RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux komainu 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 x86_64 Buildd toolchain package versions: launchpad-buildd_116~0.IS.12.04 python-lpbuildd_116~0.IS.12.04 bzr_2.5.1-0ubuntu2. Syncing the system clock with the buildd NTP service... 2 Oct 15:16:53 ntpdate[13944]: adjust time server 10.211.37.1 offset -0.000030 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5069499', '/home/buildd/filecache-default/ec2b9ebac117b63224f2bd4658a88af3242df73d'] Unpacking chroot for build PACKAGEBUILD-5069499 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5069499'] Mounting chroot for build PACKAGEBUILD-5069499 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5069499', 'deb http://ftpmaster.internal/ubuntu saucy main universe', 'deb http://ftpmaster.internal/ubuntu saucy-security main universe', 'deb http://ftpmaster.internal/ubuntu saucy-updates main universe', 'deb http://ftpmaster.internal/ubuntu saucy-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-5069499 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5069499', 'amd64'] Updating debian chroot for build PACKAGEBUILD-5069499 Ign http://ftpmaster.internal saucy InRelease Ign http://ftpmaster.internal saucy-security InRelease Ign http://archive-team.internal saucy InRelease Ign http://ftpmaster.internal saucy-updates InRelease Ign http://ftpmaster.internal saucy-proposed InRelease Ign http://archive-team.internal saucy Release.gpg Get:1 http://ftpmaster.internal saucy Release.gpg [933 B] Get:2 http://ftpmaster.internal saucy-security Release.gpg [933 B] Get:3 http://archive-team.internal saucy Release [728 B] Get:4 http://ftpmaster.internal saucy-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal saucy-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal saucy Release [49.6 kB] Get:7 http://ftpmaster.internal saucy-security Release [49.6 kB] Get:8 http://ftpmaster.internal saucy-updates Release [49.6 kB] Get:9 http://ftpmaster.internal saucy-proposed Release [49.6 kB] Get:10 http://archive-team.internal saucy/main amd64 Packages Get:11 http://ftpmaster.internal saucy/main amd64 Packages [1254 kB] Ign http://archive-team.internal saucy/main Translation-en Get:12 http://ftpmaster.internal saucy/universe amd64 Packages [5649 kB] Get:13 http://ftpmaster.internal saucy/main Translation-en [710 kB] Get:14 http://ftpmaster.internal saucy/universe Translation-en [3886 kB] Get:15 http://ftpmaster.internal saucy-security/main amd64 Packages [14 B] Get:16 http://ftpmaster.internal saucy-security/universe amd64 Packages [14 B] Get:17 http://ftpmaster.internal saucy-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal saucy-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal saucy-updates/main amd64 Packages [14 B] Get:20 http://ftpmaster.internal saucy-updates/universe amd64 Packages [14 B] Get:21 http://ftpmaster.internal saucy-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal saucy-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal saucy-proposed/main amd64 Packages [12.9 kB] Get:24 http://ftpmaster.internal saucy-proposed/universe amd64 Packages [46.8 kB] Get:25 http://ftpmaster.internal saucy-proposed/main Translation-en [6859 B] Get:26 http://ftpmaster.internal saucy-proposed/universe Translation-en [28.6 kB] Fetched 11.8 MB in 4s (2839 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: cpp-4.8 fakeroot g++-4.8 gcc-4.8 gcc-4.8-base libasan0 libatomic1 libgcc-4.8-dev libgcc1 libgomp1 libitm1 libmpfr4 libquadmath0 libstdc++-4.8-dev libstdc++6 libtsan0 libudev1 linux-libc-dev udev 19 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 28.8 MB of archives. After this operation, 2048 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! libitm1 libgomp1 gcc-4.8-base libstdc++6 libasan0 libatomic1 libtsan0 libquadmath0 cpp-4.8 libstdc++-4.8-dev g++-4.8 gcc-4.8 libgcc-4.8-dev libgcc1 libmpfr4 udev libudev1 fakeroot linux-libc-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ saucy/main libitm1 amd64 4.8.1-10ubuntu5 [37.4 kB] Get:2 http://ftpmaster.internal/ubuntu/ saucy/main libgomp1 amd64 4.8.1-10ubuntu5 [27.0 kB] Get:3 http://ftpmaster.internal/ubuntu/ saucy/main gcc-4.8-base amd64 4.8.1-10ubuntu5 [16.4 kB] Get:4 http://ftpmaster.internal/ubuntu/ saucy/main libstdc++6 amd64 4.8.1-10ubuntu5 [326 kB] Get:5 http://ftpmaster.internal/ubuntu/ saucy/main libasan0 amd64 4.8.1-10ubuntu5 [75.8 kB] Get:6 http://ftpmaster.internal/ubuntu/ saucy/main libatomic1 amd64 4.8.1-10ubuntu5 [10.3 kB] Get:7 http://ftpmaster.internal/ubuntu/ saucy/main libtsan0 amd64 4.8.1-10ubuntu5 [118 kB] Get:8 http://ftpmaster.internal/ubuntu/ saucy/main libquadmath0 amd64 4.8.1-10ubuntu5 [139 kB] Get:9 http://ftpmaster.internal/ubuntu/ saucy/main cpp-4.8 amd64 4.8.1-10ubuntu5 [5837 kB] Get:10 http://ftpmaster.internal/ubuntu/ saucy/main libstdc++-4.8-dev amd64 4.8.1-10ubuntu5 [1754 kB] Get:11 http://ftpmaster.internal/ubuntu/ saucy/main g++-4.8 amd64 4.8.1-10ubuntu5 [8699 kB] Get:12 http://ftpmaster.internal/ubuntu/ saucy/main gcc-4.8 amd64 4.8.1-10ubuntu5 [6638 kB] Get:13 http://ftpmaster.internal/ubuntu/ saucy/main libgcc-4.8-dev amd64 4.8.1-10ubuntu5 [2791 kB] Get:14 http://ftpmaster.internal/ubuntu/ saucy/main libgcc1 amd64 1:4.8.1-10ubuntu5 [43.4 kB] Get:15 http://ftpmaster.internal/ubuntu/ saucy/main libmpfr4 amd64 3.1.1-2 [202 kB] Get:16 http://ftpmaster.internal/ubuntu/ saucy/main udev amd64 204-0ubuntu15 [1037 kB] Get:17 http://ftpmaster.internal/ubuntu/ saucy/main libudev1 amd64 204-0ubuntu15 [36.1 kB] Get:18 http://ftpmaster.internal/ubuntu/ saucy/main fakeroot amd64 1.20-1 [98.9 kB] Get:19 http://ftpmaster.internal/ubuntu/ saucy/main linux-libc-dev amd64 3.11.0-11.17 [944 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.8 MB in 1s (27.6 MB/s) (Reading database ... 12043 files and directories currently installed.) Preparing to replace libitm1:amd64 4.8.1-10ubuntu4 (using .../libitm1_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libitm1:amd64 ... Preparing to replace libgomp1:amd64 4.8.1-10ubuntu4 (using .../libgomp1_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libgomp1:amd64 ... Preparing to replace gcc-4.8-base:amd64 4.8.1-10ubuntu4 (using .../gcc-4.8-base_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement gcc-4.8-base:amd64 ... Setting up gcc-4.8-base:amd64 (4.8.1-10ubuntu5) ... (Reading database ... 12043 files and directories currently installed.) Preparing to replace libstdc++6:amd64 4.8.1-10ubuntu4 (using .../libstdc++6_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libstdc++6:amd64 ... Preparing to replace libgcc1:amd64 1:4.8.1-10ubuntu4 (using .../libgcc1_1%3a4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libgcc1:amd64 ... Setting up libgcc1:amd64 (1:4.8.1-10ubuntu5) ... Setting up libstdc++6:amd64 (4.8.1-10ubuntu5) ... Processing triggers for libc-bin ... (Reading database ... 12043 files and directories currently installed.) Preparing to replace libasan0:amd64 4.8.1-10ubuntu4 (using .../libasan0_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libasan0:amd64 ... Preparing to replace libatomic1:amd64 4.8.1-10ubuntu4 (using .../libatomic1_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libatomic1:amd64 ... Preparing to replace libtsan0:amd64 4.8.1-10ubuntu4 (using .../libtsan0_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libtsan0:amd64 ... Preparing to replace libquadmath0:amd64 4.8.1-10ubuntu4 (using .../libquadmath0_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libquadmath0:amd64 ... Preparing to replace cpp-4.8 4.8.1-10ubuntu4 (using .../cpp-4.8_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement cpp-4.8 ... Preparing to replace libstdc++-4.8-dev:amd64 4.8.1-10ubuntu4 (using .../libstdc++-4.8-dev_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libstdc++-4.8-dev:amd64 ... Preparing to replace g++-4.8 4.8.1-10ubuntu4 (using .../g++-4.8_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement g++-4.8 ... Preparing to replace gcc-4.8 4.8.1-10ubuntu4 (using .../gcc-4.8_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement gcc-4.8 ... Preparing to replace libgcc-4.8-dev:amd64 4.8.1-10ubuntu4 (using .../libgcc-4.8-dev_4.8.1-10ubuntu5_amd64.deb) ... Unpacking replacement libgcc-4.8-dev:amd64 ... Preparing to replace libmpfr4:amd64 3.1.1-1 (using .../libmpfr4_3.1.1-2_amd64.deb) ... Unpacking replacement libmpfr4:amd64 ... Preparing to replace udev 204-0ubuntu14 (using .../udev_204-0ubuntu15_amd64.deb) ... Adding 'diversion of /bin/udevadm to /bin/udevadm.upgrade by fake-udev' Unpacking replacement udev ... Preparing to replace libudev1:amd64 204-0ubuntu14 (using .../libudev1_204-0ubuntu15_amd64.deb) ... Unpacking replacement libudev1:amd64 ... Preparing to replace fakeroot 1.19-2 (using .../fakeroot_1.20-1_amd64.deb) ... Unpacking replacement fakeroot ... Preparing to replace linux-libc-dev:amd64 3.11.0-9.16 (using .../linux-libc-dev_3.11.0-11.17_amd64.deb) ... Unpacking replacement linux-libc-dev:amd64 ... Setting up libitm1:amd64 (4.8.1-10ubuntu5) ... Setting up libgomp1:amd64 (4.8.1-10ubuntu5) ... Setting up libasan0:amd64 (4.8.1-10ubuntu5) ... Setting up libatomic1:amd64 (4.8.1-10ubuntu5) ... Setting up libtsan0:amd64 (4.8.1-10ubuntu5) ... Setting up libquadmath0:amd64 (4.8.1-10ubuntu5) ... Setting up libmpfr4:amd64 (3.1.1-2) ... Setting up cpp-4.8 (4.8.1-10ubuntu5) ... Setting up libgcc-4.8-dev:amd64 (4.8.1-10ubuntu5) ... Setting up libstdc++-4.8-dev:amd64 (4.8.1-10ubuntu5) ... Setting up gcc-4.8 (4.8.1-10ubuntu5) ... Setting up g++-4.8 (4.8.1-10ubuntu5) ... Setting up libudev1:amd64 (204-0ubuntu15) ... Setting up udev (204-0ubuntu15) ... 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 fakeroot (1.20-1) ... Setting up linux-libc-dev:amd64 (3.11.0-11.17) ... Processing triggers for libc-bin ... Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5069499', 'amd64', 'saucy-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=saucy-proposed', '--purpose=PRIMARY', '--architecture=amd64', '--comp=universe', 'hhsuite_2.0.16-1ubuntu1.dsc'] Initiating build PACKAGEBUILD-5069499 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 x86_64 Automatic build of hhsuite_2.0.16-1ubuntu1 on komainu by sbuild/amd64 1.170.5 Build started at 20131002-1517 ****************************************************************************** hhsuite_2.0.16-1ubuntu1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev Checking for already installed source dependencies... debhelper: missing libffindex0-dev: missing help2man: missing libpng12-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper libffindex0-dev help2man libpng12-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: apparmor-easyprof bsdmainutils dh-apparmor dh-python file gettext gettext-base groff-base intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libexpat1 libffi6 libffindex0 libgettextpo-dev libgettextpo0 libglib2.0-0 liblocale-gettext-perl libmagic1 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl python3-doc python3-tk python3.3-doc binfmt-support Recommended packages: curl wget lynx-cur libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof bsdmainutils debhelper dh-apparmor dh-python file gettext gettext-base groff-base help2man intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libexpat1 libffi6 libffindex0 libffindex0-dev libgettextpo-dev libgettextpo0 libglib2.0-0 liblocale-gettext-perl libmagic1 libpipeline1 libpng12-dev libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal zlib1g-dev 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 12.4 MB of archives. After this operation, 42.3 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libexpat1 libffi6 liblocale-gettext-perl libmagic1 libpython3.3-minimal mime-support libpython3.3-stdlib python3.3-minimal libasprintf0c2 libglib2.0-0 libpipeline1 libxml2 groff-base bsdmainutils man-db libcroco3 libunistring0 libgettextpo0 file libpython3-stdlib python3.3 python3-minimal dh-python python3 gettext-base libasprintf-dev libgettextpo-dev gettext intltool-debian po-debconf apparmor-easyprof dh-apparmor debhelper help2man zlib1g-dev libpng12-dev libffindex0 libffindex0-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ saucy/main libexpat1 amd64 2.1.0-4 [129 kB] Get:2 http://ftpmaster.internal/ubuntu/ saucy/main libffi6 amd64 3.0.13-4 [19.4 kB] Get:3 http://ftpmaster.internal/ubuntu/ saucy/main liblocale-gettext-perl amd64 1.05-7build2 [19.3 kB] Get:4 http://ftpmaster.internal/ubuntu/ saucy/main libmagic1 amd64 5.11-2ubuntu4 [170 kB] Get:5 http://ftpmaster.internal/ubuntu/ saucy/main libpython3.3-minimal amd64 3.3.2-7ubuntu2 [619 kB] Get:6 http://ftpmaster.internal/ubuntu/ saucy/main mime-support all 3.54ubuntu1 [31.7 kB] Get:7 http://ftpmaster.internal/ubuntu/ saucy/main libpython3.3-stdlib amd64 3.3.2-7ubuntu2 [2690 kB] Get:8 http://ftpmaster.internal/ubuntu/ saucy/main python3.3-minimal amd64 3.3.2-7ubuntu2 [1747 kB] Get:9 http://ftpmaster.internal/ubuntu/ saucy/main libasprintf0c2 amd64 0.18.1.1-10ubuntu3 [6864 B] Get:10 http://ftpmaster.internal/ubuntu/ saucy/main libglib2.0-0 amd64 2.38.0-1ubuntu1 [1014 kB] Get:11 http://ftpmaster.internal/ubuntu/ saucy/main libpipeline1 amd64 1.2.4-1 [27.2 kB] Get:12 http://ftpmaster.internal/ubuntu/ saucy/main libxml2 amd64 2.9.1+dfsg1-3ubuntu2 [693 kB] Get:13 http://ftpmaster.internal/ubuntu/ saucy/main groff-base amd64 1.22.2-3 [719 kB] Get:14 http://ftpmaster.internal/ubuntu/ saucy/main bsdmainutils amd64 9.0.5ubuntu1 [203 kB] Get:15 http://ftpmaster.internal/ubuntu/ saucy/main man-db amd64 2.6.5-2 [710 kB] Get:16 http://ftpmaster.internal/ubuntu/ saucy/main libcroco3 amd64 0.6.8-2 [82.6 kB] Get:17 http://ftpmaster.internal/ubuntu/ saucy/main libunistring0 amd64 0.9.3-5build1 [430 kB] Get:18 http://ftpmaster.internal/ubuntu/ saucy/main libgettextpo0 amd64 0.18.1.1-10ubuntu3 [123 kB] Get:19 http://ftpmaster.internal/ubuntu/ saucy/main file amd64 5.11-2ubuntu4 [18.4 kB] Get:20 http://ftpmaster.internal/ubuntu/ saucy/main libpython3-stdlib amd64 3.3.2-14ubuntu1 [8146 B] Get:21 http://ftpmaster.internal/ubuntu/ saucy/main python3.3 amd64 3.3.2-7ubuntu2 [129 kB] Get:22 http://ftpmaster.internal/ubuntu/ saucy/main python3-minimal amd64 3.3.2-14ubuntu1 [26.6 kB] Get:23 http://ftpmaster.internal/ubuntu/ saucy/main dh-python all 1.20130913-1 [54.4 kB] Get:24 http://ftpmaster.internal/ubuntu/ saucy/main python3 amd64 3.3.2-14ubuntu1 [9166 B] Get:25 http://ftpmaster.internal/ubuntu/ saucy/main gettext-base amd64 0.18.1.1-10ubuntu3 [77.8 kB] Get:26 http://ftpmaster.internal/ubuntu/ saucy/main libasprintf-dev amd64 0.18.1.1-10ubuntu3 [4544 B] Get:27 http://ftpmaster.internal/ubuntu/ saucy/main libgettextpo-dev amd64 0.18.1.1-10ubuntu3 [164 kB] Get:28 http://ftpmaster.internal/ubuntu/ saucy/main gettext amd64 0.18.1.1-10ubuntu3 [1039 kB] Get:29 http://ftpmaster.internal/ubuntu/ saucy/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:30 http://ftpmaster.internal/ubuntu/ saucy/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:31 http://ftpmaster.internal/ubuntu/ saucy/main apparmor-easyprof all 2.8.0-0ubuntu29 [23.6 kB] Get:32 http://ftpmaster.internal/ubuntu/ saucy/main dh-apparmor all 2.8.0-0ubuntu29 [7704 B] Get:33 http://ftpmaster.internal/ubuntu/ saucy/main debhelper all 9.20130630ubuntu1 [629 kB] Get:34 http://ftpmaster.internal/ubuntu/ saucy/main help2man amd64 1.43.3 [61.0 kB] Get:35 http://ftpmaster.internal/ubuntu/ saucy/main zlib1g-dev amd64 1:1.2.8.dfsg-1ubuntu1 [183 kB] Get:36 http://ftpmaster.internal/ubuntu/ saucy/main libpng12-dev amd64 1.2.49-4ubuntu1 [206 kB] Get:37 http://ftpmaster.internal/ubuntu/ saucy/universe libffindex0 amd64 0.9.9.1-1 [16.7 kB] Get:38 http://ftpmaster.internal/ubuntu/ saucy/universe libffindex0-dev amd64 0.9.9.1-1 [16.