn.o glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignspn.cpp:307: warning: 'uInsertPos' may be used uninitialized in this function glbalignspn.cpp:374: warning: 'uInsertPos' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 glbalignss.cpp -o glbalignss.o glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)': glbalignss.cpp:177: warning: unused variable 'ptrRowA' glbalignss.cpp:119: warning: unused variable 'uPrefixCountA' glbalignss.cpp:120: warning: unused variable 'uPrefixCountB' glbalignss.cpp:221: warning: 'uInsertPos' may be used uninitialized in this function glbalignss.cpp:283: warning: 'uInsertPos' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used glbalignss.cpp:11: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used g++ -c -g -O2 -g -Wall -O2 glbalndimer.cpp -o glbalndimer.o glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)': glbalndimer.cpp:123: warning: enumeration value 'PPSCORE_Undefined' not handled in switch glbalndimer.cpp:123: warning: enumeration value 'PPSCORE_SPN' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used glbalndimer.cpp:14: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 globals.cpp -o globals.o globals.cpp: In function 'void Log(const char*, ...)': globals.cpp:50: warning: deprecated conversion from string constant to 'char*' globals.cpp:52: warning: deprecated conversion from string constant to 'char*' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 globalslinux.cpp -o globalslinux.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 globalsother.cpp -o globalsother.o In file included from globalsother.cpp:1: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 globalswin32.cpp -o globalswin32.o In file included from globalswin32.cpp:1: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 gonnet.cpp -o gonnet.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used gonnet.cpp:137: warning: 'Gonnet160' defined but not used g++ -c -g -O2 -g -Wall -O2 gotowt.cpp -o gotowt.o g++ -c -g -O2 -g -Wall -O2 henikoffweight.cpp -o henikoffweight.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 henikoffweightpb.cpp -o henikoffweightpb.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 html.cpp -o html.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 hydro.cpp -o hydro.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 intmath.cpp -o intmath.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 local.cpp -o local.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 main.cpp -o main.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 makerootmsa.cpp -o makerootmsa.o makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)': makerootmsa.cpp:18: warning: unused variable 'uSeqLength' makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)': makerootmsa.cpp:93: warning: unused variable 'Path' makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)': makerootmsa.cpp:167: warning: unused variable 'uTreeNodeCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used makerootmsa.cpp:12: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used g++ -c -g -O2 -g -Wall -O2 makerootmsab.cpp -o makerootmsab.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 maketree.cpp -o maketree.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 mhack.cpp -o mhack.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 mpam200.cpp -o mpam200.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 msa.cpp -o msa.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used msa.cpp:385: warning: 'void FmtChar(char, unsigned int)' defined but not used msa.cpp:392: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used msa.cpp:407: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used msa.cpp:419: warning: 'void FmtPad(unsigned int)' defined but not used g++ -c -g -O2 -g -Wall -O2 msa2.cpp -o msa2.o msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)': msa2.cpp:357: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)': msa2.cpp:476: warning: unused variable 'uColCountCat' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 msadistkimura.cpp -o msadistkimura.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 msf.cpp -o msf.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used msf.cpp:24: warning: 'const char* strfind(const char*, const char*)' defined but not used g++ -c -g -O2 -g -Wall -O2 muscle.cpp -o muscle.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 muscleout.cpp -o muscleout.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 nucmx.cpp -o nucmx.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 nwdasimple.cpp -o nwdasimple.