DC-Build-Header: hhsuite 2.0.16-5 / 2015-03-26 06:38:34 +0000 DC-Task: source:hhsuite version:2.0.16-5 architecture:any chroot:unstable esttime:597 logfile:/tmp/hhsuite_2.0.16-5_unstable_clang.log modes:binary-only:parallel:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang hhsuite_2.0.16-5' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-4-233.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ hhsuite 2.0.16-5 (amd64) 26 Mar 2015 06:38 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: hhsuite Version: 2.0.16-5 Source Version: 2.0.16-5 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/hhsuite-bN52bC/hhsuite-2.0.16' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/hhsuite-bN52bC' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-f6a0dda2-83ba-46a6-904d-91b37e9435c6' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [257 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2015-03-25-1448.37.pdiff [3021 B] Get:6 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [5545 B] Get:7 http://localhost:9999 unstable/main 2015-03-26-0248.39.pdiff [3389 B] Get:8 http://localhost:9999 unstable/main 2015-03-26-0248.39.pdiff [3389 B] Get:9 http://localhost:9999 unstable/main amd64 2015-03-25-1448.37.pdiff [4095 B] Get:10 http://localhost:9999 unstable/main amd64 2015-03-25-2049.47.pdiff [4595 B] Get:11 http://localhost:9999 unstable/main amd64 2015-03-26-0248.39.pdiff [3173 B] Get:12 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [2032 B] Get:13 http://localhost:9999 unstable/main amd64 2015-03-26-0248.39.pdiff [3173 B] Get:14 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [2032 B] Fetched 306 kB in 4s (64.3 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'hhsuite' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debian-med/trunk/packages/hhsuite/trunk/ Need to get 4350 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main hhsuite 2.0.16-5 (dsc) [2200 B] Get:2 http://localhost:9999/debian/ unstable/main hhsuite 2.0.16-5 (tar) [4338 kB] Get:3 http://localhost:9999/debian/ unstable/main hhsuite 2.0.16-5 (diff) [9944 B] Fetched 4350 kB in 5s (761 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/clang ────────── + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.6 + echo 'Install of clang-3.6' Install of clang-3.6 + apt-get update Hit http://localhost:9999 unstable InRelease Get:1 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:2 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Fetched 23.6 kB in 1s (12.7 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.6 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libbsd0 libclang-common-3.6-dev libclang1-3.6 libedit2 libffi6 libllvm3.6 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.6-doc Recommended packages: llvm-3.6-dev python The following NEW packages will be installed: clang-3.6 libbsd0 libclang-common-3.6-dev libclang1-3.6 libedit2 libffi6 libllvm3.6 libobjc-4.9-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 39.2 MB of archives. After this operation, 153 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libbsd0 amd64 0.7.0-2 [67.9 kB] Get:2 http://localhost:9999/debian/ unstable/main libedit2 amd64 3.1-20140620-2 [85.1 kB] Get:3 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2+b2 [20.1 kB] Get:4 http://localhost:9999/debian/ unstable/main libllvm3.6 amd64 1:3.6-2 [8137 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.2-10 [112 kB] Get:6 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.2-10 [372 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.6 amd64 1:3.6-2 [3839 kB] Get:8 http://localhost:9999/debian/ unstable/main libclang-common-3.6-dev amd64 1:3.6-2 [706 kB] Get:9 http://localhost:9999/debian/ unstable/main clang-3.6 amd64 1:3.6-2 [25.8 MB] debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 39.2 MB in 1s (38.3 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11980 files and directories currently installed.) Preparing to unpack .../libbsd0_0.7.0-2_amd64.deb ... Unpacking libbsd0:amd64 (0.7.0-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../libedit2_3.1-20140620-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20140620-2) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.1-2+b2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2+b2) ... Selecting previously unselected package libllvm3.6:amd64. Preparing to unpack .../libllvm3.6_1%3a3.6-2_amd64.deb ... Unpacking libllvm3.6:amd64 (1:3.6-2) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.2-10_amd64.deb ... Unpacking libobjc4:amd64 (4.9.2-10) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.2-10_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.2-10) ... Selecting previously unselected package libclang1-3.6:amd64. Preparing to unpack .../libclang1-3.6_1%3a3.6-2_amd64.deb ... Unpacking libclang1-3.6:amd64 (1:3.6-2) ... Selecting previously unselected package libclang-common-3.6-dev. Preparing to unpack .../libclang-common-3.6-dev_1%3a3.6-2_amd64.deb ... Unpacking libclang-common-3.6-dev (1:3.6-2) ... Selecting previously unselected package clang-3.6. Preparing to unpack .../clang-3.6_1%3a3.6-2_amd64.deb ... Unpacking clang-3.6 (1:3.6-2) ... Setting up libbsd0:amd64 (0.7.0-2) ... Setting up libedit2:amd64 (3.1-20140620-2) ... Setting up libffi6:amd64 (3.1-2+b2) ... Setting up libllvm3.6:amd64 (1:3.6-2) ... Setting up libobjc4:amd64 (4.9.2-10) ... Setting up libobjc-4.9-dev:amd64 (4.9.2-10) ... Setting up libclang1-3.6:amd64 (1:3.6-2) ... Setting up libclang-common-3.6-dev (1:3.6-2) ... Setting up clang-3.6 (1:3.6-2) ... Processing triggers for libc-bin (2.19-17) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.6 g++-4.6 + ln -s clang-3.6 gcc-4.6 + ln -s clang-3.6 cpp-4.6 + ln -s clang-3.6 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.6 g++-4.7 + ln -s clang-3.6 gcc-4.7 + ln -s clang-3.6 cpp-4.7 + ln -s clang-3.6 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.6 g++-4.8 + ln -s clang-3.6 gcc-4.8 + ln -s clang-3.6 cpp-4.8 + ln -s clang-3.6 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.6 g++-4.9 + ln -s clang-3.6 gcc-4.9 + ln -s clang-3.6 cpp-4.9 + ln -s clang-3.6 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections + echo 'g++-4.9 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.6 g++-5 + ln -s clang-3.6 gcc-5 + ln -s clang-3.6 cpp-5 + ln -s clang-3.6 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + cd - /«BUILDDIR» + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-jdp7Rh/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/822 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12200 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libffindex0-dev (>= 0.9.6.1), help2man Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libffindex0-dev (>= 0.9.6.1), help2man dpkg-deb: building package `sbuild-build-depends-hhsuite-dummy' in `/«BUILDDIR»/resolver-g9856C/apt_archive/sbuild-build-depends-hhsuite-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install hhsuite build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man intltool-debian libasprintf0c2 libcroco3 libffindex0 libffindex0-dev libglib2.0-0 libicu52 liblocale-gettext-perl libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man intltool-debian libasprintf0c2 libcroco3 libffindex0 libffindex0-dev libglib2.0-0 libicu52 liblocale-gettext-perl libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-hhsuite-dummy 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 15.9 MB/15.9 MB of archives. After this operation, 56.2 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.4.0-1 [27.9 kB] Get:2 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.3-1 [1205 kB] Get:3 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.6 [183 kB] Get:4 http://localhost:9999/debian/ unstable/main man-db amd64 2.7.0.2-5 [1000 kB] Get:5 http://localhost:9999/debian/ unstable/main liblocale-gettext-perl amd64 1.05-8+b1 [19.0 kB] Get:6 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.19.3-2 [31.3 kB] Get:7 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.22+15-2 [249 kB] Get:8 http://localhost:9999/debian/ unstable/main libicu52 amd64 52.1-8 [6780 kB] Get:9 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.2+dfsg1-3 [934 kB] Get:10 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.42.1-1 [2401 kB] Get:11 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-3+b1 [135 kB] Get:12 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5.2+b1 [288 kB] Get:13 http://localhost:9999/debian/ unstable/main file amd64 1:5.22+15-2 [60.1 kB] Get:14 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.19.3-2 [121 kB] Get:15 http://localhost:9999/debian/ unstable/main gettext amd64 0.19.3-2 [1240 kB] Get:16 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:17 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB] Get:18 http://localhost:9999/debian/ unstable/main debhelper all 9.20150101 [813 kB] Get:19 http://localhost:9999/debian/ unstable/main help2man amd64 1.46.5 [139 kB] Get:20 http://localhost:9999/debian/ unstable/main libffindex0 amd64 0.9.9.3-2 [15.8 kB] Get:21 http://localhost:9999/debian/ unstable/main libffindex0-dev amd64 0.9.9.3-2 [15.7 kB] Preconfiguring packages ... Fetched 15.9 MB in 1s (12.6 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12200 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.4.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.0-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-1_amd64.deb ... Unpacking groff-base (1.22.3-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6_amd64.deb ... Unpacking bsdmainutils (9.0.6) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.0.2-5_amd64.deb ... Unpacking man-db (2.7.0.2-5) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.05-8+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.05-8+b1) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.19.3-2_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.19.3-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.22+15-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.22+15-2) ... Selecting previously unselected package libicu52:amd64. Preparing to unpack .../libicu52_52.1-8_amd64.deb ... Unpacking libicu52:amd64 (52.1-8) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.2+dfsg1-3_amd64.deb ... Unpacking libxml2:amd64 (2.9.2+dfsg1-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.42.1-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.42.1-1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-3+b1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.8-3+b1) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.22+15-2_amd64.deb ... Unpacking file (1:5.22+15-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.3-2_amd64.deb ... Unpacking gettext-base (0.19.3-2) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.3-2_amd64.deb ... Unpacking gettext (0.19.3-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ... Unpacking intltool-debian (0.35.0+20060710.1) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ... Unpacking po-debconf (1.0.16+nmu3) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20150101_all.deb ... Unpacking debhelper (9.20150101) ... Selecting previously unselected package help2man. Preparing to unpack .../help2man_1.46.5_amd64.deb ... Unpacking help2man (1.46.5) ... Selecting previously unselected package libffindex0. Preparing to unpack .../libffindex0_0.9.9.3-2_amd64.deb ... Unpacking libffindex0 (0.9.9.3-2) ... Selecting previously unselected package libffindex0-dev. Preparing to unpack .../libffindex0-dev_0.9.9.3-2_amd64.deb ... Unpacking libffindex0-dev (0.9.9.3-2) ... Selecting previously unselected package sbuild-build-depends-hhsuite-dummy. Preparing to unpack .../sbuild-build-depends-hhsuite-dummy.deb ... Unpacking sbuild-build-depends-hhsuite-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.4.0-1) ... Setting up groff-base (1.22.3-1) ... Setting up bsdmainutils (9.0.6) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.7.0.2-5) ... Not building database; man-db/auto-update is not 'true'. Setting up liblocale-gettext-perl (1.05-8+b1) ... Setting up libasprintf0c2:amd64 (0.19.3-2) ... Setting up libmagic1:amd64 (1:5.22+15-2) ... Setting up libicu52:amd64 (52.1-8) ... Setting up libxml2:amd64 (2.9.2+dfsg1-3) ... Setting up libglib2.0-0:amd64 (2.42.1-1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-3+b1) ... Setting up libunistring0:amd64 (0.9.3-5.2+b1) ... Setting up file (1:5.22+15-2) ... Setting up gettext-base (0.19.3-2) ... Setting up gettext (0.19.3-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up debhelper (9.20150101) ... Setting up help2man (1.46.5) ... Setting up libffindex0 (0.9.9.3-2) ... Setting up libffindex0-dev (0.9.9.3-2) ... Setting up sbuild-build-depends-hhsuite-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-17) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.24 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-17 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt7-1 Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.7 apt-utils_1.0.9.7 base-files_8 base-passwd_3.5.37 bash_4.3-12 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-5 build-essential_11.7 bzip2_1.0.6-7+b2 clang-3.6_1:3.6-2 coreutils_8.23-4 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4+b1 debconf_1.5.56 debfoster_2.7-2 debhelper_9.20150101 debian-archive-keyring_2014.3 debianutils_4.4+b1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.90-2.1 dpkg_1.17.24 dpkg-dev_1.17.24 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9+b1 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.3-2 gettext-base_0.19.3-2 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 help2man_1.46.5 hostname_3.15 init_1.22 initscripts_2.88dsf-58 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 less_458-3 libacl1_2.2.52-2 libapt-inst1.5_1.0.9.7 libapt-pkg4.12_1.0.9.7 libasan1_4.9.2-10 libasprintf0c2_0.19.3-2 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1+b1 libblkid1_2.25.2-5 libbsd0_0.7.0-2 libbz2-1.0_1.0.6-7+b2 libc-bin_2.19-17 libc-dev-bin_2.19-17 libc6_2.19-17 libc6-dev_2.19-17 libcap2_1:2.24-7 libcap2-bin_1:2.24-7 libcilkrts5_4.9.2-10 libclang-common-3.6-dev_1:3.6-2 libclang1-3.6_1:3.6-2 libcloog-isl4_0.18.2-1+b2 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3+b1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.1 libdpkg-perl_1.17.24 libedit2_3.1-20140620-2 libfakeroot_1.20.2-1 libffi6_3.1-2+b2 libffindex0_0.9.9.3-2 libffindex0-dev_0.9.9.3-2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.42.1-1 libgmp10_2:6.0.0+dfsg-6 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libicu52_52.1-8 libisl10_0.12.2-2 libitm1_4.9.2-10 libkmod2_20-1 libllvm3.6_1:3.6-2 liblocale-gettext-perl_1.05-8+b1 liblsan0_4.9.2-10 liblzma5_5.1.1alpha+20120614-2+b3 libmagic1_1:5.22+15-2 libmount1_2.25.2-5 libmpc3_1.0.3-1 libmpfr4_3.1.2-3 libncurses5_5.9+20140913-1+b1 libncursesw5_5.9+20140913-1+b1 libobjc-4.9-dev_4.9.2-10 libobjc4_4.9.2-10 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libprocps3_2:3.3.9-9 libquadmath0_4.9.2-10 libreadline6_6.3-8+b3 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1+b1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-5 libss2_1.42.12-1.1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-12 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1+b1 libtsan0_4.9.2-10 libubsan0_4.9.2-10 libudev1_215-12 libunistring0_0.9.3-5.2+b1 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3+b2 libuuid1_2.25.2-5 libxml2_2.9.2+dfsg1-3 linux-libc-dev_3.16.7-ckt7-1 login_1:4.2-3 lsb-base_4.1+Debian13+nmu1 make_4.0-8.1 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-5 multiarch-support_2.19-17 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1+b1 nvi_1.81.6-11+b1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-2 perl-base_5.20.2-2 perl-modules_5.20.2-2 po-debconf_1.0.16+nmu3 procps_2:3.3.9-9 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hhsuite-dummy_0.invalid.0 sed_4.2.2-4+b1 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.12-1 systemd_215-12 systemd-sysv_215-12 sysv-rc_2.88dsf-58 sysvinit-utils_2.88dsf-58 tar_1.27.1-2+b1 tzdata_2015b-1 udev_215-12 util-linux_2.25.2-5 xz-utils_5.1.1alpha+20120614-2+b3 zlib1g_1:1.2.8.dfsg-2+b1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Nov 7 06:12:52 2014 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./hhsuite_2.0.16-5.