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.4 MB in 0s (13.3 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 12043 files and directories currently installed.) Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-4_amd64.deb) ... Selecting previously unselected package libffi6:amd64. Unpacking libffi6:amd64 (from .../libffi6_3.0.13-4_amd64.deb) ... Selecting previously unselected package liblocale-gettext-perl. Unpacking liblocale-gettext-perl (from .../liblocale-gettext-perl_1.05-7build2_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_5.11-2ubuntu4_amd64.deb) ... Selecting previously unselected package libpython3.3-minimal:amd64. Unpacking libpython3.3-minimal:amd64 (from .../libpython3.3-minimal_3.3.2-7ubuntu2_amd64.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.54ubuntu1_all.deb) ... Selecting previously unselected package libpython3.3-stdlib:amd64. Unpacking libpython3.3-stdlib:amd64 (from .../libpython3.3-stdlib_3.3.2-7ubuntu2_amd64.deb) ... Selecting previously unselected package python3.3-minimal. Unpacking python3.3-minimal (from .../python3.3-minimal_3.3.2-7ubuntu2_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-10ubuntu3_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.38.0-1ubuntu1_amd64.deb) ... Selecting previously unselected package libpipeline1:amd64. Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.4-1_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.9.1+dfsg1-3ubuntu2_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.2-3_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.5ubuntu1_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.5-2_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.8-2_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5build1_amd64.deb) ... Selecting previously unselected package libgettextpo0:amd64. Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-10ubuntu3_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../file_5.11-2ubuntu4_amd64.deb) ... Selecting previously unselected package libpython3-stdlib:amd64. Unpacking libpython3-stdlib:amd64 (from .../libpython3-stdlib_3.3.2-14ubuntu1_amd64.deb) ... Selecting previously unselected package python3.3. Unpacking python3.3 (from .../python3.3_3.3.2-7ubuntu2_amd64.deb) ... Selecting previously unselected package python3-minimal. Unpacking python3-minimal (from .../python3-minimal_3.3.2-14ubuntu1_amd64.deb) ... Selecting previously unselected package dh-python. Unpacking dh-python (from .../dh-python_1.20130913-1_all.deb) ... Selecting previously unselected package python3. Unpacking python3 (from .../python3_3.3.2-14ubuntu1_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-10ubuntu3_amd64.deb) ... Selecting previously unselected package libasprintf-dev:amd64. Unpacking libasprintf-dev:amd64 (from .../libasprintf-dev_0.18.1.1-10ubuntu3_amd64.deb) ... Selecting previously unselected package libgettextpo-dev:amd64. Unpacking libgettextpo-dev:amd64 (from .../libgettextpo-dev_0.18.1.1-10ubuntu3_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-10ubuntu3_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2ubuntu1_all.deb) ... Selecting previously unselected package apparmor-easyprof. Unpacking apparmor-easyprof (from .../apparmor-easyprof_2.8.0-0ubuntu29_all.deb) ... Selecting previously unselected package dh-apparmor. Unpacking dh-apparmor (from .../dh-apparmor_2.8.0-0ubuntu29_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20130630ubuntu1_all.deb) ... Selecting previously unselected package help2man. Unpacking help2man (from .../help2man_1.43.3_amd64.deb) ... Selecting previously unselected package zlib1g-dev:amd64. Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.8.dfsg-1ubuntu1_amd64.deb) ... Selecting previously unselected package libpng12-dev. Unpacking libpng12-dev (from .../libpng12-dev_1.2.49-4ubuntu1_amd64.deb) ... 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Toolchain package versions: libc6-dev_2.17-93ubuntu1 make_3.81-8.2ubuntu3 dpkg-dev_1.16.10ubuntu3 gcc-4.8_4.8.1-10ubuntu5 g++-4.8_4.8.1-10ubuntu5 binutils_2.23.52.20130913-0ubuntu1 libstdc++-4.8-dev_4.8.1-10ubuntu5 libstdc++6_4.8.1-10ubuntu5 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Wed Oct 2 12:50:32 2013 UTC using RSA key ID 7D86500B gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./hhsuite_2.0.16-1ubuntu1.dsc dpkg-source: info: extracting hhsuite in hhsuite-2.0.16 dpkg-source: info: unpacking hhsuite_2.0.16.orig.tar.gz dpkg-source: info: unpacking hhsuite_2.0.16-1ubuntu1.debian.tar.gz dpkg-source: info: applying Makefile dpkg-source: info: applying paths dpkg-source: info: applying help dpkg-source: info: applying rest1 dpkg-source: info: applying perlscript_uselib dpkg-source: info: applying hardening dpkg-source: info: applying unused_variables_warning dpkg-source: info: applying unnecessary_libz dpkg-source: info: applying perl_interpreter dpkg-source: info: applying version_bump dpkg-buildpackage: source package hhsuite dpkg-buildpackage: source version 2.0.16-1ubuntu1 dpkg-source --before-build hhsuite-2.0.16 dpkg-buildpackage: host architecture amd64 /usr/bin/fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make[1]: Entering directory `/build/buildd/hhsuite-2.0.16' make -C src clean make[2]: Entering directory `/build/buildd/hhsuite-2.0.16/src' rm -f *.o cs/*.o rm -f hhconsensus hhconsensus_valgrind hhfilter_valgrind hhfilter hhalign_valgrind hhalign hhmake hhblits_valgrind hhblits hhsearch_valgrind hhsearch cstranslate make[2]: Leaving directory `/build/buildd/hhsuite-2.0.16/src' make[1]: Leaving directory `/build/buildd/hhsuite-2.0.16' debian/rules override_dh_clean make[1]: Entering directory `/build/buildd/hhsuite-2.0.16' rm -f hhalign.1 hhblits.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 dh_clean make[1]: Leaving directory `/build/buildd/hhsuite-2.0.16' debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_auto_configure -a -O--parallel dh_auto_build -a -O--parallel make[1]: Entering directory `/build/buildd/hhsuite-2.0.16' make -C data all make[2]: Entering directory `/build/buildd/hhsuite-2.0.16/data' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/build/buildd/hhsuite-2.0.16/data' make -C src all make[2]: Entering directory `/build/buildd/hhsuite-2.0.16/src' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -fopenmp -c cs/aa.cc -o cs/aa.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -fopenmp -c cs/application.cc -o cs/application.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -fopenmp -c cs/as.cc -o cs/as.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -fopenmp -c cs/assert_helpers.cc -o cs/assert_helpers.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -fopenmp -c cs/blosum_matrix.cc -o cs/blosum_matrix.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -fopenmp -c cs/getopt_pp.cc -o cs/getopt_pp.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -fopenmp -c cs/log.cc -o cs/log.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro hhblits.C -o hhblits cs/aa.o cs/application.o cs/as.o cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o -lpthread -fopenmp -lrt -lffindex g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro hhsearch.C -o hhsearch cs/aa.o cs/application.o cs/as.o cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o -lpthread -lrt g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro hhmake.C -o hhmake cs/aa.o cs/application.o cs/as.o cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro hhalign.C -o hhalign cs/aa.o cs/application.o cs/as.o cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o -DNO_FREETYPE -DHH_PNG -lpng g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro hhfilter.C -o hhfilter cs/aa.o cs/application.o cs/as.o cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro hhconsensus.C -o hhconsensus cs/aa.o cs/application.o cs/as.o cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -lm -o cstranslate cs/cstranslate_app.cc cs/aa.o cs/application.o cs/as.o cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o In file included from hhmake.C:74:0: hhutil.C: In function 'void ReadDefaultsFile(int&, char**, char*)': hhutil.C:478:67: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ hhutil.C:483:63: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ In file included from hhmake.C:81:0: hhhmm.C: In member function 'HMM& HMM::operator=(HMM&)': hhhmm.C:169:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(q.sname[k])+1]); ^ hhhmm.C:174:40: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q.seq[k])+1]); ^ hhhmm.C: In member function 'int HMM::Read(FILE*, char*)': hhhmm.C:360:57: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k-1]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C:367:57: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ^ hhhmm.C:468:47: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer(FILE*, char*)': hhhmm.C:719:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:740:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:761:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C:835:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1009:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1011:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1014:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1032:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1034:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer3(FILE*, char*)': hhhmm.C:1182:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1203:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:1224:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C:1295:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1471:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1473:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1476:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1494:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1496:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C: In member function 'void HMM::InsertCalibration(char*)': hhhmm.C:2177:39: warning: ISO C++ does not support variable-length array types [-Wvla] char** lines = new(char*[3*L+100000]); ^ hhhmm.C:2205:44: warning: ISO C++ does not support variable-length array types [-Wvla] lines[nline]=new(char[strlen(line)+1]); ^ hhhmm.C: In member function 'void HMM::AddSSPrediction(char*, char*)': hhhmm.C:2329:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred]=new(char[L+2]); ^ hhhmm.C:2336:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf]=new(char[L+2]); ^ In file included from hhmake.C:82:0: hhalignment.C: In constructor 'Alignment::Alignment(int, int)': hhalignment.C:47:30: warning: ISO C++ does not support variable-length array types [-Wvla] sname = new(char*[maxseq+2]); ^ hhalignment.C:48:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq = new(char*[maxseq+2]); ^ hhalignment.C:49:22: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int[maxres]); ^ hhalignment.C:50:26: warning: ISO C++ does not support variable-length array types [-Wvla] X = new(char*[maxseq+2]); ^ hhalignment.C:51:40: warning: ISO C++ does not support variable-length array types [-Wvla] I = new(short unsigned int*[maxseq+2]); ^ hhalignment.C:52:28: warning: ISO C++ does not support variable-length array types [-Wvla] keep = new(char[maxseq+2]); ^ hhalignment.C:53:31: warning: ISO C++ does not support variable-length array types [-Wvla] display = new(char[maxseq+2]); ^ hhalignment.C:54:27: warning: ISO C++ does not support variable-length array types [-Wvla] wg = new(float[maxseq+2]); ^ hhalignment.C:55:28: warning: ISO C++ does not support variable-length array types [-Wvla] nseqs = new(int[maxres+2]); ^ hhalignment.C: In member function 'Alignment& Alignment::operator=(Alignment&)': hhalignment.C:144:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:150:48: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(ali.sname[k])+1]); ^ hhalignment.C:156:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(ali.seq[k])+1]); ^ hhalignment.C:162:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(ali.seq[k])+2]); ^ hhalignment.C:167:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ^ hhalignment.C: In member function 'void Alignment::Read(FILE*, char*, char*)': hhalignment.C:252:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:254:47: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:256:61: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ In file included from hhmake.C:82:0: hhalignment.C:315:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(cur_name)+1]); ^ hhalignment.C:431:41: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:433:39: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:435:53: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment.C: In member function 'void Alignment::Compress(const char*)': hhalignment.C:649:36: warning: ISO C++ does not support variable-length array types [-Wvla] if (nres==NULL) nres=new(int[N_in]); ^ hhalignment.C: In member function 'void Alignment::GetSeqsFromHMM(HMM*)': hhalignment.C:923:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C:926:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C:928:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ^ hhalignment.C:949:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(q->sname[qk])+1]); ^ hhalignment.C: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)': hhalignment.C:972:33: warning: ISO C++ does not support variable-length array types [-Wvla] char *dummy = new(char[N_in+1]); ^ hhalignment.C: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)': hhalignment.C:1031:28: warning: ISO C++ does not support variable-length array types [-Wvla] char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ^ hhalignment.C:1032:30: warning: ISO C++ does not support variable-length array types [-Wvla] char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ^ hhalignment.C:1033:25: warning: ISO C++ does not support variable-length array types [-Wvla] int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ^ hhalignment.C:1034:29: warning: ISO C++ does not support variable-length array types [-Wvla] int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ^ hhalignment.C:1035:34: warning: ISO C++ does not support variable-length array types [-Wvla] int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ^ hhalignment.C:1036:22: warning: ISO C++ does not support variable-length array types [-Wvla] int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ^ hhalignment.C:1064:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1065:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:1079:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:1095:26: warning: ISO C++ does not support variable-length array types [-Wvla] ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ^ hhalignment.C: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM*)': hhalignment.C:1303:34: warning: ISO C++ does not support variable-length array types [-Wvla] float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ^ hhalignment.C:1312:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1313:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:1326:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C: In member function 'void Alignment::FrequenciesAndTransitions(HMM*, char*, bool)': hhalignment.C:1598:41: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->ncons]=new(char[L+2]); ^ hhalignment.C:1605:56: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[q->nfirst]=new(char[strlen(name)+11]); ^ hhalignment.C:1609:42: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->nfirst]=new(char[L+2]); ^ hhalignment.C:1661:52: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[nn]=new(char[strlen(sname[k])+1]); ^ hhalignment.C:1664:48: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[nn]=new(char[strlen(seq[k])+1]); ^ hhalignment.C: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM*, char*)': hhalignment.C:1764:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_I_state(HMM*, char*)': hhalignment.C:1980:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_D_state(HMM*, char*)': hhalignment.C:2173:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C: In member function 'void Alignment::MergeMasterSlave(Hit&, Alignment&, char*)': hhalignment.C:2430:39: warning: ISO C++ does not support variable-length array types [-Wvla] char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ^ hhalignment.C:2442:32: warning: ISO C++ does not support variable-length array types [-Wvla] int* imatch=new(int[hit.j2+1]); ^ hhalignment.C:2574:47: warning: ISO C++ does not support variable-length array types [-Wvla] char* new_seq=new(char[2*maxcol]); ^ hhalignment.C:2587:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[h]); ^ hhalignment.C:2590:26: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[h]); ^ hhalignment.C:2592:40: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[h]); ^ hhalignment.C:2594:52: warning: ISO C++ does not support variable-length array types [-Wvla] sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ^ hhalignment.C: In member function 'void Alignment::AddSequence(char*, int*)': hhalignment.C:2625:24: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C: In member function 'void Alignment::AddSSPrediction(char*, char*)': hhalignment.C:2663:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C:2665:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:2667:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C:2686:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C:2688:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:2690:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C: In member function 'void Alignment::GetPositionSpecificWeights(float**)': hhalignment.C:2743:24: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ In file included from hhconsensus.C:60:0: hhutil.C: In function 'void ReadDefaultsFile(int&, char**, char*)': hhutil.C:478:67: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ hhutil.C:483:63: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ In file included from hhfilter.C:74:0: hhutil.C: In function 'void ReadDefaultsFile(int&, char**, char*)': hhutil.C:478:67: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ hhutil.C:483:63: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ In file included from hhblits.C:132:0: hhutil.C: In function 'void ReadDefaultsFile(int&, char**, char*)': hhutil.C:478:67: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ hhutil.C:483:63: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ In file included from hhconsensus.C:68:0: hhhmm.C: In member function 'HMM& HMM::operator=(HMM&)': hhhmm.C:169:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(q.sname[k])+1]); ^ hhhmm.C:174:40: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q.seq[k])+1]); ^ In file included from hhsearch.C:102:0: hhutil.C: In function 'void ReadDefaultsFile(int&, char**, char*)': hhutil.C:478:67: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ hhutil.C:483:63: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ In file included from hhfilter.C:81:0: hhhmm.C: In member function 'HMM& HMM::operator=(HMM&)': hhhmm.C:169:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(q.sname[k])+1]); ^ hhhmm.C:174:40: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q.seq[k])+1]); ^ hhhmm.C: In member function 'int HMM::Read(FILE*, char*)': hhhmm.C:360:57: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k-1]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C:367:57: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ^ In file included from hhalign.C:85:0: hhutil.C: In function 'void ReadDefaultsFile(int&, char**, char*)': hhutil.C:478:67: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ hhutil.C:483:63: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ hhhmm.C: In member function 'int HMM::Read(FILE*, char*)': hhhmm.C:360:57: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k-1]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C:367:57: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ^ hhhmm.C:468:47: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+1]); ^ In file included from hhblits.C:142:0: hhhmm.C: In member function 'HMM& HMM::operator=(HMM&)': hhhmm.C:169:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(q.sname[k])+1]); ^ hhhmm.C:174:40: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q.seq[k])+1]); ^ hhhmm.C:468:47: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C: In member function 'int HMM::Read(FILE*, char*)': hhhmm.C:360:57: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k-1]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C:367:57: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ^ hhhmm.C: In member function 'int HMM::ReadHMMer(FILE*, char*)': hhhmm.C:719:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:740:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:761:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ In file included from hhsearch.C:112:0: hhhmm.C: In member function 'HMM& HMM::operator=(HMM&)': hhhmm.C:169:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(q.sname[k])+1]); ^ hhhmm.C:174:40: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q.seq[k])+1]); ^ hhhmm.C:835:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:468:47: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+1]); ^ In file included from hhalign.C:95:0: hhhmm.C: In member function 'HMM& HMM::operator=(HMM&)': hhhmm.C:169:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(q.sname[k])+1]); ^ hhhmm.C:174:40: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q.seq[k])+1]); ^ hhhmm.C: In member function 'int HMM::Read(FILE*, char*)': hhhmm.C:360:57: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k-1]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C:367:57: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ^ hhhmm.C:1009:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1011:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1014:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1032:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1034:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer(FILE*, char*)': hhhmm.C:719:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:740:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C: In member function 'int HMM::Read(FILE*, char*)': hhhmm.C:360:57: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k-1]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C:367:57: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ^ hhhmm.C:761:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C:835:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer3(FILE*, char*)': hhhmm.C:1182:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer(FILE*, char*)': hhhmm.C:719:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:468:47: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C:1203:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:740:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:1224:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C:761:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C:1295:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:835:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1009:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1011:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1014:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1032:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1034:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:468:47: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+1]); ^ hhhmm.C:1471:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1473:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1476:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer3(FILE*, char*)': hhhmm.C:1182:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1494:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1496:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1203:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer(FILE*, char*)': hhhmm.C:719:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1224:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C:740:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:1009:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:761:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C:1011:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1014:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1032:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1295:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1034:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:835:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer(FILE*, char*)': hhhmm.C:719:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:740:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:761:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer3(FILE*, char*)': hhhmm.C:1182:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1471:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1473:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1009:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:835:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1476:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1011:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1014:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1494:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1032:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1034:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1496:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1203:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:1224:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer3(FILE*, char*)': hhhmm.C:1182:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1295:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C:1203:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:1224:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ hhhmm.C:1009:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1011:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1014:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1295:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhhmm.C: In member function 'void HMM::InsertCalibration(char*)': hhhmm.C:2177:39: warning: ISO C++ does not support variable-length array types [-Wvla] char** lines = new(char*[3*L+100000]); ^ hhhmm.C:1032:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1034:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:2205:44: warning: ISO C++ does not support variable-length array types [-Wvla] lines[nline]=new(char[strlen(line)+1]); ^ hhhmm.C: In member function 'int HMM::ReadHMMer3(FILE*, char*)': hhhmm.C:1182:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[par.maxres+2]); ^ hhhmm.C: In member function 'void HMM::AddSSPrediction(char*, char*)': hhhmm.C:2329:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred]=new(char[L+2]); ^ hhhmm.C:1203:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[par.maxres+2]); ^ hhhmm.C:2336:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf]=new(char[L+2]); ^ hhhmm.C:1224:53: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[par.maxres+2]); ^ In file included from hhconsensus.C:69:0: hhalignment.C: In constructor 'Alignment::Alignment(int, int)': hhalignment.C:47:30: warning: ISO C++ does not support variable-length array types [-Wvla] sname = new(char*[maxseq+2]); ^ hhalignment.C:48:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq = new(char*[maxseq+2]); ^ hhalignment.C:49:22: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int[maxres]); ^ hhalignment.C:50:26: warning: ISO C++ does not support variable-length array types [-Wvla] X = new(char*[maxseq+2]); ^ hhalignment.C:51:40: warning: ISO C++ does not support variable-length array types [-Wvla] I = new(short unsigned int*[maxseq+2]); ^ hhalignment.C:52:28: warning: ISO C++ does not support variable-length array types [-Wvla] keep = new(char[maxseq+2]); ^ hhalignment.C:53:31: warning: ISO C++ does not support variable-length array types [-Wvla] display = new(char[maxseq+2]); ^ hhalignment.C:54:27: warning: ISO C++ does not support variable-length array types [-Wvla] wg = new(float[maxseq+2]); ^ hhalignment.C:55:28: warning: ISO C++ does not support variable-length array types [-Wvla] nseqs = new(int[maxres+2]); ^ hhhmm.C:1471:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1473:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1476:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1295:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[par.maxres+2]); ^ hhalignment.C: In member function 'Alignment& Alignment::operator=(Alignment&)': hhalignment.C:144:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:150:48: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(ali.sname[k])+1]); ^ hhhmm.C:1494:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhalignment.C:156:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(ali.seq[k])+1]); ^ hhalignment.C:162:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(ali.seq[k])+2]); ^ hhhmm.C:1496:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhalignment.C:167:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ^ hhalignment.C: In member function 'void Alignment::Read(FILE*, char*, char*)': hhalignment.C:252:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:254:47: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:256:61: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ In file included from hhconsensus.C:69:0: hhalignment.C:315:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(cur_name)+1]); ^ hhhmm.C:1471:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1471:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm.C:1473:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C: In member function 'void HMM::InsertCalibration(char*)': hhhmm.C:2177:39: warning: ISO C++ does not support variable-length array types [-Wvla] char** lines = new(char*[3*L+100000]); ^ hhhmm.C:1473:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1476:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:1494:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1496:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C:1476:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm.C:2205:44: warning: ISO C++ does not support variable-length array types [-Wvla] lines[nline]=new(char[strlen(line)+1]); ^ hhhmm.C:1494:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm.C:1496:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm.C: In member function 'void HMM::AddSSPrediction(char*, char*)': hhhmm.C:2329:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred]=new(char[L+2]); ^ hhhmm.C:2336:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf]=new(char[L+2]); ^ In file included from hhfilter.C:82:0: hhalignment.C: In constructor 'Alignment::Alignment(int, int)': hhalignment.C:47:30: warning: ISO C++ does not support variable-length array types [-Wvla] sname = new(char*[maxseq+2]); ^ hhalignment.C:48:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq = new(char*[maxseq+2]); ^ hhalignment.C:49:22: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int[maxres]); ^ hhalignment.C:50:26: warning: ISO C++ does not support variable-length array types [-Wvla] X = new(char*[maxseq+2]); ^ hhalignment.C:51:40: warning: ISO C++ does not support variable-length array types [-Wvla] I = new(short unsigned int*[maxseq+2]); ^ hhalignment.C:52:28: warning: ISO C++ does not support variable-length array types [-Wvla] keep = new(char[maxseq+2]); ^ hhalignment.C:53:31: warning: ISO C++ does not support variable-length array types [-Wvla] display = new(char[maxseq+2]); ^ hhalignment.C:431:41: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:54:27: warning: ISO C++ does not support variable-length array types [-Wvla] wg = new(float[maxseq+2]); ^ hhalignment.C:433:39: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:55:28: warning: ISO C++ does not support variable-length array types [-Wvla] nseqs = new(int[maxres+2]); ^ hhalignment.C:435:53: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment.C: In member function 'Alignment& Alignment::operator=(Alignment&)': hhalignment.C:144:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:150:48: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(ali.sname[k])+1]); ^ hhalignment.C:156:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(ali.seq[k])+1]); ^ hhalignment.C:162:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(ali.seq[k])+2]); ^ hhalignment.C:167:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ^ hhalignment.C: In member function 'void Alignment::Read(FILE*, char*, char*)': hhalignment.C:252:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:254:47: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:256:61: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhhmm.C: In member function 'void HMM::InsertCalibration(char*)': hhhmm.C:2177:39: warning: ISO C++ does not support variable-length array types [-Wvla] char** lines = new(char*[3*L+100000]); ^ hhalignment.C: In member function 'void Alignment::Compress(const char*)': hhalignment.C:649:36: warning: ISO C++ does not support variable-length array types [-Wvla] if (nres==NULL) nres=new(int[N_in]); ^ hhhmm.C:2205:44: warning: ISO C++ does not support variable-length array types [-Wvla] lines[nline]=new(char[strlen(line)+1]); ^ In file included from hhfilter.C:82:0: hhalignment.C:315:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(cur_name)+1]); ^ hhhmm.C: In member function 'void HMM::AddSSPrediction(char*, char*)': hhhmm.C:2329:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred]=new(char[L+2]); ^ hhhmm.C:2336:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf]=new(char[L+2]); ^ In file included from hhsearch.C:113:0: hhalignment.C: In constructor 'Alignment::Alignment(int, int)': hhalignment.C:47:30: warning: ISO C++ does not support variable-length array types [-Wvla] sname = new(char*[maxseq+2]); ^ hhalignment.C:48:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq = new(char*[maxseq+2]); ^ hhalignment.C:49:22: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int[maxres]); ^ hhalignment.C:50:26: warning: ISO C++ does not support variable-length array types [-Wvla] X = new(char*[maxseq+2]); ^ hhalignment.C:51:40: warning: ISO C++ does not support variable-length array types [-Wvla] I = new(short unsigned int*[maxseq+2]); ^ hhalignment.C:52:28: warning: ISO C++ does not support variable-length array types [-Wvla] keep = new(char[maxseq+2]); ^ hhalignment.C:53:31: warning: ISO C++ does not support variable-length array types [-Wvla] display = new(char[maxseq+2]); ^ hhalignment.C:54:27: warning: ISO C++ does not support variable-length array types [-Wvla] wg = new(float[maxseq+2]); ^ hhalignment.C:55:28: warning: ISO C++ does not support variable-length array types [-Wvla] nseqs = new(int[maxres+2]); ^ hhalignment.C: In member function 'Alignment& Alignment::operator=(Alignment&)': hhalignment.C:144:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:150:48: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(ali.sname[k])+1]); ^ hhalignment.C:156:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(ali.seq[k])+1]); ^ hhhmm.C: In member function 'void HMM::InsertCalibration(char*)': hhhmm.C:2177:39: warning: ISO C++ does not support variable-length array types [-Wvla] char** lines = new(char*[3*L+100000]); ^ hhalignment.C:162:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(ali.seq[k])+2]); ^ hhalignment.C:167:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ^ hhhmm.C:2205:44: warning: ISO C++ does not support variable-length array types [-Wvla] lines[nline]=new(char[strlen(line)+1]); ^ hhalignment.C: In member function 'void Alignment::GetSeqsFromHMM(HMM*)': hhalignment.C:923:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C:926:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C: In member function 'void Alignment::Read(FILE*, char*, char*)': hhalignment.C:252:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:254:47: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:928:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ^ hhalignment.C:256:61: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment.C:431:41: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:949:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(q->sname[qk])+1]); ^ hhalignment.C:433:39: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:435:53: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment.C: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)': hhalignment.C:972:33: warning: ISO C++ does not support variable-length array types [-Wvla] char *dummy = new(char[N_in+1]); ^ In file included from hhsearch.C:113:0: hhalignment.C:315:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(cur_name)+1]); ^ hhhmm.C: In member function 'void HMM::AddSSPrediction(char*, char*)': hhhmm.C:2329:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred]=new(char[L+2]); ^ hhhmm.C:2336:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf]=new(char[L+2]); ^ hhalignment.C: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)': hhalignment.C:1031:28: warning: ISO C++ does not support variable-length array types [-Wvla] char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ^ hhalignment.C:1032:30: warning: ISO C++ does not support variable-length array types [-Wvla] char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ^ hhalignment.C:1033:25: warning: ISO C++ does not support variable-length array types [-Wvla] int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ^ In file included from hhalign.C:96:0: hhalignment.C: In constructor 'Alignment::Alignment(int, int)': hhalignment.C:47:30: warning: ISO C++ does not support variable-length array types [-Wvla] sname = new(char*[maxseq+2]); ^ hhalignment.C:1034:29: warning: ISO C++ does not support variable-length array types [-Wvla] int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ^ hhalignment.C:48:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq = new(char*[maxseq+2]); ^ hhalignment.C:49:22: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int[maxres]); ^ hhalignment.C:1035:34: warning: ISO C++ does not support variable-length array types [-Wvla] int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ^ hhalignment.C:50:26: warning: ISO C++ does not support variable-length array types [-Wvla] X = new(char*[maxseq+2]); ^ hhalignment.C:51:40: warning: ISO C++ does not support variable-length array types [-Wvla] I = new(short unsigned int*[maxseq+2]); ^ hhalignment.C:52:28: warning: ISO C++ does not support variable-length array types [-Wvla] keep = new(char[maxseq+2]); ^ hhalignment.C:1036:22: warning: ISO C++ does not support variable-length array types [-Wvla] int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ^ hhalignment.C:53:31: warning: ISO C++ does not support variable-length array types [-Wvla] display = new(char[maxseq+2]); ^ hhalignment.C:54:27: warning: ISO C++ does not support variable-length array types [-Wvla] wg = new(float[maxseq+2]); ^ hhalignment.C:55:28: warning: ISO C++ does not support variable-length array types [-Wvla] nseqs = new(int[maxres+2]); ^ hhalignment.C:1064:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1065:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:1079:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:1095:26: warning: ISO C++ does not support variable-length array types [-Wvla] ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ^ hhalignment.C: In member function 'Alignment& Alignment::operator=(Alignment&)': hhalignment.C:144:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:150:48: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(ali.sname[k])+1]); ^ hhalignment.C:156:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(ali.seq[k])+1]); ^ hhalignment.C:162:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(ali.seq[k])+2]); ^ hhalignment.C:167:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ^ hhalignment.C: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM*)': hhalignment.C:1303:34: warning: ISO C++ does not support variable-length array types [-Wvla] float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ^ hhalignment.C: In member function 'void Alignment::Read(FILE*, char*, char*)': hhalignment.C:252:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:254:47: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:1312:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C: In member function 'void Alignment::Compress(const char*)': hhalignment.C:649:36: warning: ISO C++ does not support variable-length array types [-Wvla] if (nres==NULL) nres=new(int[N_in]); ^ hhalignment.C:256:61: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment.C:1313:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:1326:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ In file included from hhalign.C:96:0: hhalignment.C:315:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(cur_name)+1]); ^ hhalignment.C:431:41: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:433:39: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:435:53: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment.C: In member function 'void Alignment::FrequenciesAndTransitions(HMM*, char*, bool)': hhalignment.C:1598:41: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->ncons]=new(char[L+2]); ^ hhalignment.C:1605:56: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[q->nfirst]=new(char[strlen(name)+11]); ^ hhalignment.C:1609:42: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->nfirst]=new(char[L+2]); ^ hhalignment.C:1661:52: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[nn]=new(char[strlen(sname[k])+1]); ^ hhalignment.C: In member function 'void Alignment::Compress(const char*)': hhalignment.C:649:36: warning: ISO C++ does not support variable-length array types [-Wvla] if (nres==NULL) nres=new(int[N_in]); ^ hhalignment.C:1664:48: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[nn]=new(char[strlen(seq[k])+1]); ^ hhalignment.C:431:41: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C: In member function 'void Alignment::GetSeqsFromHMM(HMM*)': hhalignment.C:923:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C:433:39: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:435:53: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment.C:926:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C:928:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ^ hhhmm.C: In member function 'void HMM::InsertCalibration(char*)': hhhmm.C:2177:39: warning: ISO C++ does not support variable-length array types [-Wvla] char** lines = new(char*[3*L+100000]); ^ hhalignment.C:949:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(q->sname[qk])+1]); ^ hhalignment.C: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)': hhalignment.C:972:33: warning: ISO C++ does not support variable-length array types [-Wvla] char *dummy = new(char[N_in+1]); ^ hhhmm.C:2205:44: warning: ISO C++ does not support variable-length array types [-Wvla] lines[nline]=new(char[strlen(line)+1]); ^ hhalignment.C: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM*, char*)': hhalignment.C:1764:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)': hhalignment.C:1031:28: warning: ISO C++ does not support variable-length array types [-Wvla] char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ^ hhalignment.C:1032:30: warning: ISO C++ does not support variable-length array types [-Wvla] char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ^ hhalignment.C:1033:25: warning: ISO C++ does not support variable-length array types [-Wvla] int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ^ hhhmm.C: In member function 'void HMM::AddSSPrediction(char*, char*)': hhhmm.C:2329:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred]=new(char[L+2]); ^ hhalignment.C:1034:29: warning: ISO C++ does not support variable-length array types [-Wvla] int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ^ hhhmm.C:2336:34: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf]=new(char[L+2]); ^ In file included from hhblits.C:143:0: hhalignment.C: In constructor 'Alignment::Alignment(int, int)': hhalignment.C:47:30: warning: ISO C++ does not support variable-length array types [-Wvla] sname = new(char*[maxseq+2]); ^ hhalignment.C: In member function 'void Alignment::Compress(const char*)': hhalignment.C:649:36: warning: ISO C++ does not support variable-length array types [-Wvla] if (nres==NULL) nres=new(int[N_in]); ^ hhalignment.C:48:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq = new(char*[maxseq+2]); ^ hhalignment.C:49:22: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int[maxres]); ^ hhalignment.C:50:26: warning: ISO C++ does not support variable-length array types [-Wvla] X = new(char*[maxseq+2]); ^ hhalignment.C:51:40: warning: ISO C++ does not support variable-length array types [-Wvla] I = new(short unsigned int*[maxseq+2]); ^ hhalignment.C:52:28: warning: ISO C++ does not support variable-length array types [-Wvla] keep = new(char[maxseq+2]); ^ hhalignment.C:53:31: warning: ISO C++ does not support variable-length array types [-Wvla] display = new(char[maxseq+2]); ^ hhalignment.C:54:27: warning: ISO C++ does not support variable-length array types [-Wvla] wg = new(float[maxseq+2]); ^ hhalignment.C:55:28: warning: ISO C++ does not support variable-length array types [-Wvla] nseqs = new(int[maxres+2]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_I_state(HMM*, char*)': hhalignment.C:1980:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C: In member function 'Alignment& Alignment::operator=(Alignment&)': hhalignment.C:144:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C: In member function 'void Alignment::GetSeqsFromHMM(HMM*)': hhalignment.C:923:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C:150:48: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(ali.sname[k])+1]); ^ hhalignment.C:926:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C:156:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(ali.seq[k])+1]); ^ hhalignment.C:928:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ^ hhalignment.C:162:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(ali.seq[k])+2]); ^ hhalignment.C:167:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ^ hhalignment.C:949:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(q->sname[qk])+1]); ^ hhalignment.C: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)': hhalignment.C:972:33: warning: ISO C++ does not support variable-length array types [-Wvla] char *dummy = new(char[N_in+1]); ^ hhalignment.C: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)': hhalignment.C:1031:28: warning: ISO C++ does not support variable-length array types [-Wvla] char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ^ hhalignment.C:1035:34: warning: ISO C++ does not support variable-length array types [-Wvla] int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ^ hhalignment.C:1032:30: warning: ISO C++ does not support variable-length array types [-Wvla] char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ^ hhalignment.C:1036:22: warning: ISO C++ does not support variable-length array types [-Wvla] int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ^ hhalignment.C:1033:25: warning: ISO C++ does not support variable-length array types [-Wvla] int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ^ hhalignment.C: In member function 'void Alignment::Read(FILE*, char*, char*)': hhalignment.C:252:49: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:254:47: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:1034:29: warning: ISO C++ does not support variable-length array types [-Wvla] int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ^ hhalignment.C:1064:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:256:61: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment.C:1065:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:1035:34: warning: ISO C++ does not support variable-length array types [-Wvla] int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ^ hhalignment.C:1036:22: warning: ISO C++ does not support variable-length array types [-Wvla] int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ^ hhalignment.C:1079:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:1064:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1065:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:1095:26: warning: ISO C++ does not support variable-length array types [-Wvla] ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ^ hhalignment.C: In member function 'void Alignment::Transitions_from_D_state(HMM*, char*)': hhalignment.C:2173:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:1079:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ In file included from hhblits.C:143:0: hhalignment.C:315:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(cur_name)+1]); ^ hhalignment.C:1095:26: warning: ISO C++ does not support variable-length array types [-Wvla] ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ^ hhalignment.C: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM*)': hhalignment.C:1303:34: warning: ISO C++ does not support variable-length array types [-Wvla] float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ^ hhalignment.C: In member function 'void Alignment::GetSeqsFromHMM(HMM*)': hhalignment.C:923:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C:1312:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1313:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:926:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM*)': hhalignment.C:1303:34: warning: ISO C++ does not support variable-length array types [-Wvla] float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ^ hhalignment.C:928:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ^ hhalignment.C:1312:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1326:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:1313:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:1326:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:949:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(q->sname[qk])+1]); ^ hhalignment.C: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)': hhalignment.C:972:33: warning: ISO C++ does not support variable-length array types [-Wvla] char *dummy = new(char[N_in+1]); ^ hhalignment.C: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)': hhalignment.C:1031:28: warning: ISO C++ does not support variable-length array types [-Wvla] char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ^ hhalignment.C:1032:30: warning: ISO C++ does not support variable-length array types [-Wvla] char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ^ hhalignment.C:1033:25: warning: ISO C++ does not support variable-length array types [-Wvla] int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ^ hhalignment.C:1034:29: warning: ISO C++ does not support variable-length array types [-Wvla] int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ^ hhalignment.C:1035:34: warning: ISO C++ does not support variable-length array types [-Wvla] int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ^ hhalignment.C:1036:22: warning: ISO C++ does not support variable-length array types [-Wvla] int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ^ hhalignment.C:1064:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1065:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:1079:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:1095:26: warning: ISO C++ does not support variable-length array types [-Wvla] ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ^ hhalignment.C: In member function 'void Alignment::FrequenciesAndTransitions(HMM*, char*, bool)': hhalignment.C:1598:41: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->ncons]=new(char[L+2]); ^ hhalignment.C:431:41: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:1605:56: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[q->nfirst]=new(char[strlen(name)+11]); ^ hhalignment.C:433:39: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment.C:435:53: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment.C:1609:42: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->nfirst]=new(char[L+2]); ^ hhalignment.C: In member function 'void Alignment::FrequenciesAndTransitions(HMM*, char*, bool)': hhalignment.C:1598:41: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->ncons]=new(char[L+2]); ^ hhalignment.C:1605:56: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[q->nfirst]=new(char[strlen(name)+11]); ^ hhalignment.C:1609:42: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->nfirst]=new(char[L+2]); ^ hhalignment.C: In member function 'void Alignment::MergeMasterSlave(Hit&, Alignment&, char*)': hhalignment.C:2430:39: warning: ISO C++ does not support variable-length array types [-Wvla] char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ^ hhalignment.C:1661:52: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[nn]=new(char[strlen(sname[k])+1]); ^ hhalignment.C:1664:48: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[nn]=new(char[strlen(seq[k])+1]); ^ hhalignment.C:2442:32: warning: ISO C++ does not support variable-length array types [-Wvla] int* imatch=new(int[hit.j2+1]); ^ hhalignment.C: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM*)': hhalignment.C:1303:34: warning: ISO C++ does not support variable-length array types [-Wvla] float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ^ hhalignment.C:1312:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1661:52: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[nn]=new(char[strlen(sname[k])+1]); ^ hhalignment.C:1313:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:1664:48: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[nn]=new(char[strlen(seq[k])+1]); ^ hhalignment.C:1326:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:2574:47: warning: ISO C++ does not support variable-length array types [-Wvla] char* new_seq=new(char[2*maxcol]); ^ hhalignment.C:2587:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[h]); ^ hhalignment.C: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM*, char*)': hhalignment.C:1764:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:2590:26: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[h]); ^ hhalignment.C: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM*, char*)': hhalignment.C:1764:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:2592:40: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[h]); ^ hhalignment.C:2594:52: warning: ISO C++ does not support variable-length array types [-Wvla] sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ^ hhalignment.C: In member function 'void Alignment::Compress(const char*)': hhalignment.C:649:36: warning: ISO C++ does not support variable-length array types [-Wvla] if (nres==NULL) nres=new(int[N_in]); ^ hhalignment.C: In member function 'void Alignment::AddSequence(char*, int*)': hhalignment.C:2625:24: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C: In member function 'void Alignment::AddSSPrediction(char*, char*)': hhalignment.C:2663:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C:2665:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C: In member function 'void Alignment::FrequenciesAndTransitions(HMM*, char*, bool)': hhalignment.C:1598:41: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->ncons]=new(char[L+2]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_I_state(HMM*, char*)': hhalignment.C:1980:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:1605:56: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[q->nfirst]=new(char[strlen(name)+11]); ^ hhalignment.C:2667:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_I_state(HMM*, char*)': hhalignment.C:1980:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:1609:42: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->nfirst]=new(char[L+2]); ^ hhalignment.C:2686:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C:2688:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:2690:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C:1661:52: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[nn]=new(char[strlen(sname[k])+1]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_D_state(HMM*, char*)': hhalignment.C:2173:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:1664:48: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[nn]=new(char[strlen(seq[k])+1]); ^ hhalignment.C: In member function 'void Alignment::GetPositionSpecificWeights(float**)': hhalignment.C:2743:24: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_D_state(HMM*, char*)': hhalignment.C:2173:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ In file included from hhconsensus.C:70:0: hhhalfalignment.C: In constructor 'HalfAlignment::HalfAlignment(int)': hhhalfalignment.C:46:25: warning: ISO C++ does not support variable-length array types [-Wvla] h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ^ hhhalfalignment.C:47:27: warning: ISO C++ does not support variable-length array types [-Wvla] s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ^ hhhalfalignment.C:48:26: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ^ hhhalfalignment.C:49:26: warning: ISO C++ does not support variable-length array types [-Wvla] m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ^ hhalignment.C: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM*, char*)': hhalignment.C:1764:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C: In member function 'void Alignment::MergeMasterSlave(Hit&, Alignment&, char*)': hhalignment.C:2430:39: warning: ISO C++ does not support variable-length array types [-Wvla] char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ^ hhalignment.C: In member function 'void Alignment::GetSeqsFromHMM(HMM*)': hhalignment.C:923:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_I_state(HMM*, char*)': hhalignment.C:1980:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:2442:32: warning: ISO C++ does not support variable-length array types [-Wvla] int* imatch=new(int[hit.j2+1]); ^ hhalignment.C:926:42: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(q->seq[qk])+1]); ^ hhalignment.C:928:56: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ^ hhalignment.C:949:50: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(q->sname[qk])+1]); ^ hhalignment.C: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)': hhalignment.C:972:33: warning: ISO C++ does not support variable-length array types [-Wvla] char *dummy = new(char[N_in+1]); ^ hhalignment.C:2574:47: warning: ISO C++ does not support variable-length array types [-Wvla] char* new_seq=new(char[2*maxcol]); ^ hhalignment.C: In member function 'void Alignment::MergeMasterSlave(Hit&, Alignment&, char*)': hhalignment.C:2430:39: warning: ISO C++ does not support variable-length array types [-Wvla] char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ^ hhalignment.C:2587:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[h]); ^ hhalignment.C:2442:32: warning: ISO C++ does not support variable-length array types [-Wvla] int* imatch=new(int[hit.j2+1]); ^ hhalignment.C:2590:26: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[h]); ^ hhalignment.C: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)': hhalignment.C:1031:28: warning: ISO C++ does not support variable-length array types [-Wvla] char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ^ hhalignment.C:2592:40: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[h]); ^ hhalignment.C:1032:30: warning: ISO C++ does not support variable-length array types [-Wvla] char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ^ hhalignment.C:1033:25: warning: ISO C++ does not support variable-length array types [-Wvla] int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ^ hhalignment.C:2594:52: warning: ISO C++ does not support variable-length array types [-Wvla] sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_D_state(HMM*, char*)': hhalignment.C:2173:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:1034:29: warning: ISO C++ does not support variable-length array types [-Wvla] int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ^ hhalignment.C:1035:34: warning: ISO C++ does not support variable-length array types [-Wvla] int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ^ hhalignment.C:1036:22: warning: ISO C++ does not support variable-length array types [-Wvla] int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ^ hhalignment.C:1064:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1065:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C: In member function 'void Alignment::AddSequence(char*, int*)': hhalignment.C:2625:24: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:2574:47: warning: ISO C++ does not support variable-length array types [-Wvla] char* new_seq=new(char[2*maxcol]); ^ hhalignment.C:1079:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C:1095:26: warning: ISO C++ does not support variable-length array types [-Wvla] ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ^ hhalignment.C:2587:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[h]); ^ hhalignment.C: In member function 'void Alignment::AddSSPrediction(char*, char*)': hhalignment.C:2663:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C:2590:26: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[h]); ^ hhalignment.C:2665:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:2592:40: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[h]); ^ hhalignment.C:2667:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C:2594:52: warning: ISO C++ does not support variable-length array types [-Wvla] sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ^ hhalignment.C:2686:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C:2688:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C: In member function 'void Alignment::AddSequence(char*, int*)': hhalignment.C:2625:24: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:2690:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C: In member function 'void Alignment::AddSSPrediction(char*, char*)': hhalignment.C:2663:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM*)': hhalignment.C:1303:34: warning: ISO C++ does not support variable-length array types [-Wvla] float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ^ hhalignment.C: In member function 'void Alignment::GetPositionSpecificWeights(float**)': hhalignment.C:2743:24: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:2665:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:1312:26: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment.C:1313:26: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment.C:2667:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C:1326:25: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment.C: In member function 'void Alignment::MergeMasterSlave(Hit&, Alignment&, char*)': hhalignment.C:2430:39: warning: ISO C++ does not support variable-length array types [-Wvla] char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ^ hhalignment.C:2686:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C:2688:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:2442:32: warning: ISO C++ does not support variable-length array types [-Wvla] int* imatch=new(int[hit.j2+1]); ^ hhalignment.C:2690:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C: In member function 'void Alignment::GetPositionSpecificWeights(float**)': hhalignment.C:2743:24: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C:2574:47: warning: ISO C++ does not support variable-length array types [-Wvla] char* new_seq=new(char[2*maxcol]); ^ In file included from hhsearch.C:114:0: hhhit.C: In member function 'void Hit::AllocateBacktraceMatrix(int, int)': hhhit.C:141:20: warning: ISO C++ does not support variable-length array types [-Wvla] bMM=new(char*[Nq]); ^ hhhit.C:142:20: warning: ISO C++ does not support variable-length array types [-Wvla] bMI=new(char*[Nq]); ^ hhalignment.C:2587:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[h]); ^ hhhit.C:143:20: warning: ISO C++ does not support variable-length array types [-Wvla] bIM=new(char*[Nq]); ^ hhhit.C:144:20: warning: ISO C++ does not support variable-length array types [-Wvla] bDG=new(char*[Nq]); ^ hhhit.C:145:20: warning: ISO C++ does not support variable-length array types [-Wvla] bGD=new(char*[Nq]); ^ hhhit.C:146:25: warning: ISO C++ does not support variable-length array types [-Wvla] cell_off=new(char*[Nq]); ^ hhalignment.C:2590:26: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[h]); ^ hhhit.C:149:26: warning: ISO C++ does not support variable-length array types [-Wvla] bMM[i]=new(char[Nt]); ^ hhhit.C:150:26: warning: ISO C++ does not support variable-length array types [-Wvla] bMI[i]=new(char[Nt]); ^ hhhit.C:151:26: warning: ISO C++ does not support variable-length array types [-Wvla] bIM[i]=new(char[Nt]); ^ hhalignment.C:2592:40: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[h]); ^ hhhit.C:152:26: warning: ISO C++ does not support variable-length array types [-Wvla] bGD[i]=new(char[Nt]); ^ hhhit.C:153:26: warning: ISO C++ does not support variable-length array types [-Wvla] bDG[i]=new(char[Nt]); ^ hhhit.C:154:31: warning: ISO C++ does not support variable-length array types [-Wvla] cell_off[i]=new(char[Nt]); ^ hhalignment.C:2594:52: warning: ISO C++ does not support variable-length array types [-Wvla] sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ^ hhalignment.C: In member function 'void Alignment::FrequenciesAndTransitions(HMM*, char*, bool)': hhalignment.C:1598:41: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->ncons]=new(char[L+2]); ^ hhalignment.C:1605:56: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[q->nfirst]=new(char[strlen(name)+11]); ^ hhhit.C: In member function 'void Hit::AllocateForwardMatrix(int, int)': hhhit.C:192:23: warning: ISO C++ does not support variable-length array types [-Wvla] F_MM=new(double*[Nq]); ^ hhhit.C:199:25: warning: ISO C++ does not support variable-length array types [-Wvla] scale=new(double[Nq+1]); // need Nq+3? ^ hhhit.C:202:31: warning: ISO C++ does not support variable-length array types [-Wvla] F_MM[i] = new(double[Nt]); ^ hhalignment.C:1609:42: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[q->nfirst]=new(char[L+2]); ^ hhalignment.C: In member function 'void Alignment::AddSequence(char*, int*)': hhalignment.C:2625:24: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhhit.C: In member function 'void Hit::AllocateBackwardMatrix(int, int)': hhhit.C:252:23: warning: ISO C++ does not support variable-length array types [-Wvla] B_MM=new(double*[Nq]); ^ hhhit.C:261:31: warning: ISO C++ does not support variable-length array types [-Wvla] B_MM[i] = new(double[Nt]); ^ hhalignment.C: In member function 'void Alignment::AddSSPrediction(char*, char*)': hhalignment.C:2663:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhhit.C: In member function 'void Hit::AllocateIndices(int)': hhhit.C:291:19: warning: ISO C++ does not support variable-length array types [-Wvla] i = new(int[len]); ^ hhhit.C:292:19: warning: ISO C++ does not support variable-length array types [-Wvla] j = new(int[len]); ^ hhalignment.C:2665:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:1661:52: warning: ISO C++ does not support variable-length array types [-Wvla] q->sname[nn]=new(char[strlen(sname[k])+1]); ^ hhalignment.C:1664:48: warning: ISO C++ does not support variable-length array types [-Wvla] q->seq[nn]=new(char[strlen(seq[k])+1]); ^ hhalignment.C:2667:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C:2686:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C:2688:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:2690:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C: In member function 'void Alignment::GetPositionSpecificWeights(float**)': hhalignment.C:2743:24: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment.C: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM*, char*)': hhalignment.C:1764:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ In file included from hhalign.C:97:0: hhhit.C: In member function 'void Hit::AllocateBacktraceMatrix(int, int)': hhhit.C:141:20: warning: ISO C++ does not support variable-length array types [-Wvla] bMM=new(char*[Nq]); ^ hhhit.C:142:20: warning: ISO C++ does not support variable-length array types [-Wvla] bMI=new(char*[Nq]); ^ hhhit.C:143:20: warning: ISO C++ does not support variable-length array types [-Wvla] bIM=new(char*[Nq]); ^ hhhit.C:144:20: warning: ISO C++ does not support variable-length array types [-Wvla] bDG=new(char*[Nq]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_I_state(HMM*, char*)': hhalignment.C:1980:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhhit.C:145:20: warning: ISO C++ does not support variable-length array types [-Wvla] bGD=new(char*[Nq]); ^ hhhit.C:146:25: warning: ISO C++ does not support variable-length array types [-Wvla] cell_off=new(char*[Nq]); ^ hhhit.C:149:26: warning: ISO C++ does not support variable-length array types [-Wvla] bMM[i]=new(char[Nt]); ^ hhhit.C:150:26: warning: ISO C++ does not support variable-length array types [-Wvla] bMI[i]=new(char[Nt]); ^ hhhit.C:151:26: warning: ISO C++ does not support variable-length array types [-Wvla] bIM[i]=new(char[Nt]); ^ hhhit.C:152:26: warning: ISO C++ does not support variable-length array types [-Wvla] bGD[i]=new(char[Nt]); ^ hhhit.C:153:26: warning: ISO C++ does not support variable-length array types [-Wvla] bDG[i]=new(char[Nt]); ^ hhhit.C:154:31: warning: ISO C++ does not support variable-length array types [-Wvla] cell_off[i]=new(char[Nt]); ^ hhhit.C: In member function 'void Hit::AllocateForwardMatrix(int, int)': hhhit.C:192:23: warning: ISO C++ does not support variable-length array types [-Wvla] F_MM=new(double*[Nq]); ^ hhhit.C:199:25: warning: ISO C++ does not support variable-length array types [-Wvla] scale=new(double[Nq+1]); // need Nq+3? ^ hhhit.C:202:31: warning: ISO C++ does not support variable-length array types [-Wvla] F_MM[i] = new(double[Nt]); ^ hhhit.C: In member function 'void Hit::AllocateBackwardMatrix(int, int)': hhhit.C:252:23: warning: ISO C++ does not support variable-length array types [-Wvla] B_MM=new(double*[Nq]); ^ hhhit.C:261:31: warning: ISO C++ does not support variable-length array types [-Wvla] B_MM[i] = new(double[Nt]); ^ hhhit.C: In member function 'void Hit::AllocateIndices(int)': hhhit.C:291:19: warning: ISO C++ does not support variable-length array types [-Wvla] i = new(int[len]); ^ hhhit.C:292:19: warning: ISO C++ does not support variable-length array types [-Wvla] j = new(int[len]); ^ hhalignment.C: In member function 'void Alignment::Transitions_from_D_state(HMM*, char*)': hhalignment.C:2173:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhhit.C: In member function 'void Hit::Backtrace(HMM*, HMM*)': hhhit.C:1147:30: warning: ISO C++ does not support variable-length array types [-Wvla] S = new( float[nsteps+1]); ^ hhhit.C:1148:30: warning: ISO C++ does not support variable-length array types [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit.C: In member function 'void Hit::BacktraceMAC(HMM*, HMM*)': hhhit.C:1487:30: warning: ISO C++ does not support variable-length array types [-Wvla] S = new( float[nsteps+1]); ^ hhhit.C:1488:30: warning: ISO C++ does not support variable-length array types [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit.C:1489:37: warning: ISO C++ does not support variable-length array types [-Wvla] P_posterior = new( float[nsteps+1]); ^ hhalignment.C: In member function 'void Alignment::MergeMasterSlave(Hit&, Alignment&, char*)': hhalignment.C:2430:39: warning: ISO C++ does not support variable-length array types [-Wvla] char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ^ hhalignment.C:2442:32: warning: ISO C++ does not support variable-length array types [-Wvla] int* imatch=new(int[hit.j2+1]); ^ hhalignment.C:2574:47: warning: ISO C++ does not support variable-length array types [-Wvla] char* new_seq=new(char[2*maxcol]); ^ hhalignment.C:2587:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[h]); ^ hhalignment.C:2590:26: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[h]); ^ hhalignment.C:2592:40: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[h]); ^ hhhit.C: In member function 'void Hit::InitializeBacktrace(HMM*, HMM*)': hhhit.C:1795:43: warning: ISO C++ does not support variable-length array types [-Wvla] longname=new(char[strlen(t->longname)+1]); ^ hhalignment.C:2594:52: warning: ISO C++ does not support variable-length array types [-Wvla] sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ^ hhhit.C:1796:39: warning: ISO C++ does not support variable-length array types [-Wvla] name =new(char[strlen(t->name)+1]); ^ hhhit.C:1797:39: warning: ISO C++ does not support variable-length array types [-Wvla] file =new(char[strlen(t->file)+1]); ^ hhhit.C:1808:30: warning: ISO C++ does not support variable-length array types [-Wvla] this->i = new( int[i2+j2+2]); ^ hhalignment.C: In member function 'void Alignment::AddSequence(char*, int*)': hhalignment.C:2625:24: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhhit.C:1809:30: warning: ISO C++ does not support variable-length array types [-Wvla] this->j = new( int[i2+j2+2]); ^ hhhit.C:1810:31: warning: ISO C++ does not support variable-length array types [-Wvla] states = new( char[i2+j2+2]); ^ hhhit.C:1813:32: warning: ISO C++ does not support variable-length array types [-Wvla] sname=new(char*[t->n_display]); ^ hhhit.C:1814:32: warning: ISO C++ does not support variable-length array types [-Wvla] seq =new(char*[t->n_display]); ^ hhhit.C:1833:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(t->sname[k])+1]); ^ hhalignment.C: In member function 'void Alignment::AddSSPrediction(char*, char*)': hhalignment.C:2663:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhhit.C:1834:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k] = new(char[strlen(t->seq[k])+1]); ^ hhalignment.C:2665:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhhit.C:1840:34: warning: ISO C++ does not support variable-length array types [-Wvla] dbfile = new(char[strlen(ptr)+1]); ^ hhhit.C: In member function 'void Hit::Backtrace(HMM*, HMM*)': hhhit.C:1147:30: warning: ISO C++ does not support variable-length array types [-Wvla] S = new( float[nsteps+1]); ^ hhalignment.C:2667:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhhit.C:1148:30: warning: ISO C++ does not support variable-length array types [-Wvla] S_ss = new( float[nsteps+1]); ^ hhalignment.C:2686:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[L+2]); ^ hhalignment.C:2688:28: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment.C:2690:42: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[L+2]); ^ hhalignment.C: In member function 'void Alignment::GetPositionSpecificWeights(float**)': hhalignment.C:2743:24: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhhit.C: In member function 'void Hit::BacktraceMAC(HMM*, HMM*)': hhhit.C:1487:30: warning: ISO C++ does not support variable-length array types [-Wvla] S = new( float[nsteps+1]); ^ hhhit.C:1488:30: warning: ISO C++ does not support variable-length array types [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit.C:1489:37: warning: ISO C++ does not support variable-length array types [-Wvla] P_posterior = new( float[nsteps+1]); ^ In file included from hhsearch.C:115:0: hhhalfalignment.C: In constructor 'HalfAlignment::HalfAlignment(int)': hhhalfalignment.C:46:25: warning: ISO C++ does not support variable-length array types [-Wvla] h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ^ hhhalfalignment.C:47:27: warning: ISO C++ does not support variable-length array types [-Wvla] s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ^ hhhalfalignment.C:48:26: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ^ hhhalfalignment.C:49:26: warning: ISO C++ does not support variable-length array types [-Wvla] m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ^ In file included from hhblits.C:144:0: hhhit.C: In member function 'void Hit::AllocateBacktraceMatrix(int, int)': hhhit.C:141:20: warning: ISO C++ does not support variable-length array types [-Wvla] bMM=new(char*[Nq]); ^ hhhit.C:142:20: warning: ISO C++ does not support variable-length array types [-Wvla] bMI=new(char*[Nq]); ^ hhhit.C:143:20: warning: ISO C++ does not support variable-length array types [-Wvla] bIM=new(char*[Nq]); ^ hhhit.C:144:20: warning: ISO C++ does not support variable-length array types [-Wvla] bDG=new(char*[Nq]); ^ hhhit.C:145:20: warning: ISO C++ does not support variable-length array types [-Wvla] bGD=new(char*[Nq]); ^ hhhit.C:146:25: warning: ISO C++ does not support variable-length array types [-Wvla] cell_off=new(char*[Nq]); ^ hhhit.C:149:26: warning: ISO C++ does not support variable-length array types [-Wvla] bMM[i]=new(char[Nt]); ^ hhhit.C:150:26: warning: ISO C++ does not support variable-length array types [-Wvla] bMI[i]=new(char[Nt]); ^ hhhit.C:151:26: warning: ISO C++ does not support variable-length array types [-Wvla] bIM[i]=new(char[Nt]); ^ hhhit.C:152:26: warning: ISO C++ does not support variable-length array types [-Wvla] bGD[i]=new(char[Nt]); ^ hhhit.C:153:26: warning: ISO C++ does not support variable-length array types [-Wvla] bDG[i]=new(char[Nt]); ^ hhhit.C:154:31: warning: ISO C++ does not support variable-length array types [-Wvla] cell_off[i]=new(char[Nt]); ^ hhhit.C: In member function 'void Hit::AllocateForwardMatrix(int, int)': hhhit.C:192:23: warning: ISO C++ does not support variable-length array types [-Wvla] F_MM=new(double*[Nq]); ^ hhhit.C:199:25: warning: ISO C++ does not support variable-length array types [-Wvla] scale=new(double[Nq+1]); // need Nq+3? ^ hhhit.C:202:31: warning: ISO C++ does not support variable-length array types [-Wvla] F_MM[i] = new(double[Nt]); ^ hhhit.C: In member function 'void Hit::AllocateBackwardMatrix(int, int)': hhhit.C:252:23: warning: ISO C++ does not support variable-length array types [-Wvla] B_MM=new(double*[Nq]); ^ hhhit.C:261:31: warning: ISO C++ does not support variable-length array types [-Wvla] B_MM[i] = new(double[Nt]); ^ hhhit.C: In member function 'void Hit::InitializeBacktrace(HMM*, HMM*)': hhhit.C:1795:43: warning: ISO C++ does not support variable-length array types [-Wvla] longname=new(char[strlen(t->longname)+1]); ^ hhhit.C:1796:39: warning: ISO C++ does not support variable-length array types [-Wvla] name =new(char[strlen(t->name)+1]); ^ hhhit.C: In member function 'void Hit::AllocateIndices(int)': hhhit.C:291:19: warning: ISO C++ does not support variable-length array types [-Wvla] i = new(int[len]); ^ hhhit.C:292:19: warning: ISO C++ does not support variable-length array types [-Wvla] j = new(int[len]); ^ hhhit.C:1797:39: warning: ISO C++ does not support variable-length array types [-Wvla] file =new(char[strlen(t->file)+1]); ^ hhhit.C:1808:30: warning: ISO C++ does not support variable-length array types [-Wvla] this->i = new( int[i2+j2+2]); ^ hhhit.C:1809:30: warning: ISO C++ does not support variable-length array types [-Wvla] this->j = new( int[i2+j2+2]); ^ hhhit.C:1810:31: warning: ISO C++ does not support variable-length array types [-Wvla] states = new( char[i2+j2+2]); ^ hhhit.C:1813:32: warning: ISO C++ does not support variable-length array types [-Wvla] sname=new(char*[t->n_display]); ^ hhhit.C:1814:32: warning: ISO C++ does not support variable-length array types [-Wvla] seq =new(char*[t->n_display]); ^ hhhit.C:1833:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(t->sname[k])+1]); ^ hhhit.C:1834:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k] = new(char[strlen(t->seq[k])+1]); ^ hhhit.C:1840:34: warning: ISO C++ does not support variable-length array types [-Wvla] dbfile = new(char[strlen(ptr)+1]); ^ In file included from hhalign.C:98:0: hhhalfalignment.C: In constructor 'HalfAlignment::HalfAlignment(int)': hhhalfalignment.C:46:25: warning: ISO C++ does not support variable-length array types [-Wvla] h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ^ hhhalfalignment.C:47:27: warning: ISO C++ does not support variable-length array types [-Wvla] s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ^ hhhalfalignment.C:48:26: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ^ hhhalfalignment.C:49:26: warning: ISO C++ does not support variable-length array types [-Wvla] m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ^ hhhit.C: In member function 'void Hit::Backtrace(HMM*, HMM*)': hhhit.C:1147:30: warning: ISO C++ does not support variable-length array types [-Wvla] S = new( float[nsteps+1]); ^ hhhit.C:1148:30: warning: ISO C++ does not support variable-length array types [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit.C: In member function 'void Hit::BacktraceMAC(HMM*, HMM*)': hhhit.C:1487:30: warning: ISO C++ does not support variable-length array types [-Wvla] S = new( float[nsteps+1]); ^ hhhit.C:1488:30: warning: ISO C++ does not support variable-length array types [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit.C:1489:37: warning: ISO C++ does not support variable-length array types [-Wvla] P_posterior = new( float[nsteps+1]); ^ hhhit.C: In member function 'void Hit::InitializeBacktrace(HMM*, HMM*)': hhhit.C:1795:43: warning: ISO C++ does not support variable-length array types [-Wvla] longname=new(char[strlen(t->longname)+1]); ^ hhhit.C:1796:39: warning: ISO C++ does not support variable-length array types [-Wvla] name =new(char[strlen(t->name)+1]); ^ hhhit.C:1797:39: warning: ISO C++ does not support variable-length array types [-Wvla] file =new(char[strlen(t->file)+1]); ^ hhhit.C:1808:30: warning: ISO C++ does not support variable-length array types [-Wvla] this->i = new( int[i2+j2+2]); ^ hhhit.C:1809:30: warning: ISO C++ does not support variable-length array types [-Wvla] this->j = new( int[i2+j2+2]); ^ hhhit.C:1810:31: warning: ISO C++ does not support variable-length array types [-Wvla] states = new( char[i2+j2+2]); ^ hhhit.C:1813:32: warning: ISO C++ does not support variable-length array types [-Wvla] sname=new(char*[t->n_display]); ^ hhhit.C:1814:32: warning: ISO C++ does not support variable-length array types [-Wvla] seq =new(char*[t->n_display]); ^ hhhit.C:1833:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(t->sname[k])+1]); ^ hhhit.C:1834:44: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k] = new(char[strlen(t->seq[k])+1]); ^ hhhit.C:1840:34: warning: ISO C++ does not support variable-length array types [-Wvla] dbfile = new(char[strlen(ptr)+1]); ^ In file included from hhblits.C:145:0: hhhalfalignment.C: In constructor 'HalfAlignment::HalfAlignment(int)': hhhalfalignment.C:46:25: warning: ISO C++ does not support variable-length array types [-Wvla] h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ^ hhhalfalignment.C:47:27: warning: ISO C++ does not support variable-length array types [-Wvla] s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ^ hhhalfalignment.C:48:26: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ^ hhhalfalignment.C:49:26: warning: ISO C++ does not support variable-length array types [-Wvla] m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ^ hhsearch.C: In function 'void ProcessArguments(int, char**)': hhsearch.C:375:56: warning: ISO C++ does not support variable-length array types [-Wvla] par.dbfiles = new(char[strlen(argv[i])+1]); ^ hhsearch.C:445:52: warning: ISO C++ does not support variable-length array types [-Wvla] par.exclstr = new(char[strlen(argv[i])+1]); ^ hhsearch.C: In function 'void perform_realign(char**, int)': hhsearch.C:672:54: warning: ISO C++ does not support variable-length array types [-Wvla] Qali.longname = new(char[strlen(q->longname)+1]); ^ hhsearch.C:705:57: warning: ISO C++ does not support variable-length array types [-Wvla] hit[bin]->dbfile = new(char[strlen(hit_cur.dbfile)+1]); ^ hhsearch.C:963:59: warning: ISO C++ does not support variable-length array types [-Wvla] hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ^ hhsearch.C: In function 'int main(int, char**)': hhsearch.C:1268:25: warning: ISO C++ does not support variable-length array types [-Wvla] format = new(int[bins]); ^ hhsearch.C:1304:62: warning: ISO C++ does not support variable-length array types [-Wvla] dbfiles[ndb]=new(char[strlen(dbfile)+1]); ^ hhsearch.C:1317:58: warning: ISO C++ does not support variable-length array types [-Wvla] dbfiles[ndb]=new(char[strlen(dbfile_cur)+1]); ^ hhsearch.C:1433:66: warning: ISO C++ does not support variable-length array types [-Wvla] hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ^ In file included from hhblits.C:262:0: hhprefilter.C: In function 'void init_no_prefiltering()': hhprefilter.C:794:52: warning: ISO C++ does not support variable-length array types [-Wvla] dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]); ^ hhprefilter.C: In function 'void init_prefilter()': hhprefilter.C:846:45: warning: ISO C++ does not support variable-length array types [-Wvla] dbnames[num_dbs]=new(char[strlen(word)+1]); ^ hhprefilter.C: In function 'void prefilter_db()': hhprefilter.C:1045:42: warning: ISO C++ does not support variable-length array types [-Wvla] __m128i** workspace = new(__m128i*[cpu]); ^ hhprefilter.C:1144:56: warning: ISO C++ does not support variable-length array types [-Wvla] dbfiles_old[ndb_old]=new(char[strlen(db_name)+1]); ^ hhprefilter.C:1150:56: warning: ISO C++ does not support variable-length array types [-Wvla] dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]); ^ hhblits.C: In function 'void ReadQueryA3MFile()': hhblits.C:781:54: warning: ISO C++ does not support variable-length array types [-Wvla] Qali.longname = new(char[strlen(q->longname)+1]); ^ hhblits.C: In function 'void DoViterbiSearch(char**, int, bool)': hhblits.C:914:55: warning: ISO C++ does not support variable-length array types [-Wvla] hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ^ hhblits.C: In function 'void RescoreWithViterbiKeepAlignment(int)': hhblits.C:1120:51: warning: ISO C++ does not support variable-length array types [-Wvla] dbfiles[ndb]=new(char[strlen(hit_cur.dbfile)+1]); ^ hhblits.C: In function 'void perform_realign(char**, int)': hhblits.C:1406:57: warning: ISO C++ does not support variable-length array types [-Wvla] hit[bin]->dbfile = new(char[strlen(hit_cur.dbfile)+1]); ^ hhblits.C:1716:59: warning: ISO C++ does not support variable-length array types [-Wvla] hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ^ hhalign.C: In function 'void ProcessArguments(int, char**)': hhalign.C:442:45: warning: ISO C++ does not support variable-length array types [-Wvla] pngfile = new(char[strlen(argv[i])+1]); ^ hhalign.C:452:47: warning: ISO C++ does not support variable-length array types [-Wvla] strucfile = new(char[strlen(argv[i])+1]); ^ hhalign.C:474:44: warning: ISO C++ does not support variable-length array types [-Wvla] tcfile = new(char[strlen(argv[i])+1]); ^ hhalign.C:491:45: warning: ISO C++ does not support variable-length array types [-Wvla] par.exclstr = new(char[strlen(argv[i])+1]); ^ hhalign.C:539:46: warning: ISO C++ does not support variable-length array types [-Wvla] dmapfile = new(char[strlen(argv[i])+1]); ^ hhblits.C: In function 'int main(int, char**)': hhblits.C:2140:25: warning: ISO C++ does not support variable-length array types [-Wvla] format = new(int[bins]); ^ hhblits.C:2240:58: warning: ISO C++ does not support variable-length array types [-Wvla] dbfiles_new[ndb_new]=new(char[strlen(dbfiles_old[a])+1]); ^ hhalign.C: In function 'int main(int, char**)': hhalign.C:943:34: warning: ISO C++ does not support variable-length array types [-Wvla] Pstruc = new(float*[q->L+2]); ^ hhalign.C:944:65: warning: ISO C++ does not support variable-length array types [-Wvla] for (int i=0; iL+2; i++) Pstruc[i] = new(float[t->L+2]); ^ hhalign.C:945:34: warning: ISO C++ does not support variable-length array types [-Wvla] Sstruc = new(float*[q->L+2]); ^ hhalign.C:946:65: warning: ISO C++ does not support variable-length array types [-Wvla] for (int i=0; iL+2; i++) Sstruc[i] = new(float[t->L+2]); ^ hhalign.C:1182:35: warning: ISO C++ does not support variable-length array types [-Wvla] float** s=new(float*[q->L+2]); ^ hhalign.C:1184:29: warning: ISO C++ does not support variable-length array types [-Wvla] if(!(s[i]=new(float[t->L+2]))) MemoryError("image map"); ^ hhalign.C:1220:30: warning: ISO C++ does not support variable-length array types [-Wvla] ali = new(int*[q->L+2]); ^ hhalign.C:1223:29: warning: ISO C++ does not support variable-length array types [-Wvla] ali[i] = new(int[t->L+2]); ^ hhalign.C:1229:33: warning: ISO C++ does not support variable-length array types [-Wvla] alisto = new(int*[q->L+2]); ^ hhalign.C:1232:32: warning: ISO C++ does not support variable-length array types [-Wvla] alisto[i] = new(int[t->L+2]); ^ make[2]: Leaving directory `/build/buildd/hhsuite-2.0.16/src' make[1]: Leaving directory `/build/buildd/hhsuite-2.0.16' dh_auto_test -a -O--parallel /usr/bin/fakeroot debian/rules binary-arch dh binary-arch --parallel dh_testroot -a -O--parallel dh_prep -a -O--parallel dh_auto_install -a -O--parallel make[1]: Entering directory `/build/buildd/hhsuite-2.0.16' mkdir -p /build/buildd/hhsuite-2.0.16/debian/tmp/usr/bin install src/hhblits /build/buildd/hhsuite-2.0.16/debian/tmp/usr/bin/hhblits install src/hhalign /build/buildd/hhsuite-2.0.16/debian/tmp/usr/bin/hhalign install src/hhconsensus /build/buildd/hhsuite-2.0.16/debian/tmp/usr/bin/hhconsensus install src/hhfilter /build/buildd/hhsuite-2.0.16/debian/tmp/usr/bin/hhfilter install src/hhmake /build/buildd/hhsuite-2.0.16/debian/tmp/usr/bin/hhmake install src/hhsearch /build/buildd/hhsuite-2.0.16/debian/tmp/usr/bin/hhsearch mkdir -p /build/buildd/hhsuite-2.0.16/debian/tmp/usr/lib/hhsuite mkdir -p /build/buildd/hhsuite-2.0.16/debian/tmp/usr/lib/hhsuite/bin install src/cstranslate /build/buildd/hhsuite-2.0.16/debian/tmp/usr/lib/hhsuite/bin/cstranslate mkdir -p /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/data /build/buildd/hhsuite-2.0.16/debian/tmp/usr/lib/hhsuite/data install --mode=0644 data/context_data.lib /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/data/context_data.lib install --mode=0644 data/cs219.lib /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/data/cs219.lib install --mode=0644 data/do_not_delete /build/buildd/hhsuite-2.0.16/debian/tmp/usr/lib/hhsuite/data/do_not_delete install --mode=0644 data/do_not_delete.phr /build/buildd/hhsuite-2.0.16/debian/tmp/usr/lib/hhsuite/data/do_not_delete.phr install --mode=0644 data/do_not_delete.pin /build/buildd/hhsuite-2.0.16/debian/tmp/usr/lib/hhsuite/data/do_not_delete.pin install --mode=0644 data/do_not_delete.psq /build/buildd/hhsuite-2.0.16/debian/tmp/usr/lib/hhsuite/data/do_not_delete.psq mkdir -p /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts install --mode=0644 scripts/Align.pm /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/Align.pm install --mode=0644 scripts/HHPaths.pm /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/HHPaths.pm install scripts/addss.pl /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/addss.pl install scripts/create_profile_from_hhm.pl /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/create_profile_from_hhm.pl install scripts/create_profile_from_hmmer.pl /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/create_profile_from_hmmer.pl install scripts/hhmakemodel.pl /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/hhmakemodel.pl install scripts/reformat.pl /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/reformat.pl install scripts/splitfasta.pl /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/splitfasta.pl install scripts/multithread.pl /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/multithread.pl install scripts/hhblitsdb.pl /build/buildd/hhsuite-2.0.16/debian/tmp/usr/share/hhsuite/scripts/hhblitsdb.pl make[1]: Leaving directory `/build/buildd/hhsuite-2.0.16' dh_install -a -O--parallel dh_installdocs -a -O--parallel dh_installchangelogs -a -O--parallel dh_installexamples -a -O--parallel debian/rules override_dh_installman make[1]: Entering directory `/build/buildd/hhsuite-2.0.16' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string 2.0.16 -n "$n_hhalign" 'debian/tmp/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string 2.0.16 -n "$n_hhblits" 'debian/tmp/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string 2.0.16 -n "$n_hhconsensus" 'debian/tmp/usr/bin/hhconsensus' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhconsensus.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string 2.0.16 -n "$n_hhfilter" 'debian/tmp/usr/bin/hhfilter' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhfilter.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string 2.0.16 -n "$n_hhmake" 'debian/tmp/usr/bin/hhmake' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhmake.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string 2.0.16 -n "$n_hhsearch" 'debian/tmp/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1' dh_installman make[1]: Leaving directory `/build/buildd/hhsuite-2.0.16' dh_perl -a -O--parallel dh_link -a -O--parallel dh_compress -a -O--parallel dh_fixperms -a -O--parallel debian/rules override_dh_strip make[1]: Entering directory `/build/buildd/hhsuite-2.0.16' dh_strip --dbg-package=hhsuite-dbg -Xlibffindex.a -Xlibffindex.so dh_strip debug symbol extraction: all non-arch-all packages for this build platform amd64: hhsuite hhsuite-data hhsuite-dbg dh_strip debug symbol extraction: not adding gnu debuglinks since --dbg-package is given dh_strip debug symbol extraction: packages to act on: hhsuite hhsuite-data hhsuite-dbg dh_strip debug symbol extraction: ignored packages: we have -dbg package(s), not installing anything into ddeb find: `/build/buildd/hhsuite-2.0.16/debian/hhsuite-dbgsym': No such file or directory dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-deb: warning: '/build/buildd/hhsuite-2.0.16/debian/hhsuite-dbgsym/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `hhsuite-dbgsym' in `../hhsuite-dbgsym_2.0.16-1ubuntu1_amd64.ddeb'. hhsuite-data is already stripped, ignoring find: `/build/buildd/hhsuite-2.0.16/debian/hhsuite-data-dbgsym': No such file or directory dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-deb: warning: '/build/buildd/hhsuite-2.0.16/debian/hhsuite-data-dbgsym/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `hhsuite-data-dbgsym' in `../hhsuite-data-dbgsym_2.0.16-1ubuntu1_amd64.ddeb'. make[1]: Leaving directory `/build/buildd/hhsuite-2.0.16' dh_makeshlibs -a -O--parallel dh_shlibdeps -a -O--parallel dh_installdeb -a -O--parallel dh_gencontrol -a -O--parallel dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package hhsuite-data: unused substitution variable ${perl:Depends} dpkg-gencontrol: warning: Depends field of package hhsuite-dbg: unknown substitution variable ${shlibs:Depends} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a -O--parallel dh_builddeb -a -O--parallel INFO: pkgstriptranslations version 118 pkgstriptranslations: processing hhsuite (in debian/hhsuite); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/hhsuite/DEBIAN/control, package hhsuite, directory debian/hhsuite Searching for duplicated docs in dependency hhsuite-data... symlinking changelog.Debian.gz in hhsuite to file in hhsuite-data pkgstripfiles: PNG optimization for package hhsuite took 0 s dpkg-deb: warning: 'debian/hhsuite/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `hhsuite' in `../hhsuite_2.0.16-1ubuntu1_amd64.deb'. INFO: pkgstriptranslations version 118 pkgstriptranslations: processing hhsuite-data (in debian/hhsuite-data); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/hhsuite-data/DEBIAN/control, package hhsuite-data, directory debian/hhsuite-data pkgstripfiles: PNG optimization for package hhsuite-data took 0 s dpkg-deb: warning: 'debian/hhsuite-data/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `hhsuite-data' in `../hhsuite-data_2.0.16-1ubuntu1_amd64.deb'. INFO: pkgstriptranslations version 118 pkgstriptranslations: processing hhsuite-dbg (in debian/hhsuite-dbg); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/hhsuite-dbg/DEBIAN/control, package hhsuite-dbg, directory debian/hhsuite-dbg Searching for duplicated docs in dependency hhsuite... symlinking changelog.Debian.gz in hhsuite-dbg to file in hhsuite-data pkgstripfiles: PNG optimization for package hhsuite-dbg took 0 s dpkg-deb: warning: 'debian/hhsuite-dbg/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `hhsuite-dbg' in `../hhsuite-dbg_2.0.16-1ubuntu1_amd64.deb'. dpkg-genchanges -B -mUbuntu/amd64 Build Daemon >../hhsuite_2.0.16-1ubuntu1_amd64.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build hhsuite-2.0.16 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20131002-1518 Publishing debug debs. chroot-autobuild/build/buildd/hhsuite_2.0.16-1ubuntu1_amd64.deb: new debian package, version 2.0. size 1654860 bytes: control archive= 1783 bytes. 1583 bytes, 28 lines control 1643 bytes, 25 lines md5sums Package: hhsuite Version: 2.0.16-1ubuntu1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 2925 Depends: libc6 (>= 2.14), libffindex0 (>= 0.9.8), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libpng12-0 (>= 1.2.13-4), libstdc++6 (>= 4.4.0), ffindex (>= 0.9.6.1), hhsuite-data (= 2.0.16-1ubuntu1) Section: science Priority: extra Homepage: http://toolkit.genzentrum.lmu.de/sections/search Description: sensitive protein sequence searching based on HMM-HMM alignment HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). . This package contains HHsearch and HHblits among other programs and utilities. . HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous proteins. HHsearch is often used for protein structure prediction to detect homologous templates and to build highly accurate query-template pairwise alignments for homology modeling. . HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and, using an iterative search strategy, adds significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/hhsuite-data_2.0.16-1ubuntu1_amd64.deb: new debian package, version 2.0. size 2516062 bytes: control archive= 1044 bytes. 670 bytes, 15 lines control 1047 bytes, 14 lines md5sums Package: hhsuite-data Source: hhsuite Version: 2.0.16-1ubuntu1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 6055 Section: science Priority: extra Homepage: http://toolkit.genzentrum.lmu.de/sections/search Description: sensitive protein sequence searching based on HMM-HMM alignment (data) HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). . This package contains architecture independent scripts and data files. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/hhsuite-dbg_2.0.16-1ubuntu1_amd64.deb: new debian package, version 2.0. size 3750108 bytes: control archive= 840 bytes. 680 bytes, 16 lines control 539 bytes, 8 lines md5sums Package: hhsuite-dbg Source: hhsuite Version: 2.0.16-1ubuntu1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 13347 Depends: hhsuite (= 2.0.16-1ubuntu1) Section: debug Priority: extra Homepage: http://toolkit.genzentrum.lmu.de/sections/search Description: sensitive protein sequence searching based on HMM-HMM alignment (debug) HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). . This package contains the debugging symbols. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/hhsuite_2.0.16-1ubuntu1_amd64.deb: drwxr-xr-x root/root 0 2013-10-02 15:18 ./ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/bin/ -rwxr-xr-x root/root 273784 2013-10-02 15:18 ./usr/bin/hhmake -rwxr-xr-x root/root 479032 2013-10-02 15:18 ./usr/bin/hhalign -rwxr-xr-x root/root 466680 2013-10-02 15:18 ./usr/bin/hhblits -rwxr-xr-x root/root 421440 2013-10-02 15:18 ./usr/bin/hhsearch -rwxr-xr-x root/root 277888 2013-10-02 15:18 ./usr/bin/hhconsensus -rwxr-xr-x root/root 249184 2013-10-02 15:18 ./usr/bin/hhfilter drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/hhsuite/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/hhsuite/data/ -rw-r--r-- root/root 112 2013-10-02 15:18 ./usr/lib/hhsuite/data/do_not_delete.pin -rw-r--r-- root/root 433 2013-10-02 15:18 ./usr/lib/hhsuite/data/do_not_delete.psq -rw-r--r-- root/root 1986 2013-10-02 15:18 ./usr/lib/hhsuite/data/do_not_delete -rw-r--r-- root/root 135 2013-10-02 15:18 ./usr/lib/hhsuite/data/do_not_delete.phr drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/hhsuite/bin/ -rwxr-xr-x root/root 154672 2013-10-02 15:18 ./usr/lib/hhsuite/bin/cstranslate drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/doc-base/ -rw-r--r-- root/root 276 2012-02-22 11:20 ./usr/share/doc-base/hhsuite drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/doc/hhsuite/ -rw-r--r-- root/root 316913 2013-02-18 13:44 ./usr/share/doc/hhsuite/hhsuite-userguide.pdf.gz -rw-r--r-- root/root 3378 2012-06-27 14:54 ./usr/share/doc/hhsuite/copyright -rw-r--r-- root/root 2485 2013-02-18 13:44 ./usr/share/doc/hhsuite/README.gz drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/doc/hhsuite/examples/ -rw-r--r-- root/root 21793 2013-02-18 13:44 ./usr/share/doc/hhsuite/examples/query.hhm.gz -rw-r--r-- root/root 238386 2013-02-18 13:44 ./usr/share/doc/hhsuite/examples/query.hhr.gz -rw-r--r-- root/root 506 2013-02-18 13:44 ./usr/share/doc/hhsuite/examples/query.seq -rw-r--r-- root/root 11079 2013-02-18 13:44 ./usr/share/doc/hhsuite/examples/query.a3m.gz drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/man/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/man/man1/ -rw-r--r-- root/root 2961 2013-10-02 15:18 ./usr/share/man/man1/hhsearch.1.gz -rw-r--r-- root/root 1544 2013-10-02 15:18 ./usr/share/man/man1/hhmake.1.gz -rw-r--r-- root/root 3020 2013-10-02 15:18 ./usr/share/man/man1/hhblits.1.gz -rw-r--r-- root/root 925 2013-10-02 15:18 ./usr/share/man/man1/hhfilter.1.gz -rw-r--r-- root/root 3259 2013-10-02 15:18 ./usr/share/man/man1/hhalign.1.gz -rw-r--r-- root/root 1012 2013-10-02 15:18 ./usr/share/man/man1/hhconsensus.1.gz lrwxrwxrwx root/root 0 2013-10-02 15:18 ./usr/lib/hh -> hhsuite lrwxrwxrwx root/root 0 2013-10-02 15:18 ./usr/share/doc/hhsuite/changelog.Debian.gz -> ../hhsuite-data/changelog.Debian.gz chroot-autobuild/build/buildd/hhsuite-data_2.0.16-1ubuntu1_amd64.deb: drwxr-xr-x root/root 0 2013-10-02 15:18 ./ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/hhsuite/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/hhsuite/data/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/hhsuite/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/hhsuite/data/ -rw-r--r-- root/root 5922161 2013-10-02 15:18 ./usr/share/hhsuite/data/context_data.lib -rw-r--r-- root/root 51634 2013-10-02 15:18 ./usr/share/hhsuite/data/cs219.lib drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/hhsuite/scripts/ -rwxr-xr-x root/root 28464 2013-10-02 15:18 ./usr/share/hhsuite/scripts/reformat.pl -rwxr-xr-x root/root 5724 2013-10-02 15:18 ./usr/share/hhsuite/scripts/multithread.pl -rw-r--r-- root/root 23774 2013-10-02 15:18 ./usr/share/hhsuite/scripts/Align.pm -rwxr-xr-x root/root 4661 2013-10-02 15:18 ./usr/share/hhsuite/scripts/create_profile_from_hhm.pl -rwxr-xr-x root/root 28064 2013-10-02 15:18 ./usr/share/hhsuite/scripts/addss.pl -rwxr-xr-x root/root 47961 2013-10-02 15:18 ./usr/share/hhsuite/scripts/hhmakemodel.pl -rwxr-xr-x root/root 6822 2013-10-02 15:18 ./usr/share/hhsuite/scripts/create_profile_from_hmmer.pl -rwxr-xr-x root/root 19300 2013-10-02 15:18 ./usr/share/hhsuite/scripts/hhblitsdb.pl -rw-r--r-- root/root 4721 2013-10-02 15:18 ./usr/share/hhsuite/scripts/HHPaths.pm -rwxr-xr-x root/root 3653 2013-10-02 15:18 ./usr/share/hhsuite/scripts/splitfasta.pl drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/doc/hhsuite-data/ -rw-r--r-- root/root 691 2013-10-02 12:50 ./usr/share/doc/hhsuite-data/changelog.Debian.gz -rw-r--r-- root/root 3378 2012-06-27 14:54 ./usr/share/doc/hhsuite-data/copyright lrwxrwxrwx root/root 0 2013-10-02 15:18 ./usr/lib/hhsuite/data/context_data.lib -> ../../../share/hhsuite/data/context_data.lib lrwxrwxrwx root/root 0 2013-10-02 15:18 ./usr/lib/hhsuite/data/cs219.lib -> ../../../share/hhsuite/data/cs219.lib lrwxrwxrwx root/root 0 2013-10-02 15:18 ./usr/lib/hhsuite/scripts -> ../../share/hhsuite/scripts chroot-autobuild/build/buildd/hhsuite-dbg_2.0.16-1ubuntu1_amd64.deb: drwxr-xr-x root/root 0 2013-10-02 15:18 ./ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/debug/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/debug/usr/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/debug/usr/bin/ -rw-r--r-- root/root 1673187 2013-10-02 15:18 ./usr/lib/debug/usr/bin/hhmake -rw-r--r-- root/root 2425243 2013-10-02 15:18 ./usr/lib/debug/usr/bin/hhalign -rw-r--r-- root/root 2457378 2013-10-02 15:18 ./usr/lib/debug/usr/bin/hhblits -rw-r--r-- root/root 2198336 2013-10-02 15:18 ./usr/lib/debug/usr/bin/hhsearch -rw-r--r-- root/root 1696430 2013-10-02 15:18 ./usr/lib/debug/usr/bin/hhconsensus -rw-r--r-- root/root 1514362 2013-10-02 15:18 ./usr/lib/debug/usr/bin/hhfilter drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/debug/usr/lib/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/debug/usr/lib/hhsuite/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/lib/debug/usr/lib/hhsuite/bin/ -rw-r--r-- root/root 1644968 2013-10-02 15:18 ./usr/lib/debug/usr/lib/hhsuite/bin/cstranslate drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2013-10-02 15:18 ./usr/share/doc/hhsuite-dbg/ -rw-r--r-- root/root 3378 2012-06-27 14:54 ./usr/share/doc/hhsuite-dbg/copyright lrwxrwxrwx root/root 0 2013-10-02 15:18 ./usr/share/doc/hhsuite-dbg/changelog.Debian.gz -> ../hhsuite-data/changelog.Debian.gz hhsuite_2.0.16-1ubuntu1_amd64.changes: Format: 1.8 Date: Wed, 02 Oct 2013 13:50:20 +0100 Source: hhsuite Binary: hhsuite hhsuite-data hhsuite-dbg Architecture: amd64 Version: 2.0.16-1ubuntu1 Distribution: saucy-proposed Urgency: low Maintainer: Ubuntu/amd64 Build Daemon Changed-By: Colin Watson Description: hhsuite - sensitive protein sequence searching based on HMM-HMM alignment hhsuite-data - sensitive protein sequence searching based on HMM-HMM alignment ( hhsuite-dbg - sensitive protein sequence searching based on HMM-HMM alignment ( Changes: hhsuite (2.0.16-1ubuntu1) saucy; urgency=low . * Make hhsuite-data Architecture: amd64 even though it contains architecture-independent files; it's useless on other architectures, and an Architecture: all package does not get built on Ubuntu build daemons unless either all binary packages are Architecture: all or at least one package builds on i386. Checksums-Sha1: d2035d16921185bbbc3db8697b4e8729f270cec9 1654860 hhsuite_2.0.16-1ubuntu1_amd64.deb ba43eed4936b3caa8c2e8c5d7b025e5568e14b05 2516062 hhsuite-data_2.0.16-1ubuntu1_amd64.deb c589bc396058d5836c26cfe99e56cd8ab9ef0061 3750108 hhsuite-dbg_2.0.16-1ubuntu1_amd64.deb Checksums-Sha256: 294e24f373d023cc316855a32a1e495901004bef4ca09a9cd42c6ee983fd7efd 1654860 hhsuite_2.0.16-1ubuntu1_amd64.deb af4aff8244ffeee06c1ed25e17e92e65fbf1eaf80ee82546a6bc5162b22c5347 2516062 hhsuite-data_2.0.16-1ubuntu1_amd64.deb 7e95c46c8c4f745fa53a4e0e26318d416cbbad96625ed77a637b9f1d22a9c779 3750108 hhsuite-dbg_2.0.16-1ubuntu1_amd64.deb Files: c14c71756ce0367690d6239d3623fd3e 1654860 science extra hhsuite_2.0.16-1ubuntu1_amd64.deb 88a003a14f5569bba4f61daac8590e0c 2516062 science extra hhsuite-data_2.0.16-1ubuntu1_amd64.deb f883b8e2c34feed4a2d6680cc491a13e 3750108 debug extra hhsuite-dbg_2.0.16-1ubuntu1_amd64.deb Original-Maintainer: Debian Med Packaging Team ****************************************************************************** Built successfully ****************************************************************************** Finished at 20131002-1518 Build needed 00:00:48, 81708k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5069499'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5069499/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5069499'] Unmounting chroot for build PACKAGEBUILD-5069499... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5069499'] Removing build PACKAGEBUILD-5069499