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 nwdasimple2.cpp -o nwdasimple2.o In file included from nwdasimple2.cpp:3: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 nwdasmall.cpp -o nwdasmall.o In file included from nwdasmall.cpp:4: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 nwrec.cpp -o nwrec.o g++ -c -g -O2 -g -Wall -O2 nwsmall.cpp -o nwsmall.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 objscore.cpp -o objscore.o objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)': objscore.cpp:31: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch objscore.cpp:31: warning: enumeration value 'OBJSCORE_SPM' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 objscore2.cpp -o objscore2.o objscore2.cpp: In function 'SCORE TermGapScore(bool)': objscore2.cpp:22: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)': objscore2.cpp:62: warning: unused variable 'scoreGaps' objscore2.cpp:63: warning: unused variable 'bGapping1' objscore2.cpp:64: warning: unused variable 'bGapping2' objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)': objscore2.cpp:314: warning: unused variable 'uColCount2' objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)': objscore2.cpp:493: warning: unused variable 'w' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 objscoreda.cpp -o objscoreda.o In file included from objscoreda.cpp:4: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 onexception.cpp -o onexception.o onexception.cpp: In function 'void OnException()': onexception.cpp:11: warning: format not a string literal and no format arguments intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 options.cpp -o options.o options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:84: warning: missing braces around initializer for 'VALUE_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' options.cpp:124: warning: missing braces around initializer for 'FLAG_OPT' intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 outweights.cpp -o outweights.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 pam200mafft.cpp -o pam200mafft.o pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' pam200mafft.cpp:32: warning: missing braces around initializer for 'float [23]' intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used pam200mafft.cpp:6: warning: 'PAM200' defined but not used g++ -c -g -O2 -g -Wall -O2 params.cpp -o params.o params.cpp: In function 'void SetPPScore(bool)': params.cpp:441: warning: enumeration value 'PPSCORE_Undefined' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 phy.cpp -o phy.o phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)': phy.cpp:665: warning: unused variable 'dEdgeLength' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 phy2.cpp -o phy2.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 phy3.cpp -o phy3.o phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)': phy3.cpp:125: warning: unused variable 'dThisDist' phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)': phy3.cpp:167: warning: unused variable 'uLeafCount' phy3.cpp:190: warning: unused variable 'dAllMaxDist' phy3.cpp:191: warning: unused variable 'uMaxFrom' phy3.cpp:192: warning: unused variable 'uMaxTo' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used phy3.cpp:45: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used g++ -c -g -O2 -g -Wall -O2 phy4.cpp -o phy4.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 phyfromclust.cpp -o phyfromclust.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 phyfromfile.cpp -o phyfromfile.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 physeq.cpp -o physeq.o physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const': physeq.cpp:60: warning: comparison between signed and unsigned integer expressions physeq.cpp:71: warning: comparison between signed and unsigned integer expressions physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const': physeq.cpp:112: warning: comparison between signed and unsigned integer expressions physeq.cpp:124: warning: comparison between signed and unsigned integer expressions intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 phytofile.cpp -o phytofile.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 posgap.cpp -o posgap.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 ppscore.cpp -o ppscore.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 profdb.cpp -o profdb.o In file included from clustsetmsa.h:8, from profdb.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22: warning: enumeration value 'DISTANCE_Undefined' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Edit' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 profile.cpp -o profile.