RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux postal04 3.13.0-16-generic #36-Ubuntu SMP Tue Mar 4 23:03:28 UTC 2014 ppc64le Buildd toolchain package versions: launchpad-buildd_121~0.IS.08.04.0 python-lpbuildd_121~0.IS.08.04.0 dpkg-dev_1.17.5ubuntu4. Syncing the system clock with the buildd NTP service... 11 Mar 08:53:56 ntpdate[14508]: adjust time server 10.211.37.1 offset -0.000012 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5710758', '/home/buildd/filecache-default/aabc9cb3b8af7e262bbf6bfae32b9f7021db16d4'] Unpacking chroot for build PACKAGEBUILD-5710758 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5710758'] Mounting chroot for build PACKAGEBUILD-5710758 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5710758', 'deb http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu trusty main universe', 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu trusty main', 'deb http://ftpmaster.internal/ubuntu trusty main universe'] Overriding sources.list in build-PACKAGEBUILD-5710758 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5710758', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-5710758 Ign http://ftpmaster.internal trusty InRelease Ign http://ppa.launchpad.net trusty InRelease Ign http://rebuild-test.internal trusty InRelease Ign http://archive-team.internal trusty InRelease Get:1 http://ftpmaster.internal trusty Release.gpg [933 B] Get:2 http://ppa.launchpad.net trusty Release.gpg [316 B] Ign http://rebuild-test.internal trusty Release.gpg Ign http://archive-team.internal trusty Release.gpg Get:3 http://ftpmaster.internal trusty Release [58.5 kB] Get:4 http://rebuild-test.internal trusty Release [58.5 kB] Get:5 http://ppa.launchpad.net trusty Release [14.0 kB] Hit http://archive-team.internal trusty Release Ign http://ppa.launchpad.net trusty Release Ign http://archive-team.internal trusty/main ppc64el Packages/DiffIndex Get:6 http://ppa.launchpad.net trusty/main ppc64el Packages [11.8 kB] Get:7 http://ftpmaster.internal trusty/main ppc64el Packages [1235 kB] Get:8 http://rebuild-test.internal trusty/main ppc64el Packages [1115 kB] Ign http://ppa.launchpad.net trusty/main Translation-en Ign http://archive-team.internal trusty/main Translation-en Hit http://archive-team.internal trusty/main ppc64el Packages Get:9 http://rebuild-test.internal trusty/universe ppc64el Packages [2182 kB] Get:10 http://ftpmaster.internal trusty/universe ppc64el Packages [5066 kB] Get:11 http://rebuild-test.internal trusty/main Translation-en [726 kB] Get:12 http://rebuild-test.internal trusty/universe Translation-en [1643 kB] Get:13 http://ftpmaster.internal trusty/main Translation-en [765 kB] Get:14 http://ftpmaster.internal trusty/universe Translation-en [4053 kB] Fetched 16.9 MB in 9s (1785 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net trusty Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 1E9377A2BA9EF27F Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libtasn1-3 Use 'apt-get autoremove' to remove it. The following NEW packages will be installed: libtasn1-6 The following packages will be upgraded: apt apt-transport-https base-files bash binutils bsdutils cpp-4.8 dpkg dpkg-dev g++-4.8 gcc-4.8 gcc-4.8-base gcc-4.9-base gnupg gpgv initramfs-tools initramfs-tools-bin libapt-pkg4.12 libatomic1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcloog-isl4 libdpkg-perl libgcc-4.8-dev libgcc1 libgnutls26 libgomp1 libitm1 libmount1 libp11-kit0 libreadline6 libsqlite3-0 libstdc++-4.8-dev libstdc++6 libudev1 libuuid1 linux-libc-dev mount multiarch-support pkg-create-dbgsym policyrcd-script-zg2 readline-common tzdata udev util-linux 48 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 36.5 MB of archives. After this operation, 166 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! base-files bash dpkg libc6-dev libc-dev-bin linux-libc-dev libc-bin gcc-4.9-base libgcc1 libc6 libitm1 libgomp1 libatomic1 libcloog-isl4 g++-4.8 gcc-4.8 cpp-4.8 libstdc++-4.8-dev binutils libgcc-4.8-dev gcc-4.8-base libstdc++6 libapt-pkg4.12 readline-common libreadline6 gpgv gnupg apt libp11-kit0 libtasn1-6 libgnutls26 libsqlite3-0 udev libudev1 multiarch-support initramfs-tools initramfs-tools-bin apt-transport-https dpkg-dev libdpkg-perl policyrcd-script-zg2 Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main mount ppc64el 2.20.1-5.1ubuntu15 [114 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libc6-dev ppc64el 2.19-0ubuntu3~ppa1 [1949 kB] Get:3 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main base-files ppc64el 7.2ubuntu4 [61.2 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main tzdata all 2014a-1 [180 kB] Get:5 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main bash ppc64el 4.3-2ubuntu1 [608 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main util-linux ppc64el 2.20.1-5.1ubuntu15 [455 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libc-dev-bin ppc64el 2.19-0ubuntu3~ppa1 [66.3 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main bsdutils ppc64el 1:2.20.1-5.1ubuntu15 [33.3 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libc-bin ppc64el 2.19-0ubuntu3~ppa1 [1158 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main libuuid1 ppc64el 2.20.1-5.1ubuntu15 [11.5 kB] Get:11 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main dpkg ppc64el 1.17.5ubuntu5 [1977 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libblkid1 ppc64el 2.20.1-5.1ubuntu15 [60.6 kB] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libc6 ppc64el 2.19-0ubuntu3~ppa1 [4420 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libmount1 ppc64el 2.20.1-5.1ubuntu15 [53.2 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main pkg-create-dbgsym all 0.64 [7564 B] Get:16 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libitm1 ppc64el 4.8.2-16ubuntu6x1 [28.9 kB] Get:17 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libgomp1 ppc64el 4.8.2-16ubuntu6x1 [22.0 kB] Get:18 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libatomic1 ppc64el 4.8.2-16ubuntu6x1 [7888 B] Get:19 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main g++-4.8 ppc64el 4.8.2-16ubuntu6x1 [6200 kB] Get:20 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main linux-libc-dev ppc64el 3.13.0-16.36 [757 kB] Get:21 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main gcc-4.9-base ppc64el 4.9-20140303-0ubuntu3 [14.0 kB] Get:22 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main gcc-4.8 ppc64el 4.8.2-16ubuntu6x1 [4834 kB] Get:23 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libgcc1 ppc64el 1:4.9-20140303-0ubuntu3 [28.9 kB] Get:24 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libcloog-isl4 ppc64el 0.18.2-1 [57.1 kB] Get:25 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main binutils ppc64el 2.24-4ubuntu1 [2240 kB] Get:26 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main cpp-4.8 ppc64el 4.8.2-16ubuntu6x1 [4427 kB] Get:27 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libstdc++-4.8-dev ppc64el 4.8.2-16ubuntu6x1 [1087 kB] Get:28 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libgcc-4.8-dev ppc64el 4.8.2-16ubuntu6x1 [245 kB] Get:29 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main gcc-4.8-base ppc64el 4.8.2-16ubuntu6x1 [15.2 kB] Get:30 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main libstdc++6 ppc64el 4.8.2-16ubuntu6x1 [270 kB] Get:31 http://ppa.launchpad.net/ubuntu-toolchain-r/aarch64/ubuntu/ trusty/main multiarch-support ppc64el 2.19-0ubuntu3~ppa1 [4488 B] Get:32 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libapt-pkg4.12 ppc64el 0.9.15.4ubuntu2 [622 kB] Get:33 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main readline-common all 6.3-1ubuntu1 [51.2 kB] Get:34 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libreadline6 ppc64el 6.3-1ubuntu1 [113 kB] Get:35 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main gpgv ppc64el 1.4.16-1ubuntu2 [167 kB] Get:36 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main gnupg ppc64el 1.4.16-1ubuntu2 [637 kB] Get:37 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main apt ppc64el 0.9.15.4ubuntu2 [957 kB] Get:38 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libp11-kit0 ppc64el 0.20.2-1ubuntu2 [75.4 kB] Get:39 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libtasn1-6 ppc64el 3.4-3 [42.6 kB] Get:40 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libgnutls26 ppc64el 2.12.23-12ubuntu2 [358 kB] Get:41 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libsqlite3-0 ppc64el 3.8.2-1ubuntu2 [315 kB] Get:42 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main udev ppc64el 204-5ubuntu13 [721 kB] Get:43 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libudev1 ppc64el 204-5ubuntu13 [32.8 kB] Get:44 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main initramfs-tools all 0.103ubuntu4 [44.2 kB] Get:45 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main initramfs-tools-bin ppc64el 0.103ubuntu4 [8638 B] Get:46 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main apt-transport-https ppc64el 0.9.15.4ubuntu2 [24.8 kB] Get:47 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main dpkg-dev all 1.17.5ubuntu5 [726 kB] Get:48 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libdpkg-perl all 1.17.5ubuntu5 [178 kB] Get:49 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main policyrcd-script-zg2 all 0.1-2 [5232 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 36.5 MB in 6s (5377 kB/s) (Reading database ... 