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_2.0.16-5.debian.tar.xz 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 unused_variables_warning dpkg-source: info: applying unnecessary_libz dpkg-source: info: applying perl_interpreter dpkg-source: info: applying version_bump dpkg-source: info: applying add_Makefile_in_data.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=10 HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-f6a0dda2-83ba-46a6-904d-91b37e9435c6 SCHROOT_UID=1001 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package hhsuite dpkg-buildpackage: source version 2.0.16-5 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build hhsuite-2.0.16 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make[1]: Entering directory '/«PKGBUILDDIR»' make -C src clean make[2]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src' make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules override_dh_clean make[1]: Entering directory '/«PKGBUILDDIR»' rm -f hhalign.1 hhblits.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 dh_clean make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_auto_configure -a -O--parallel debian/rules override_dh_auto_build make[1]: Entering directory '/«PKGBUILDDIR»' dh_auto_build -- NO_PNG=1 make[2]: Entering directory '/«PKGBUILDDIR»' make -C data all make[3]: Entering directory '/«PKGBUILDDIR»/data' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/«PKGBUILDDIR»/data' make -C src all make[3]: Entering directory '/«PKGBUILDDIR»/src' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/blosum_matrix.cc -o cs/blosum_matrix.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/as.cc -o cs/as.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/log.cc -o cs/log.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/application.cc -o cs/application.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/getopt_pp.cc -o cs/getopt_pp.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/assert_helpers.cc -o cs/assert_helpers.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/aa.cc -o cs/aa.o clang: warning: -Wl,-z,relro: 'linker' input unused clangclangclangclang: warning: -Wl,-z,relro: 'linker' input unused : warning: -Wl,-z,relro: 'linker' input unused : warning: -Wl,-z,relro: 'linker' input unused clang: warning: -Wl,-z,relro: 'linker' input unused : warning: -Wl,-z,relro: 'linker' input unused clang: warning: -Wl,-z,relro: 'linker' input unused g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhblits.C -o hhblits cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o -lpthread -fopenmp -lrt -lffindex g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhsearch.C -o hhsearch cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o -lpthread -lrt g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhmake.C -o hhmake cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhalign.C -o hhalign cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhfilter.C -o hhfilter cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhconsensus.C -o hhconsensus cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -lm -o cstranslate cs/cstranslate_app.cc cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o In file included from cs/cstranslate_app.cc:4: In file included from cs/alignment-inl.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ In file included from cs/cstranslate_app.cc:4: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ cs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhblits.C:123: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ In file included from hhalign.C:78: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ In file included from In file included from hhconsensus.C:52: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ hhblits.C:123: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ cs/alignment-inl.hIn file included from :827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhfilter.C:66: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ hhsearch.C:93: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ In file included from hhblits.C:123: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhmake.C:66: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ In file included from cs/cstranslate_app.cc:7: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhconsensus.C:52: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from hhalign.C:78: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ cs/alignment-inl.hIn file included from :827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ hhsearch.C:93: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.hcs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ :8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ cs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhfilter.C:66: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from hhconsensus.C:52: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhalign.C:78: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct cs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhsearch.C:93: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhmake.C:66: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ cs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhfilter.C:66: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhmake.C:66: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhblits.C:132: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhconsensus.C:60: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhblits.C:142: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ In file included from hhsearch.C:102: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ In file included from hhalign.C:85: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from ./hhhmm.Chhconsensus.C:68: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from :360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ hhfilter.C:74: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C3 warnings and 1 error generated. make[3]: *** [cstranslate] Error 1 make[3]: *** Waiting for unfinished jobs.... Makefile:80: recipe for target 'cstranslate' failed ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ :719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ In file included from hhmake.C:74: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ In file included from hhsearch.C:112: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C./hhhmm.CIn file included from hhalign.C:95: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ::1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ 360:39./hhhmm.C: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ :740:40: warning:: 1011when type is in parentheses, array cannot have dynamic size:./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ 23 seq[nss_pred] = new(char[par.maxres+2]);: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~~~~~~~~~~ ~ ~ ^~~ ~./hhhmm.C ./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ In file included from ./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ hhfilter.C:81: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ :1203:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C:1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ :1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ In file included from ./hhhmm.Chhmake.C:81: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1203:40: warning:: 1473when type is in parentheses, array cannot have dynamic size: 23 seq[nss_pred] = new(char[par.maxres+2]);: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C ~ ^~~ ~ ./hhhmm.C:1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ :1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ :./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ 719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C./hhhmm.C:719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ :1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ : 740./hhhmm.C:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ : 1014./hhhmm.C:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]);:1032:25 : ~ ^~~~~~~~~~~~ ~ warning : ./hhhmm.Cwhen type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ :1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C./hhhmm.C:1203:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]);:2329:30: ~ ^~~ ~ warning : when type is in parentheses, array cannot have dynamic size./hhhmm.C seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ :1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ In file included from :1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.Chhblits.C:143: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ :48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15./hhhmm.C:: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ 740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhalignment.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~./hhhmm.C: ./hhalignment.C./hhhmm.C761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:150:25: warning: when type is in parentheses, array cannot have dynamic size ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ :1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: ./hhalignment.Cwhen type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ :1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1203:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ./hhhmm.C:252:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C::2205256::2943:: warning./hhhmm.Cwarning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ ./hhhmm.C:1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1182:40::1473 :warning23: :when type is in parentheses, array cannot have dynamic size warning seq[nsa_dssp] = new(char[par.maxres+2]);: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~~~~~~~~~~ ~ ~ ^~~ ~ ./hhhmm.C ./hhhmm.C:1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1203:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ :315:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ :1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ :2329:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ In file included from hhconsensus.C:69: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C./hhhmm.C:1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ :./hhhmm.C52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhalignment.C./hhhmm.