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 profilefrommsa.cpp -o profilefrommsa.o profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)': profilefrommsa.cpp:131: warning: comparison between signed and unsigned integer expressions profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)': profilefrommsa.cpp:230: warning: enumeration value 'ALPHA_Undefined' not handled in switch profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)': profilefrommsa.cpp:245: warning: unused variable 'uSeqCount' profilefrommsa.cpp:253: warning: unused variable 'uHydrophobicRunLength' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used profilefrommsa.cpp:15: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 progalign.cpp -o progalign.o progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)': progalign.cpp:41: warning: unused variable 'uIterCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 progress.cpp -o progress.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 progressivealign.cpp -o progressivealign.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 pwpath.cpp -o pwpath.o pwpath.cpp: In member function 'void PWPath::Validate() const': pwpath.cpp:79: warning: unused variable 'LastEdge' pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)': pwpath.cpp:212: warning: unused variable 'uEdgeIndex' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 readmx.cpp -o readmx.o readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]': readmx.cpp:83: warning: comparison between signed and unsigned integer expressions readmx.cpp:84: warning: comparison between signed and unsigned integer expressions intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used readmx.cpp:30: warning: 'unsigned int MxCharToLetter(char)' defined but not used g++ -c -g -O2 -g -Wall -O2 realigndiffs.cpp -o realigndiffs.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 realigndiffse.cpp -o realigndiffse.o realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)': realigndiffse.cpp:72: warning: unused variable 'uNewRight' realigndiffse.cpp:75: warning: unused variable 'uOldRight' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 refine.cpp -o refine.o In file included from clustsetmsa.h:8, from refine.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22: warning: enumeration value 'DISTANCE_Undefined' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Edit' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 refinehoriz.cpp -o refinehoriz.o refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)': refinehoriz.cpp:247: warning: 'bRight' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 refinesubfams.cpp -o refinesubfams.o refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)': refinesubfams.cpp:63: warning: unused variable 'uNodeCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 refinetree.cpp -o refinetree.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 refinetreee.cpp -o refinetreee.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 refinevert.cpp -o refinevert.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 refinew.cpp -o refinew.o refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)': refinew.cpp:22: warning: unused variable 'uColCountCat' refinew.cpp: In function 'void RefineW(const MSA&, MSA&)': refinew.cpp:125: warning: unused variable 'uOutCols' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 savebest.cpp -o savebest.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 scoredist.cpp -o scoredist.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 scoregaps.cpp -o scoregaps.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used scoregaps.cpp:37: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used scoregaps.cpp:80: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used g++ -c -g -O2 -g -Wall -O2 scorehistory.cpp -o scorehistory.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 scorepp.cpp -o scorepp.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 seq.cpp -o seq.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 seqvect.cpp -o seqvect.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 setblosumweights.cpp -o setblosumweights.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 setgscweights.cpp -o setgscweights.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 setnewhandler.cpp -o setnewhandler.