11636 files and directories currently installed.) Preparing to unpack .../base-files_7.2ubuntu4_ppc64el.deb ... Unpacking base-files (7.2ubuntu4) over (7.2ubuntu3) ... Setting up base-files (7.2ubuntu4) ... (Reading database ... 11636 files and directories currently installed.) Preparing to unpack .../bash_4.3-2ubuntu1_ppc64el.deb ... Unpacking bash (4.3-2ubuntu1) over (4.2-5ubuntu3) ... Setting up bash (4.3-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 11637 files and directories currently installed.) Preparing to unpack .../dpkg_1.17.5ubuntu5_ppc64el.deb ... Unpacking dpkg (1.17.5ubuntu5) over (1.17.5ubuntu4) ... Setting up dpkg (1.17.5ubuntu5) ... (Reading database ... 11637 files and directories currently installed.) Preparing to unpack .../mount_2.20.1-5.1ubuntu15_ppc64el.deb ... Unpacking mount (2.20.1-5.1ubuntu15) over (2.20.1-5.1ubuntu14) ... Setting up mount (2.20.1-5.1ubuntu15) ... (Reading database ... 11637 files and directories currently installed.) Preparing to unpack .../tzdata_2014a-1_all.deb ... Unpacking tzdata (2014a-1) over (2013i-1) ... Setting up tzdata (2014a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Mar 11 12:54:19 UTC 2014. Universal Time is now: Tue Mar 11 12:54:19 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 11637 files and directories currently installed.) Preparing to unpack .../util-linux_2.20.1-5.1ubuntu15_ppc64el.deb ... Unpacking util-linux (2.20.1-5.1ubuntu15) over (2.20.1-5.1ubuntu14) ... Setting up util-linux (2.20.1-5.1ubuntu15) ... (Reading database ... 11637 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.19-0ubuntu3~ppa1_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.19-0ubuntu3~ppa1) over (2.19-0ubuntu2) ... Preparing to unpack .../libc-dev-bin_2.19-0ubuntu3~ppa1_ppc64el.deb ... 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(Reading database ... 11638 files and directories currently installed.) Preparing to unpack .../gpgv_1.4.16-1ubuntu2_ppc64el.deb ... Unpacking gpgv (1.4.16-1ubuntu2) over (1.4.16-1ubuntu1) ... Setting up gpgv (1.4.16-1ubuntu2) ... (Reading database ... 11638 files and directories currently installed.) Preparing to unpack .../gnupg_1.4.16-1ubuntu2_ppc64el.deb ... Unpacking gnupg (1.4.16-1ubuntu2) over (1.4.16-1ubuntu1) ... Setting up gnupg (1.4.16-1ubuntu2) ... (Reading database ... 11638 files and directories currently installed.) Preparing to unpack .../apt_0.9.15.4ubuntu2_ppc64el.deb ... Unpacking apt (0.9.15.4ubuntu2) over (0.9.15.4ubuntu1) ... Setting up apt (0.9.15.4ubuntu2) ... Processing triggers for libc-bin (2.19-0ubuntu3~ppa1) ... (Reading database ... 11638 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.20.1-5.1ubuntu15_ppc64el.deb ... Unpacking bsdutils (1:2.20.1-5.1ubuntu15) over (1:2.20.1-5.1ubuntu14) ... Setting up bsdutils (1:2.20.1-5.1ubuntu15) ... (Reading database ... 11638 files and directories currently installed.) Preparing to unpack .../libuuid1_2.20.1-5.1ubuntu15_ppc64el.deb ... Unpacking libuuid1:ppc64el (2.20.1-5.1ubuntu15) over (2.20.1-5.1ubuntu14) ... Setting up libuuid1:ppc64el (2.20.1-5.1ubuntu15) ... Processing triggers for libc-bin (2.19-0ubuntu3~ppa1) ... (Reading database ... 11638 files and directories currently installed.) Preparing to unpack .../libblkid1_2.20.1-5.1ubuntu15_ppc64el.deb ... Unpacking libblkid1:ppc64el (2.20.1-5.1ubuntu15) over (2.20.1-5.1ubuntu14) ... Setting up libblkid1:ppc64el (2.20.1-5.1ubuntu15) ... Processing triggers for libc-bin (2.19-0ubuntu3~ppa1) ... (Reading database ... 11638 files and directories currently installed.) Preparing to unpack .../libmount1_2.20.1-5.1ubuntu15_ppc64el.deb ... Unpacking libmount1:ppc64el (2.20.1-5.1ubuntu15) over (2.20.1-5.1ubuntu14) ... Setting up libmount1:ppc64el (2.20.1-5.1ubuntu15) ... Processing triggers for libc-bin (2.19-0ubuntu3~ppa1) ... (Reading database ... 11638 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.20.2-1ubuntu2_ppc64el.deb ... Unpacking libp11-kit0:ppc64el (0.20.2-1ubuntu2) over (0.20.2-1ubuntu1) ... Selecting previously unselected package libtasn1-6:ppc64el. Preparing to unpack .../libtasn1-6_3.4-3_ppc64el.deb ... Unpacking libtasn1-6:ppc64el (3.4-3) ... Preparing to unpack .../libgnutls26_2.12.23-12ubuntu2_ppc64el.deb ... Unpacking libgnutls26:ppc64el (2.12.23-12ubuntu2) over (2.12.23-1ubuntu5) ... Preparing to unpack .../libsqlite3-0_3.8.2-1ubuntu2_ppc64el.deb ... Unpacking libsqlite3-0:ppc64el (3.8.2-1ubuntu2) over (3.8.2-1ubuntu2) ... Preparing to unpack .../udev_204-5ubuntu13_ppc64el.deb ... Adding 'diversion of /bin/udevadm to /bin/udevadm.upgrade by fake-udev' Unpacking udev (204-5ubuntu13) over (204-5ubuntu11) ... Preparing to unpack .../libudev1_204-5ubuntu13_ppc64el.deb ... 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Setting up libtasn1-6:ppc64el (3.4-3) ... Setting up libgnutls26:ppc64el (2.12.23-12ubuntu2) ... Setting up libsqlite3-0:ppc64el (3.8.2-1ubuntu2) ... Setting up libudev1:ppc64el (204-5ubuntu13) ... Setting up udev (204-5ubuntu13) ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /bin/udevadm to /bin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up initramfs-tools-bin (0.103ubuntu4) ... Setting up initramfs-tools (0.103ubuntu4) ... update-initramfs: deferring update (trigger activated) Setting up apt-transport-https (0.9.15.4ubuntu2) ... Setting up libdpkg-perl (1.17.5ubuntu5) ... Setting up dpkg-dev (1.17.5ubuntu5) ... Setting up pkg-create-dbgsym (0.64) ... Setting up policyrcd-script-zg2 (0.1-2) ... Processing triggers for libc-bin (2.19-0ubuntu3~ppa1) ... Processing triggers for initramfs-tools (0.103ubuntu4) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5710758', 'ppc64el', 'trusty', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty', '--purpose=COPY', '--architecture=ppc64el', '--comp=universe', 'muscle_3.8.31-1.dsc'] Initiating build PACKAGEBUILD-5710758 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.13.0-16-generic #36-Ubuntu SMP Tue Mar 4 23:03:28 UTC 2014 ppc64le Automatic build of muscle_3.8.31-1 on postal04 by sbuild/ppc64el 1.170.5 Build started at 20140311-0854 ****************************************************************************** muscle_3.8.31-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 8), cdbs Checking for already installed source dependencies... debhelper: missing cdbs: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper cdbs Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libtasn1-3 Use 'apt-get autoremove' to remove it. The following extra packages will be installed: apparmor-easyprof autoconf automake autotools-dev bsdmainutils dh-apparmor dh-python dh-translations file gettext gettext-base groff-base intltool intltool-debian libasprintf0c2 libcroco3 libencode-locale-perl libexpat1 libfile-listing-perl libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-html-perl libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libmpdec2 libnet-http-perl libnet-ssleay-perl libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsigsegv2 libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 m4 man-db mime-support netbase po-debconf python python-minimal python-scour python2.7 python2.7-minimal python3 python3-minimal python3.4 python3.4-minimal Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation devscripts dh-make gettext-doc groff libdata-dump-perl libcrypt-ssleay-perl libauthen-ntlm-perl less www-browser libmail-box-perl python-doc python-tk python-rsvg python-cairo python2.7-doc binfmt-support python3-doc python3-tk python3.4-doc Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info libhtml-format-perl libio-socket-inet6-perl libio-socket-ip-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof autoconf automake autotools-dev bsdmainutils cdbs debhelper dh-apparmor dh-python dh-translations file gettext gettext-base groff-base intltool intltool-debian libasprintf0c2 libcroco3 libencode-locale-perl libexpat1 libfile-listing-perl libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-html-perl libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libmpdec2 libnet-http-perl libnet-ssleay-perl libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsigsegv2 libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 m4 man-db mime-support netbase po-debconf python python-minimal python-scour python2.7 python2.7-minimal python3 python3-minimal python3.4 python3.4-minimal 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded. Need to get 16.1 MB of archives. After this operation, 70.6 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libexpat1 libmagic1 libasprintf0c2 libglib2.0-0 libpipeline1 libxml2 groff-base bsdmainutils man-db libcroco3 libmpdec2 mime-support libsigsegv2 libunistring0 libpython2.7-minimal python2.7-minimal python3-minimal libpython3-stdlib python3 file netbase gettext-base m4 autoconf autotools-dev automake gettext intltool-debian po-debconf apparmor-easyprof dh-apparmor debhelper liburi-perl libencode-locale-perl libhttp-date-perl libfile-listing-perl libhtml-tagset-perl libhtml-parser-perl libhtml-tree-perl libio-html-perl liblwp-mediatypes-perl libhttp-message-perl libhttp-cookies-perl libhttp-negotiate-perl libnet-ssleay-perl libio-socket-ssl-perl libnet-http-perl liblwp-protocol-https-perl libwww-robotrules-perl libwww-perl libxml-parser-perl intltool libpython2.7-stdlib python2.7 python-minimal libpython-stdlib python python-scour cdbs Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.4-minimal ppc64el 3.4~rc3-0ubuntu1 [441 kB] Get:2 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libexpat1 ppc64el 2.1.0-4ubuntu1 [80.1 kB] Get:3 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libmagic1 ppc64el 1:5.14-2ubuntu2 [194 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.4-stdlib ppc64el 3.4~rc3-0ubuntu1 [1974 kB] Get:5 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libasprintf0c2 ppc64el 0.18.3.1-1ubuntu2 [6742 B] Get:6 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libglib2.0-0 ppc64el 2.39.91-0ubuntu2 [996 kB] Get:7 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libpipeline1 ppc64el 1.2.6-2 [22.6 kB] Get:8 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libxml2 ppc64el 2.9.1+dfsg1-3ubuntu4 [601 kB] Get:9 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main groff-base ppc64el 1.22.2-5 [1249 kB] Get:10 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main bsdmainutils ppc64el 9.0.5ubuntu1 [173 kB] Get:11 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main man-db ppc64el 2.6.6-1 [846 kB] Get:12 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libcroco3 ppc64el 0.6.8-2ubuntu1 [75.5 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main python3.4-minimal ppc64el 3.4~rc3-0ubuntu1 [1145 kB] Get:14 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libmpdec2 ppc64el 2.4.0-6 [83.9 kB] Get:15 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main mime-support all 3.54ubuntu1 [29.3 kB] Get:16 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libsigsegv2 ppc64el 2.10-2 [13.8 kB] Get:17 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libunistring0 ppc64el 0.9.3-5ubuntu3 [263 kB] Get:18 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libpython2.7-minimal ppc64el 2.7.6-7 [307 kB] Get:19 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main python2.7-minimal ppc64el 2.7.6-7 [931 kB] Get:20 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main python3-minimal ppc64el 3.4~rc1-1 [23.3 kB] Get:21 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libpython3-stdlib ppc64el 3.4~rc1-1 [6970 B] Get:22 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main python3 ppc64el 3.4~rc1-1 [8660 B] Get:23 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main file ppc64el 1:5.14-2ubuntu2 [19.3 kB] Get:24 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main netbase all 5.2 [12.9 kB] Get:25 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main gettext-base ppc64el 0.18.3.1-1ubuntu2 [47.2 kB] Get:26 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main m4 ppc64el 1.4.17-2ubuntu1 [194 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main python3.4 ppc64el 3.4~rc3-0ubuntu1 [160 kB] Get:28 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main autoconf all 2.69-5 [322 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main dh-python all 1.20140128-1ubuntu4 [50.9 kB] Get:30 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main autotools-dev all 20130810.1 [40.1 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main dh-translations all 119 [21.5 kB] Get:32 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main automake all 1:1.14.1-2ubuntu1 [510 kB] Get:33 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main gettext ppc64el 0.18.3.1-1ubuntu2 [840 kB] Get:34 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [24.6 kB] Get:35 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [207 kB] Get:36 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main apparmor-easyprof all 2.8.0-0ubuntu38 [20.0 kB] Get:37 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main dh-apparmor all 2.8.0-0ubuntu38 [7310 B] Get:38 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main debhelper all 9.20131227ubuntu1 [603 kB] Get:39 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main liburi-perl all 1.60-1 [84.0 kB] Get:40 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libencode-locale-perl all 1.03-1 [11.7 kB] Get:41 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libhttp-date-perl all 6.02-1 [9780 B] Get:42 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libfile-listing-perl all 6.04-1 [9244 B] Get:43 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libhtml-tagset-perl all 3.20-2 [12.2 kB] Get:44 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libhtml-parser-perl ppc64el 3.71-1build1 [94.9 kB] Get:45 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libhtml-tree-perl all 5.03-1 [197 kB] Get:46 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libio-html-perl all 1.00-1 [14.5 kB] Get:47 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main liblwp-mediatypes-perl all 6.02-1 [19.4 kB] Get:48 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libhttp-message-perl all 6.06-1 [73.7 kB] Get:49 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libhttp-cookies-perl all 6.00-2 [21.8 kB] Get:50 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libhttp-negotiate-perl all 6.00-2 [12.6 kB] Get:51 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libnet-ssleay-perl ppc64el 1.58-1 [231 kB] Get:52 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libio-socket-ssl-perl all 1.965-1ubuntu1 [73.8 kB] Get:53 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libnet-http-perl all 6.06-1 [22.8 kB] Get:54 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main liblwp-protocol-https-perl all 6.04-2 [7354 B] Get:55 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libwww-robotrules-perl all 6.01-1 [13.3 kB] Get:56 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libwww-perl all 6.05-2 [146 kB] Get:57 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libxml-parser-perl ppc64el 2.41-1build3 [199 kB] Get:58 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main intltool all 0.50.2-2 [44.4 kB] Get:59 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libpython2.7-stdlib ppc64el 2.7.6-7 [1771 kB] Get:60 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main python2.7 ppc64el 2.7.6-7 [194 kB] Get:61 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main python-minimal ppc64el 2.7.5-5ubuntu3 [27.6 kB] Get:62 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main libpython-stdlib ppc64el 2.7.5-5ubuntu3 [7020 B] Get:63 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main python ppc64el 2.7.5-5ubuntu3 [133 kB] Get:64 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main python-scour all 0.26-3build1 [40.6 kB] Get:65 http://rebuild-test.internal/ubuntu-test-rebuild-20140307/ubuntu/ trusty/main cdbs all 0.4.122ubuntu2 [42.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.1 MB in 9s (1746 kB/s) Selecting previously unselected package libexpat1:ppc64el. (Reading database ... 11647 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-4ubuntu1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.1.0-4ubuntu1) ... Selecting previously unselected package libmagic1:ppc64el. Preparing to unpack .../libmagic1_1%3a5.14-2ubuntu2_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.14-2ubuntu2) ... Selecting previously unselected package libasprintf0c2:ppc64el. Preparing to unpack .../libasprintf0c2_0.18.3.1-1ubuntu2_ppc64el.deb ... Unpacking libasprintf0c2:ppc64el (0.18.3.1-1ubuntu2) ... Selecting previously unselected package libglib2.0-0:ppc64el. Preparing to unpack .../libglib2.0-0_2.39.91-0ubuntu2_ppc64el.deb ... Unpacking libglib2.0-0:ppc64el (2.39.91-0ubuntu2) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../libpipeline1_1.2.6-2_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.2.6-2) ... Selecting previously unselected package libxml2:ppc64el. 