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); :1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ :252:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1203:40: warning: ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ when type is in parentheses, array cannot have dynamic size ./hhalignment.C:256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhalignment.C./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C./hhhmm.C:315:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ :1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); : ~ ^~~ ~1295 : 36:431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ : warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhalignment.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ./hhhmm.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ :649:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ ./hhhmm.C./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C./hhalignment.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ :431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ :2329:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ In file included from hhsearch.C:113: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhhmm.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhhmm.C./hhalignment.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ :156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:2329:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ :649:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C./hhhmm.C:2177:28: warning:: 252when type is in parentheses, array cannot have dynamic size: 31 char** lines = new(char*[3*L+100000]);: warning: when type is in parentheses, array cannot have dynamic size ~ ^~~~~~~~~~ ~ seq[k]=new(char[strlen(cur_seq)+2]); ./hhalignment.C:923:23: ./hhhmm.Cwarning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:928:35: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ :256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2336::30949:: 27warning:: when type is in parentheses, array cannot have dynamic sizewarning : seq[nss_conf]=new(char[L+2]);when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~ ~ ~ ^~~~~~~~~~~~~~~~~~~~~~ ~In file included from ./hhalignment.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ ./hhalignment.C :972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ ./hhalignment.Chhalign.C:96: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: :when type is in parentheses, array cannot have dynamic size 1031 I = new(short unsigned int*[maxseq+2]);:21: warning : ~ ^~~~~~~~ ~ when type is in parentheses, array cannot have dynamic size ./hhhmm.C 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:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1033:21: warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax)./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~ ~ ~ ^~~~~~~~ ~ ./hhalignment.C ./hhalignment.C::541034::1825:: warningwarning: : when type is in parentheses, array cannot have dynamic sizewhen type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~~~~~~ ~ ~ ^~~ ~ ./hhalignment.C ./hhalignment.C:55:19: warning:: when type is in parentheses, array cannot have dynamic size1035 : nseqs = new(int[maxres+2]);27::315:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ warning ~ ^~~~~~~~ ~: when type is in parentheses, array cannot have dynamic size ./hhalignment.C int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C:1036:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k:144: 20 ~ ^~~~ ~: warning./hhalignment.C: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ : 1065./hhalignment.C:21:2329:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ : warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhhmm.C:2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]);In file included from hhfilter.C:82: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]);./hhalignment.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ~ ^~~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1095:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ : 162 ::156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1303:30: warning: when type is in parentheses, array cannot have dynamic size float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~ ~ ./hhalignment.C:1312:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1313::162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:252:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~: 1326 :./hhalignment.C./hhalignment.C20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhhmm.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ./hhhmm.C:252:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C::2562205::4329:: warningwarning: : when type is in parentheses, array cannot have dynamic sizewhen type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~ ~ :254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:315:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:923:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:315:31:./hhalignment.C warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ :926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ ./hhalignment.C./hhalignment.C:1598:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1031:21: warning: when type is in parentheses, array cannot have dynamic size 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:1609:38: warning: when type is in parentheses, array cannot have dynamic size ~ ^~~~~~ ~ q->seq[q->nfirst]=new(char[L+2]); ./hhalignment.C ~ ^~~ ~ ./hhalignment.C:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1033:21: warning: when type is in parentheses, array cannot have dynamic size :2329:30 int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax): warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ~ ^~~ ~ ./hhhmm.C./hhalignment.C:1034:25: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment.C:1035:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid):2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ ~ ^~~~~~ ~ ./hhalignment.C:1036:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ In file included from hhmake.C:82: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ./hhalignment.