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 spfast.cpp -o spfast.o spfast.cpp: In function 'char* GapTypeToStr(int)': spfast.cpp:18: warning: deprecated conversion from string constant to 'char*' spfast.cpp:19: warning: deprecated conversion from string constant to 'char*' spfast.cpp:20: warning: deprecated conversion from string constant to 'char*' spfast.cpp:21: warning: deprecated conversion from string constant to 'char*' spfast.cpp:24: warning: deprecated conversion from string constant to 'char*' spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)': spfast.cpp:252: warning: unused variable 'uSeqCount' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used spfast.cpp:14: warning: 'char* GapTypeToStr(int)' defined but not used spfast.cpp:59: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used g++ -c -g -O2 -g -Wall -O2 sptest.cpp -o sptest.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 stabilize.cpp -o stabilize.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 subfam.cpp -o subfam.o subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)': subfam.cpp:173: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 subfams.cpp -o subfams.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used subfams.cpp:10: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used subfams.cpp:40: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used subfams.cpp:52: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used g++ -c -g -O2 -g -Wall -O2 sw.cpp -o sw.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used sw.cpp:21: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used g++ -c -g -O2 -g -Wall -O2 termgaps.cpp -o termgaps.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 textfile.cpp -o textfile.o textfile.cpp: In member function 'void TextFile::PutChar(char)': textfile.cpp:107: warning: unused variable 'i' textfile.cpp: In member function 'void TextFile::PutString(const char*)': textfile.cpp:120: warning: unused variable 'iError' In function 'void* memset(void*, int, size_t)', inlined from 'bool TextFile::GetLine(char*, unsigned int)' at textfile.cpp:60: /usr/include/bits/string3.h:82: warning: call to '__warn_memset_zero_len' declared with attribute warning: memset used with constant zero length parameter; this could be due to transposed parameters intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 threewaywt.cpp -o threewaywt.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 tomhydro.cpp -o tomhydro.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 traceback.cpp -o traceback.o traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)': traceback.cpp:21: warning: unused variable 'uPrefixCountB' traceback.cpp:68: warning: 'cPrevEdgeType' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 tracebackopt.cpp -o tracebackopt.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 tracebacksw.cpp -o tracebacksw.o tracebacksw.cpp: In function 'void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)': tracebacksw.cpp:22: warning: unused variable 'uPrefixCountB' tracebacksw.cpp:29: warning: unused variable 'scoreMax' tracebacksw.cpp:43: warning: 'cPrevEdgeType' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 treefrommsa.cpp -o treefrommsa.o In file included from clustsetmsa.h:8, from treefrommsa.cpp:5: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22: warning: enumeration value 'DISTANCE_Undefined' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch msadist.h:22: warning: enumeration value 'DISTANCE_Edit' not handled in switch intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 typetostr.cpp -o typetostr.o typetostr.cpp: In function 'const char* SecsToStr(long unsigned int)': typetostr.cpp:13: warning: format '%02d' expects type 'int', but argument 3 has type 'long int' typetostr.cpp:13: warning: format '%02d' expects type 'int', but argument 4 has type 'long int' typetostr.cpp:13: warning: format '%02d' expects type 'int', but argument 5 has type 'long int' intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 upgma2.cpp -o upgma2.o upgma2.cpp: In member function 'virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const': upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp:371: warning: missing braces around initializer for 'dist_t [5]' upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)': upgma2.cpp:252: warning: 'dtNewDist' may be used uninitialized in this function intmath.h: At global scope: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used upgma2.cpp:68: warning: 'void ListState()' defined but not used g++ -c -g -O2 -g -Wall -O2 usage.cpp -o usage.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 validateids.cpp -o validateids.o In file included from validateids.cpp:4: intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 vtml2.cpp -o vtml2.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -c -g -O2 -g -Wall -O2 writescorefile.cpp -o writescorefile.o intmath.h:59: warning: 'double ScoreToDouble(SCORE)' defined but not used g++ -g -O2 -g -Wall -O2 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsother.o globalswin32.o gonnet.o gotowt.