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Preparing to unpack .../cdbs_0.4.122ubuntu2_all.deb ... Unpacking cdbs (0.4.122ubuntu2) ... Setting up libexpat1:ppc64el (2.1.0-4ubuntu1) ... Setting up libmagic1:ppc64el (1:5.14-2ubuntu2) ... Setting up libasprintf0c2:ppc64el (0.18.3.1-1ubuntu2) ... Setting up libglib2.0-0:ppc64el (2.39.91-0ubuntu2) ... No schema files found: doing nothing. Setting up libpipeline1:ppc64el (1.2.6-2) ... Setting up libxml2:ppc64el (2.9.1+dfsg1-3ubuntu4) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.6-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:ppc64el (0.6.8-2ubuntu1) ... Setting up libmpdec2:ppc64el (2.4.0-6) ... Setting up libpython3.4-minimal:ppc64el (3.4~rc3-0ubuntu1) ... 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Toolchain package versions: libc6-dev_2.19-0ubuntu3~ppa1 make_3.81-8.2ubuntu3 dpkg-dev_1.17.5ubuntu5 gcc-4.8_4.8.2-16ubuntu6x1 g++-4.8_4.8.2-16ubuntu6x1 binutils_2.24-4ubuntu1 libstdc++-4.8-dev_4.8.2-16ubuntu6x1 libstdc++6_4.8.2-16ubuntu6x1 ------------------------------------------------------------------------------ gpgv: Signature made Sun Nov 13 09:46:18 2011 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./muscle_3.8.31-1.dsc dpkg-source: info: extracting muscle in muscle-3.8.31 dpkg-source: info: unpacking muscle_3.8.31.orig.tar.gz dpkg-source: info: applying muscle_3.8.31-1.diff.gz dpkg-buildpackage: source package muscle dpkg-buildpackage: source version 1:3.8.31-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build muscle-3.8.31 dpkg-buildpackage: host architecture ppc64el dpkg-source: warning: unknown information field 'Dm-Upload-Allowed' in input data in general section of control info file /usr/bin/fakeroot debian/rules clean test -x debian/rules dh_clean rm -f *.o make.err make.out muscle debian/rules build-arch test -x debian/rules mkdir -p "." g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aligngivenpath.o aligngivenpath.cpp aligngivenpath.cpp: In function 'void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)': aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ In file included from muscle.h:34:0, from aligngivenpath.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aligngivenpathsw.o aligngivenpathsw.cpp aligngivenpathsw.cpp: In function 'void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)': aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)': aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ In file included from muscle.h:34:0, from aligngivenpathsw.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aligntwomsas.o aligntwomsas.cpp In file included from muscle.h:34:0, from aligntwomsas.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aligntwoprofs.o aligntwoprofs.cpp In file included from muscle.h:34:0, from aligntwoprofs.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aln.o aln.cpp In file included from muscle.h:34:0, from aln.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o alpha.o alpha.cpp alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)': alpha.cpp:84:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (Alpha) ^ In file included from muscle.h:34:0, from alpha.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o anchors.o anchors.cpp anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)': anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable] unsigned uWindowCenter = uBestColIndex + uWindowLength/2; ^ In file included from muscle.h:34:0, from anchors.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function] static void FindBestColsGrade(const SCORE Score[], unsigned uCount, ^ anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function] static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[], ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o bittraceback.o bittraceback.cpp bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)': bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable] char Bits = TraceBack[uLengthA][uLengthB]; ^ In file included from muscle.h:34:0, from bittraceback.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function] static const char *BitsToStr(char Bits) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o blosum62.o blosum62.cpp In file included from muscle.h:34:0, from blosum62.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o blosumla.o blosumla.cpp In file included from muscle.h:34:0, from blosumla.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable] static float Blosum62LA[20][20] = ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o clust.o clust.cpp clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)': clust.cpp:167:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)': clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)': clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)': clust.cpp:295:9: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] switch (m_CentroidStyle) ^ clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)': clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable] const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex); ^ clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const': clust.cpp:611:9: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ In file included from muscle.h:34:0, from clust.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o cluster.o cluster.cpp cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)': cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable] bool bFound = false; ^ cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable] double dMaxDist = 0.0; ^ cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized in this function [-Wmaybe-uninitialized] ClusterNode &Child2 = m_Nodes[uIndexClosest2]; ^ cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized in this function [-Wmaybe-uninitialized] ClusterNode &Child1 = m_Nodes[uIndexClosest1]; ^ In file included from muscle.h:34:0, from cluster.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o clwwt.o clwwt.cpp In file included from muscle.h:34:0, from clwwt.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o color.o color.cpp In file included from muscle.h:34:0, from color.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function] static int BlosumScore(char c1, char c2) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o cons.o cons.cpp In file included from muscle.h:34:0, from cons.cpp:7: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o diaglist.o diaglist.cpp diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)': diaglist.cpp:12:23: warning: 'uStartPosB' may be used uninitialized in this function [-Wmaybe-uninitialized] m_Diags[m_uCount] = d; ^ diaglist.cpp:52:11: note: 'uStartPosB' was declared here unsigned uStartPosB; ^ diaglist.cpp:12:23: warning: 'uStartPosA' may be used uninitialized in this function [-Wmaybe-uninitialized] m_Diags[m_uCount] = d; ^ diaglist.cpp:51:11: note: 'uStartPosA' was declared here unsigned uStartPosA; ^ In file included from muscle.h:34:0, from diaglist.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o diffobjscore.o diffobjscore.cpp diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)': diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable] const unsigned uColCount = msa.GetColCount(); ^ In file included from muscle.h:34:0, from diffobjscore.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o diffpaths.o diffpaths.cpp In file included from muscle.h:34:0, from diffpaths.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o difftrees.o difftrees.cpp difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)': difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable] const unsigned uLeafCount2 = Tree2.GetLeafCount(); ^ In file included from muscle.h:34:0, from difftrees.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o difftreese.o difftreese.cpp In file included from muscle.h:34:0, from difftreese.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o distcalc.o distcalc.cpp In file included from muscle.h:34:0, from distcalc.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o distfunc.o distfunc.cpp In file included from muscle.h:34:0, from distfunc.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o distpwkimura.o distpwkimura.cpp In file included from muscle.h:34:0, from distpwkimura.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o domuscle.o domuscle.cpp In file included from muscle.h:34:0, from domuscle.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dosp.o dosp.cpp In file included from muscle.h:34:0, from dosp.