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm textfile.o: In function `memset': /usr/include/bits/string3.h:82: warning: memset used with constant zero length parameter; this could be due to transposed parameters strip muscle make[1]: Leaving directory `/build/buildd/muscle-3.70+fix1' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks /usr/bin/fakeroot debian/rules binary-arch test -x debian/rules dh_testroot dh_clean -k dh_installdirs -A mkdir -p "." DEB_MAKE_CHECK_TARGET unset, not running checks DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target dh_installdirs -pmuscle dh_installdocs -pmuscle dh_installexamples -pmuscle dh_installman -pmuscle dh_installinfo -pmuscle dh_installmenu -pmuscle dh_installcron -pmuscle dh_installinit -pmuscle dh_installdebconf -pmuscle dh_installemacsen -pmuscle dh_installcatalogs -pmuscle dh_installpam -pmuscle dh_installlogrotate -pmuscle dh_installlogcheck -pmuscle dh_installchangelogs -pmuscle dh_installudev -pmuscle dh_lintian -pmuscle dh_install -pmuscle dh_link -pmuscle dh_installmime -pmuscle dh_strip -pmuscle dh_strip debug symbol extraction: all non-arch-all packages for this build platform lpia: muscle dh_strip debug symbol extraction: packages to act on: muscle dh_strip debug symbol extraction: ignored packages: pkgstriptranslations: processing control file: ./debian/muscle-dbgsym/DEBIAN/control, package muscle-dbgsym, directory ./debian/muscle-dbgsym pkgstriptranslations: muscle-dbgsym does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball pkgmaintainermangler: Maintainer field overridden to "Ubuntu MOTU Developers " warning, `/build/buildd/muscle-3.70+fix1/debian/muscle-dbgsym/DEBIAN/control' contains user-defined field `Original-Maintainer' dpkg-deb: ignoring 1 warnings about the control file(s) dpkg-deb: building package `muscle-dbgsym' in `../muscle-dbgsym_3.70+fix1-2_lpia.ddeb'. dh_compress -pmuscle dh_fixperms -pmuscle dh_makeshlibs -pmuscle dh_installdeb -pmuscle dh_perl -pmuscle dh_shlibdeps -pmuscle dh_gencontrol -pmuscle dpkg-gencontrol: warning: unknown substitution variable ${misc:Depends} # symlink identical documentation to depending packages [ -n "$CDBS_NO_DOC_SYMLINKING" ] || \ [ -h debian/muscle/usr/share/doc ] || \ [ ! -d debian/muscle/usr/share/doc ] || \ for dep in `perl -ne 'if (/^(Pre-)?Depends:/) {s/^\w+://; foreach (split /,/) { split; print($_[0], "\n"); } }' debian/muscle/DEBIAN/control`; do \ if [ -d debian/$dep/usr/share/doc ]; then \ echo "Searching for duplicated docs in dependency $dep..."; \ rootdir=`pwd`; \ (cd debian/muscle/usr/share/doc/muscle; find -type f ! -name copyright | while read f; do \ thisfile="$rootdir/debian/muscle/usr/share/doc/muscle/$f"; \ depfile="$rootdir/debian/$dep/usr/share/doc/$dep/$f"; \ if [ -f $depfile -o -L $depfile ] && zcmp $thisfile $depfile >/dev/null; then \ echo " symlinking $f in muscle to file in $dep"; \ rm $thisfile; ln -s /usr/share/doc/$dep/$f $thisfile; \ fi; \ done ); \ fi; \ done # symlink identical Gnome help files within packages if [ -z "$CDBS_NO_GNOME_HELP_SYMLINKING" ] && [ -d debian/muscle/usr/share/gnome/help ]; then \ cd debian/muscle && LC_ALL=C fdupes -r1nq usr/share/gnome/help | while read s; do \ set -- $(echo $s | tr ' ' '\n' | sort); \ f=$1; shift; \ for d; do \ echo "symlinking duplicate Gnome help file $d to $f"; \ rm $d; ln -s /$f $d; \ done; \ done; \ fi dh_link -p muscle dh_md5sums -pmuscle dh_builddeb -pmuscle pkgstriptranslations: processing control file: ./debian/muscle/DEBIAN/control, package muscle, directory ./debian/muscle pkgstriptranslations: muscle does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball pkgmaintainermangler: Maintainer field overridden to "Ubuntu MOTU Developers " warning, `debian/muscle/DEBIAN/control' contains user-defined field `Original-Maintainer' dpkg-deb: ignoring 1 warnings about the control file(s) dpkg-deb: building package `muscle' in `../muscle_3.70+fix1-2_lpia.deb'. dpkg-genchanges -B -mUbuntu/lpia Build Daemon >../muscle_3.70+fix1-2_lpia.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20080509-2312 Publishing debug debs. chroot-autobuild/build/buildd/muscle_3.70+fix1-2_lpia.deb: new debian package, version 2.0. size 160672 bytes: control archive= 1094 bytes. 829 bytes, 20 lines control 457 bytes, 7 lines md5sums 213 bytes, 7 lines * postinst #!/bin/sh 217 bytes, 8 lines * prerm #!