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dpreglist.o dpreglist.cpp dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)': dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable] const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1; ^ In file included from muscle.h:34:0, from dpreglist.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o drawtree.o drawtree.cpp In file included from muscle.h:34:0, from drawtree.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o edgelist.o edgelist.cpp In file included from muscle.h:34:0, from edgelist.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o enumopts.o enumopts.cpp In file included from muscle.h:34:0, from enumopts.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o enumtostr.o enumtostr.cpp In file included from muscle.h:34:0, from enumtostr.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o estring.o estring.cpp estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)': estring.cpp:409:3: warning: 'cType' may be used uninitialized in this function [-Wmaybe-uninitialized] switch (cType) ^ In file included from muscle.h:34:0, from estring.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function] static bool CanMultiplyEstrings(const short es1[], const short es2[]) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fasta.o fasta.cpp fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)': fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable] unsigned uSeqCount = 0; ^ fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable] unsigned uColCount = uInsane; ^ In file included from muscle.h:34:0, from fasta.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fasta2.o fasta2.cpp In file included from muscle.h:34:0, from fasta2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastclust.o fastclust.cpp In file included from muscle.h:34:0, from fastclust.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdist.o fastdist.cpp In file included from muscle.h:34:0, from fastdist.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistjones.o fastdistjones.cpp In file included from muscle.h:34:0, from fastdistjones.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistkbit.o fastdistkbit.cpp In file included from muscle.h:34:0, from fastdistkbit.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistkmer.o fastdistkmer.cpp fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)': fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable] double KD = KimuraDist(EstimatedPctId); ^ In file included from muscle.h:34:0, from fastdistkmer.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistmafft.o fastdistmafft.cpp fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)': fastdistmafft.cpp:238:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from muscle.h:34:0, from fastdistmafft.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastdistnuc.o fastdistnuc.cpp fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)': fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from muscle.h:34:0, from fastdistnuc.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable] static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]); ^ fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastscorepath2.o fastscorepath2.cpp In file included from muscle.h:34:0, from fastscorepath2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o finddiags.o finddiags.cpp In file included from muscle.h:34:0, from finddiags.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function] static char *TupleToStr(int t) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o finddiagsn.o finddiagsn.cpp finddiagsn.cpp: In function 'char* TupleToStr(int)': finddiagsn.cpp:16:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < K; ++i) ^ In file included from muscle.h:34:0, from finddiagsn.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function] static char *TupleToStr(int t) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalign.o glbalign.cpp In file included from muscle.h:34:0, from glbalign.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalign352.o glbalign352.cpp In file included from muscle.h:34:0, from glbalign352.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbaligndiag.o glbaligndiag.cpp In file included from muscle.h:34:0, from glbaligndiag.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignle.o glbalignle.cpp glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignle.cpp:427:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^ In file included from muscle.h:34:0, from glbalignle.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignsimple.o glbalignsimple.cpp In file included from muscle.h:34:0, from glbalignsimple.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function] static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB, ^ glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignsp.o glbalignsp.cpp glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignsp.cpp:366:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^ glbalignsp.cpp:305:41: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^ In file included from muscle.h:34:0, from glbalignsp.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignspn.o glbalignspn.cpp glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)': glbalignspn.cpp:401:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^ glbalignspn.cpp:340:41: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^ In file included from muscle.h:34:0, from glbalignspn.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalignss.o glbalignss.cpp glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)': glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable] const SCORE *ptrRowA = MxRowA[i]; ^ glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable] const unsigned uPrefixCountA = uLengthA + 1; ^ glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ glbalignss.cpp:310:33: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] iTraceBack = (int) uInsertPos - (int) uLengthB; ^ glbalignss.cpp:252:41: warning: 'uInsertPos' may be used uninitialized in this function [-Wmaybe-uninitialized] *ptrTraceBack_ij = (int) uInsertPos - (int) j; ^ In file included from muscle.h:34:0, from glbalignss.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function] static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o glbalndimer.o glbalndimer.cpp glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)': glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^ glbalndimer.cpp:123:9: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from glbalndimer.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globals.o globals.cpp In file included from muscle.h:34:0, from globals.cpp:6: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globalslinux.o globalslinux.cpp globalslinux.cpp: In function 'double GetNAN()': globalslinux.cpp:17:28: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] double dNAN = *( double* )nan; ^ In file included from muscle.h:34:0, from globalslinux.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globalsosx.o globalsosx.cpp g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globalsother.o globalsother.cpp In file included from muscle.h:34:0, from globalsother.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o globalswin32.o globalswin32.cpp In file included from muscle.h:34:0, from globalswin32.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o gonnet.o gonnet.cpp In file included from muscle.h:34:0, from gonnet.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable] static SCORE Gonnet160[20][20] = ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o henikoffweight.o henikoffweight.cpp In file included from muscle.h:34:0, from henikoffweight.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o henikoffweightpb.o henikoffweightpb.cpp In file included from muscle.h:34:0, from henikoffweightpb.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o html.o html.cpp In file included from muscle.h:34:0, from html.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o hydro.o hydro.cpp In file included from muscle.h:34:0, from hydro.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o intmath.o intmath.cpp In file included from muscle.h:34:0, from intmath.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o local.o local.cpp In file included from muscle.h:34:0, from local.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o main.o main.cpp In file included from muscle.h:34:0, from main.cpp:3: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o makerootmsa.o makerootmsa.cpp makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)': makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable] const unsigned uSeqLength = s.Length(); ^ makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)': makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable] const PWPath &Path = Nodes[uNodeIndex].m_Path; ^ makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)': makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable] const unsigned uTreeNodeCount = GuideTree.GetNodeCount(); ^ In file included from muscle.h:34:0, from makerootmsa.