/bin/sh Package: muscle Version: 3.70+fix1-2 Architecture: lpia Maintainer: Ubuntu MOTU Developers Original-Maintainer: Debian-Med Packaging Team Installed-Size: 476 Depends: libc6 (>= 2.7-1), libgcc1 (>= 1:4.3), libstdc++6 (>= 4.3) Enhances: seaview Conflicts: muscle-doc Replaces: muscle-doc Provides: muscle-doc Section: science Priority: optional Homepage: http://www.drive5.com/muscle/ Description: Multiple alignment program of protein sequences MUSCLE is a multiple alignment program for protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there. chroot-autobuild/build/buildd/muscle_3.70+fix1-2_lpia.deb: drwxr-xr-x root/root 0 2008-05-09 23:11 ./ drwxr-xr-x root/root 0 2008-05-09 23:11 ./usr/ drwxr-xr-x root/root 0 2008-05-09 23:11 ./usr/bin/ -rwxr-xr-x root/root 308808 2008-05-09 23:11 ./usr/bin/muscle drwxr-xr-x root/root 0 2008-05-09 23:11 ./usr/share/ drwxr-xr-x root/root 0 2008-05-09 23:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2008-05-09 23:11 ./usr/share/doc/muscle/ -rw-r--r-- root/root 96687 2008-05-09 23:11 ./usr/share/doc/muscle/muscle.html -rw-r--r-- root/root 779 2008-05-09 23:11 ./usr/share/doc/muscle/README.Debian -rw-r--r-- root/root 1176 2008-05-09 23:11 ./usr/share/doc/muscle/copyright -rw-r--r-- root/root 1140 2008-05-09 23:11 ./usr/share/doc/muscle/changelog.Debian.gz drwxr-xr-x root/root 0 2008-05-09 23:11 ./usr/share/doc-base/ -rw-r--r-- root/root 716 2008-05-09 23:11 ./usr/share/doc-base/muscle-manual drwxr-xr-x root/root 0 2008-05-09 23:11 ./usr/share/man/ drwxr-xr-x root/root 0 2008-05-09 23:11 ./usr/share/man/man1/ -rw-r--r-- root/root 1291 2008-05-09 23:11 ./usr/share/man/man1/muscle.1.gz muscle_3.70+fix1-2_lpia.changes: Format: 1.7 Date: Thu, 14 Feb 2008 10:44:17 +0900 Source: muscle Binary: muscle Architecture: lpia Version: 3.70+fix1-2 Distribution: intrepid Urgency: low Maintainer: Ubuntu/lpia Build Daemon Changed-By: Charles Plessy Description: muscle - Multiple alignment program of protein sequences Closes: 465607 Changes: muscle (3.70+fix1-2) unstable; urgency=low . * debian/control Conflicts: and Replaces: muscle-doc (Closes: #465607) Files: f09d4f3c73772101e643024436347be0 160672 science optional muscle_3.70+fix1-2_lpia.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/muscle-3.70+fix1 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --root=/home/buildd/build-587248-1518481/chroot-autobuild --purge intltool-debian groff-base m4 gettext file libhtml-parser-perl intltool automake1.7 cdbs libwww-perl liburi-perl html2text gettext-base debhelper libhtml-tree-perl ifupdown autotools-dev po-debconf net-tools libxml-parser-perl libmagic1 libhtml-tagset-perl libexpat1 netbase bsdmainutils fdupes update-inetd man-db autoconf (Reading database ... 11912 files and directories currently installed.) Removing cdbs ... Removing debhelper ... Removing po-debconf ... Removing fdupes ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. dpkg - warning: while removing man-db, directory `/usr/share/doc/man-db/examples' not empty so not removed. dpkg - warning: while removing man-db, directory `/usr/share/doc/man-db' not empty so not removed. dpkg - warning: while removing man-db, directory `/usr/share/man-db' not empty so not removed. dpkg - warning: while removing man-db, directory `/usr/share/bug/man-db' not empty so not removed. dpkg - warning: while removing man-db, directory `/usr/lib/man-db' not empty so not removed. Removing intltool-debian ... Removing groff-base ... Purging configuration files for groff-base ... Removing intltool ... Removing automake1.7 ... Removing html2text ... Purging configuration files for html2text ... Removing autotools-dev ... Removing libxml-parser-perl ... Removing libexpat1 ... Purging configuration files for libexpat1 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing autoconf ... Purging configuration files for autoconf ... Removing m4 ... Removing gettext ... Removing file ... Purging configuration files for file ... Removing libwww-perl ... Removing gettext-base ... Removing libhtml-tree-perl ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing netbase ... Purging configuration files for netbase ... Removing update-inetd ... Purging configuration files for update-inetd ... Removing libhtml-parser-perl ... Removing liburi-perl ... Removing ifupdown ... Purging configuration files for ifupdown ... Removing net-tools ... Removing libhtml-tagset-perl ... Processing triggers for libc6 ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20080509-2312 Build needed 00:00:31, 5712k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '587248-1518481'] Scanning for processes to kill in build 587248-1518481... Scanning for processes to kill in build /home/buildd/build-587248-1518481/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '587248-1518481'] Unmounting chroot for build 587248-1518481... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '587248-1518481'] Removing build 587248-1518481