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function] static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o makerootmsab.o makerootmsab.cpp In file included from muscle.h:34:0, from makerootmsab.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o maketree.o maketree.cpp In file included from muscle.h:34:0, from maketree.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o mhack.o mhack.cpp In file included from muscle.h:34:0, from mhack.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o mpam200.o mpam200.cpp In file included from muscle.h:34:0, from mpam200.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o msa.o msa.cpp In file included from muscle.h:34:0, from msa.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function] static void FmtChar(char c, unsigned uWidth) ^ msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function] static void FmtInt(unsigned u, unsigned uWidth) ^ msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function] static void FmtInt0(unsigned u, unsigned uWidth) ^ msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function] static void FmtPad(unsigned n) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o msa2.o msa2.cpp msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)': msa2.cpp:357:9: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] switch (Method) ^ msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)': msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ In file included from muscle.h:34:0, from msa2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o msadistkimura.o msadistkimura.cpp In file included from muscle.h:34:0, from msadistkimura.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o msf.o msf.cpp In file included from muscle.h:34:0, from msf.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function] static const char *strfind(const char *s, const char *t) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o muscle.o muscle.cpp In file included from muscle.h:34:0, from muscle.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o muscleout.o muscleout.cpp In file included from muscle.h:34:0, from muscleout.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nucmx.o nucmx.cpp In file included from muscle.h:34:0, from nucmx.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwdasimple.o nwdasimple.cpp In file included from muscle.h:34:0, from nwdasimple.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwdasimple2.o nwdasimple2.cpp In file included from muscle.h:34:0, from nwdasimple2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwdasmall.o nwdasmall.cpp In file included from muscle.h:34:0, from nwdasmall.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwrec.o nwrec.cpp g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o nwsmall.o nwsmall.cpp In file included from muscle.h:34:0, from nwsmall.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o objscore.o objscore.cpp objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)': objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch] switch (OS) ^ objscore.cpp:31:9: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from objscore.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o objscore2.o objscore2.cpp objscore2.cpp: In function 'SCORE TermGapScore(bool)': objscore2.cpp:22:9: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] switch (g_TermGaps) ^ objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)': objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable] SCORE scoreGaps = 0; ^ objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable] bool bGapping1 = false; ^ objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable] bool bGapping2 = false; ^ objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^ objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^ objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)': objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^ objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^ objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)': objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable] const unsigned uColCount2 = msa2.GetColCount(); ^ objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)': objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable] const WEIGHT w = w1*w2; ^ In file included from muscle.h:34:0, from objscore2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o objscoreda.o objscoreda.cpp In file included from muscle.h:34:0, from objscoreda.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o onexception.o onexception.cpp In file included from muscle.h:34:0, from onexception.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o options.o options.cpp In file included from muscle.h:34:0, from options.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o outweights.o outweights.cpp In file included from muscle.h:34:0, from outweights.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o pam200mafft.o pam200mafft.cpp In file included from muscle.h:34:0, from pam200mafft.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable] static float PAM200[23][23] = ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o params.o params.cpp params.cpp: In function 'void SetPPScore(bool)': params.cpp:441:9: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^ In file included from muscle.h:34:0, from params.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phy.o phy.cpp phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)': phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable] double dEdgeLength = GetEdgeLength(uNode1, uNode2); ^ In file included from muscle.h:34:0, from phy.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phy2.o phy2.cpp In file included from muscle.h:34:0, from phy2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phy3.o phy3.cpp phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)': phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable] const double dThisDist = tree.GetEdgeLength(uNode1, uNode2); ^ phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)': phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable] const unsigned uLeafCount = tree.GetLeafCount(); ^ phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable] double dAllMaxDist = -1e20; ^ phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable] unsigned uMaxFrom = NULL_NEIGHBOR; ^ phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable] unsigned uMaxTo = NULL_NEIGHBOR; ^ phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)': phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable] unsigned uMostDistantLeaf = NULL_NEIGHBOR; ^ In file included from muscle.h:34:0, from phy3.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function] static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phy4.o phy4.cpp In file included from muscle.h:34:0, from phy4.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phyfromclust.o phyfromclust.cpp In file included from muscle.h:34:0, from phyfromclust.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phyfromfile.o phyfromfile.cpp In file included from muscle.h:34:0, from phyfromfile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o physeq.o physeq.cpp physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const': physeq.cpp:60:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (Col == ColCount) ^ physeq.cpp:71:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (Col == ColCount) ^ physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const': physeq.cpp:112:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (Col == ColCount) ^ physeq.cpp:124:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (Col == ColCount) ^ In file included from muscle.h:34:0, from physeq.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o phytofile.o phytofile.cpp In file included from muscle.h:34:0, from phytofile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o posgap.o posgap.cpp In file included from muscle.h:34:0, from posgap.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o ppscore.o ppscore.cpp In file included from muscle.h:34:0, from ppscore.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o profdb.o profdb.cpp In file included from clustsetmsa.h:8:0, from profdb.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] switch(m_Distance) ^ msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from profdb.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o profile.o profile.cpp In file included from muscle.h:34:0, from profile.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o profilefrommsa.o profilefrommsa.cpp profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)': profilefrommsa.cpp:131:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (-1 == PP.m_uResidueGroup) ^ profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)': profilefrommsa.cpp:230:9: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (g_Alpha) ^ profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)': profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = a.GetSeqCount(); ^ profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable] unsigned uHydrophobicRunLength = 0; ^ In file included from muscle.h:34:0, from profilefrommsa.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o progalign.o progalign.cpp progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)': progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable] const unsigned uIterCount = uSeqCount - 1; ^ In file included from muscle.h:34:0, from progalign.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o progress.o progress.cpp In file included from muscle.h:34:0, from progress.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o progressivealign.o progressivealign.cpp In file included from muscle.h:34:0, from progressivealign.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o pwpath.o pwpath.cpp pwpath.cpp: In member function 'void PWPath::Validate() const': pwpath.cpp:79:16: warning: unused variable 'LastEdge' [-Wunused-variable] const PWEdge &LastEdge = GetEdge(uEdgeCount - 1); ^ pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)': pwpath.cpp:212:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable] unsigned uEdgeIndex = 0; ^ In file included from muscle.h:34:0, from pwpath.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o readmx.o readmx.cpp readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]': readmx.cpp:83:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < MAX_ALPHA; ++i) ^ readmx.cpp:84:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0; j < MAX_ALPHA; ++j) ^ In file included from muscle.h:34:0, from readmx.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function] static unsigned MxCharToLetter(char c) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o realigndiffs.o realigndiffs.cpp In file included from muscle.h:34:0, from realigndiffs.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o realigndiffse.o realigndiffse.cpp realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)': realigndiffse.cpp:72:13: warning: unused variable 'uNewRight' [-Wunused-variable] unsigned uNewRight = NewTree.GetRight(uNewNodeIndex); ^ realigndiffse.cpp:75:13: warning: unused variable 'uOldRight' [-Wunused-variable] unsigned uOldRight = OldTree.GetRight(uOld); ^ In file included from muscle.h:34:0, from realigndiffse.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refine.o refine.cpp In file included from clustsetmsa.h:8:0, from refine.cpp:9: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] switch(m_Distance) ^ msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from refine.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinehoriz.o refinehoriz.cpp In file included from muscle.h:34:0, from refinehoriz.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinesubfams.o refinesubfams.cpp refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)': refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable] const unsigned uNodeCount = tree.GetNodeCount(); ^ In file included from muscle.h:34:0, from refinesubfams.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinetree.o refinetree.cpp In file included from muscle.h:34:0, from refinetree.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinetreee.o refinetreee.cpp In file included from muscle.h:34:0, from refinetreee.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinevert.o refinevert.cpp In file included from muscle.h:34:0, from refinevert.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o refinew.o refinew.cpp refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)': refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ refinew.cpp: In function 'void RefineW(const MSA&, MSA&)': refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable] unsigned uOutCols = msaOut.GetColCount(); ^ In file included from muscle.h:34:0, from refinew.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o savebest.o savebest.cpp In file included from muscle.h:34:0, from savebest.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o scoredist.o scoredist.cpp In file included from muscle.h:34:0, from scoredist.cpp:3: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o scoregaps.o scoregaps.cpp In file included from muscle.h:34:0, from scoregaps.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function] static void FreeGapInfo(GAPINFO *GI) ^ scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function] static SCORE Penalty(unsigned Length, bool Term) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o scorehistory.o scorehistory.cpp In file included from muscle.h:34:0, from scorehistory.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o scorepp.o scorepp.cpp In file included from muscle.h:34:0, from scorepp.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o seq.o seq.cpp In file included from muscle.h:34:0, from seq.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o seqvect.o seqvect.cpp In file included from muscle.h:34:0, from seqvect.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o setblosumweights.o setblosumweights.cpp In file included from muscle.h:34:0, from setblosumweights.cpp:42: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o setgscweights.o setgscweights.cpp In file included from muscle.h:34:0, from setgscweights.cpp:104: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o setnewhandler.o setnewhandler.cpp In file included from muscle.h:34:0, from setnewhandler.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o spfast.o spfast.cpp spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)': spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ In file included from muscle.h:34:0, from spfast.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function] static const char *GapTypeToStr(int GapType) ^ spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function] static SCORE SPColBrute(const MSA &msa, unsigned uColIndex) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o sptest.o sptest.cpp In file included from muscle.h:34:0, from sptest.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o stabilize.o stabilize.cpp In file included from muscle.h:34:0, from stabilize.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o subfam.o subfam.cpp subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)': subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable] int NotUsed = system(CmdLine); ^ In file included from muscle.h:34:0, from subfam.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o subfams.o subfams.cpp In file included from muscle.h:34:0, from subfams.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ subfams.cpp:10:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function] static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2) ^ subfams.cpp:40:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function] static void InitializeSingleSource(DistFunc &DF, unsigned uIndex) ^ subfams.cpp:52:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function] static void Relax(DistFunc &DF, unsigned u, unsigned v) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o sw.o sw.cpp In file included from muscle.h:34:0, from sw.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o termgaps.o termgaps.cpp In file included from muscle.h:34:0, from termgaps.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o textfile.o textfile.cpp textfile.cpp: In member function 'void TextFile::PutChar(char)': textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable] int i = fputc(c, m_ptrFile); ^ textfile.cpp: In member function 'void TextFile::PutString(const char*)': textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable] int iError = fputs(szLine, m_ptrFile); ^ textfile.cpp: In member function 'void TextFile::SkipLine()': textfile.cpp:332:3: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized] if ('\n' == c) ^ In file included from muscle.h:34:0, from textfile.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o threewaywt.o threewaywt.cpp In file included from muscle.h:34:0, from threewaywt.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o tomhydro.o tomhydro.cpp In file included from muscle.h:34:0, from tomhydro.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o traceback.o traceback.cpp traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)': traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ traceback.cpp:59:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized] if ('S' == cEdgeType) ^ In file included from muscle.h:34:0, from traceback.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o tracebackopt.o tracebackopt.cpp In file included from muscle.h:34:0, from tracebackopt.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o tracebacksw.o tracebacksw.cpp tracebacksw.cpp: In function 'void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)': tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable] SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB); ^ tracebacksw.cpp:34:3: warning: 'cPrevEdgeType' may be used uninitialized in this function [-Wmaybe-uninitialized] if ('S' == cEdgeType) ^ In file included from muscle.h:34:0, from tracebacksw.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o treefrommsa.o treefrommsa.cpp In file included from clustsetmsa.h:8:0, from treefrommsa.cpp:5: msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)': msadist.h:22:9: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch] switch(m_Distance) ^ msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch] msadist.h:22:9: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch] In file included from muscle.h:34:0, from treefrommsa.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o typetostr.o typetostr.cpp In file included from muscle.h:34:0, from typetostr.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o upgma2.o upgma2.cpp upgma2.cpp: In member function 'virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const': upgma2.cpp:373:24: warning: array subscript is above array bounds [-Warray-bounds] Dist[j] = TestDist[i][j]; ^ upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)': upgma2.cpp:292:26: warning: 'dtNewDist' may be used uninitialized in this function [-Wmaybe-uninitialized] g_Dist[vL] = dtNewDist; ^ In file included from muscle.h:34:0, from upgma2.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function] static void ListState() ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o usage.o usage.cpp In file included from muscle.h:34:0, from usage.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o validateids.o validateids.cpp In file included from muscle.h:34:0, from validateids.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o vtml2.o vtml2.cpp In file included from muscle.h:34:0, from vtml2.cpp:1: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o writescorefile.o writescorefile.cpp writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)': writescorefile.cpp:40:17: warning: 'Score' may be used uninitialized in this function [-Wmaybe-uninitialized] dSum += Score; ^ writescorefile.cpp:27:11: note: 'Score' was declared here double Score; ^ In file included from muscle.h:34:0, from writescorefile.cpp:1: intmath.h: At global scope: intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o /usr/bin/fakeroot debian/rules binary-arch test -x debian/rules dh_testroot dh_prep dh_installdirs -A mkdir -p "." g++ -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o Adding cdbs dependencies to debian/muscle.substvars dh_installdirs -pmuscle dh_installdocs -pmuscle dh_installexamples -pmuscle dh_installman -pmuscle dh_installinfo -pmuscle dh_installmenu -pmuscle dh_installcron -pmuscle dh_installinit -pmuscle dh_installdebconf -pmuscle dh_installemacsen -pmuscle dh_installcatalogs -pmuscle dh_installpam -pmuscle dh_installlogrotate -pmuscle dh_installlogcheck -pmuscle dh_installchangelogs -pmuscle dh_installudev -pmuscle dh_lintian -pmuscle dh_bugfiles -pmuscle dh_install -pmuscle dh_link -pmuscle dh_installmime -pmuscle dh_installgsettings -pmuscle dh_strip -pmuscle dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform ppc64el: muscle dh_strip debug symbol extraction: packages to act on: muscle dh_strip debug symbol extraction: ignored packages: dpkg-gencontrol: warning: unknown information field 'Dm-Upload-Allowed' in input data in general section of control info file dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: building ddeb package dpkg-deb: building package `muscle-dbgsym' in `../muscle-dbgsym_3.8.31-1_ppc64el.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 information field 'Dm-Upload-Allowed' in input data in general section of control info file dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -pmuscle ; fi dh_md5sums -pmuscle dh_builddeb -pmuscle INFO: pkgstriptranslations version 119 pkgstriptranslations: processing muscle (in debian/muscle); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/muscle/DEBIAN/control, package muscle, directory debian/muscle pkgstripfiles: PNG optimization for package muscle took 0 s dpkg-deb: warning: 'debian/muscle/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `muscle' in `../muscle_3.8.31-1_ppc64el.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../muscle_3.8.31-1_ppc64el.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: warning: unknown information field 'Dm-Upload-Allowed' in input data in general section of control info file dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build muscle-3.8.31 dpkg-source: warning: unknown information field 'Dm-Upload-Allowed' in input data in general section of control info file dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20140311-0855 Publishing debug debs. chroot-autobuild/build/buildd/muscle_3.8.31-1_ppc64el.deb: new debian package, version 2.0. size 170662 bytes: control archive=909 bytes. 848 bytes, 20 lines control 457 bytes, 7 lines md5sums Package: muscle Version: 1:3.8.31-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 620 Depends: libc6 (>= 2.17), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.1.1) Enhances: seaview, t-coffee 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_3.8.31-1_ppc64el.deb: drwxr-xr-x root/root 0 2014-03-11 08:55 ./ drwxr-xr-x root/root 0 2014-03-11 08:55 ./usr/ drwxr-xr-x root/root 0 2014-03-11 08:55 ./usr/bin/ -rwxr-xr-x root/root 491776 2014-03-11 08:55 ./usr/bin/muscle drwxr-xr-x root/root 0 2014-03-11 08:55 ./usr/share/ drwxr-xr-x root/root 0 2014-03-11 08:55 ./usr/share/man/ drwxr-xr-x root/root 0 2014-03-11 08:55 ./usr/share/man/man1/ -rw-r--r-- root/root 1291 2014-03-11 08:55 ./usr/share/man/man1/muscle.1.gz drwxr-xr-x root/root 0 2014-03-11 08:55 ./usr/share/doc-base/ -rw-r--r-- root/root 703 2014-03-11 08:54 ./usr/share/doc-base/muscle-manual drwxr-xr-x root/root 0 2014-03-11 08:55 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-03-11 08:55 ./usr/share/doc/muscle/ -rw-r--r-- root/root 96687 2014-03-11 08:54 ./usr/share/doc/muscle/muscle.html -rw-r--r-- root/root 1008 2014-03-11 08:54 ./usr/share/doc/muscle/copyright -rw-r--r-- root/root 1408 2014-03-11 08:54 ./usr/share/doc/muscle/changelog.Debian.gz -rw-r--r-- root/root 779 2014-03-11 08:54 ./usr/share/doc/muscle/README.Debian muscle_3.8.31-1_ppc64el.changes: Format: 1.8 Date: Sun, 13 Nov 2011 18:38:06 +0900 Source: muscle Binary: muscle Architecture: ppc64el Version: 1:3.8.31-1 Distribution: trusty Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Charles Plessy Description: muscle - Multiple alignment program of protein sequences Closes: 643443 Changes: muscle (1:3.8.31-1) unstable; urgency=low . [ Charles Plessy ] * New upstream release (Closes: #643443). * debian/control: Enhances: t-coffee. * Changed the doc-base section according to the new policy. * Updated my email address. * Updated debian/watch to new version scheme and download location. * Repack usptream archive and implemented a get-orig-source target (debian/rules, debian/README.source, debian/copyright). * Use Debhelper 8 (debian/control, debian/compat). * Build directly from debian/rules targets. * Corrected VCS URLs in debian/control. * Conforms to Debian Policy 3.9.2 (debian/control, no changes needed). . [ David Paleino ] * removed myself from Uploaders (debian/control). Checksums-Sha1: fe6e65e05dc1c4a7780dc3c0cac1984b972c3f7f 170662 muscle_3.8.31-1_ppc64el.deb Checksums-Sha256: 9ccf6e326ba337d2adbbde4d165f6b52a31496b4e77ee475ee2755dc2f4bd161 170662 muscle_3.8.31-1_ppc64el.deb Files: 9d51beab3eaad7ed36b59ee1ede93aef 170662 science optional muscle_3.8.31-1_ppc64el.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20140311-0855 Build needed 00:00:31, 11844k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5710758'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5710758/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5710758'] Unmounting chroot for build PACKAGEBUILD-5710758... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5710758'] Removing build PACKAGEBUILD-5710758