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ~ ^~~~ ~ ./hhalignment.C:150:./hhalignment.C25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ :1065:21: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C:1095:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ ./hhalignment.C./hhalignment.C:252:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~:1764:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C::256649::4331:: warningwarning: ./hhalignment.C: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ :1303:30: warning: when type is in parentheses, array cannot have dynamic size float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~ ~ ./hhalignment.C:1312:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1826:57: warning: add explicit braces to avoid dangling else [-Wdangling-else]: 1313 if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0; ^ :431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ :1598:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:2173:16: warning: :when type is in parentheses, array cannot have dynamic size1609 : n = new(int*[L+2]);38: warning : ~ ^~~ ~when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ./hhalignment.C ~ ^~~ ~ ./hhalignment.C:2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ :1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C./hhalignment.C:649:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1764:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C./hhalignment.C:1826:57: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ :2430:28: warning: when type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ~ ^~~~~~~~~~ ~ ./hhalignment.C:2442./hhalignment.C:23: warning: when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ :431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1031:21:: 435warning:: 35when type is in parentheses, array cannot have dynamic size: 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 seqidwarning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C ./hhalignment.C:2574:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ ./hhalignment.C:1980:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2587:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2590:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2047:55: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0;: 2592 ^: 38:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1033:21: warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ~ ^~~ ~ ./hhalignment.C:1034:25: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment.C:1035./hhalignment.C:2173:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ :27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C:1036:18./hhalignment.C: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment.C:2594:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2625:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1065:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1095:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ :2663:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2665:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2667:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1303:30: warning: when type is in parentheses, array cannot have dynamic size float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ./hhalignment.C:2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:923:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C ~ ^~~ ~ ./hhalignment.C:1312:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1313:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1326:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ In file included from hhblits.C:144: ./hhhit.C:66:15: error: inline declaration of '_mm_flog2_ps' follows non-inline definition inline __m128 _mm_flog2_ps(__m128 X); // Fast SSE2 log2 for four floats ^ ./util.C:129:8: note: previous definition is here __m128 _mm_flog2_ps(__m128 X) ^ In file included from ./hhalignment.C:649:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.Chhblits.C:144: ./hhhit.C:141:17: warning: when type is in parentheses, array cannot have dynamic size bMM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:142:17: warning: when type is in parentheses, array cannot have dynamic size bMI=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:143:17: warning: when type is in parentheses, array cannot have dynamic size bIM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:144:17: warning: when type is in parentheses, array cannot have dynamic size bDG=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:145:17: warning: when type is in parentheses, array cannot have dynamic size bGD=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:146:22: warning: when type is in parentheses, array cannot have dynamic size cell_off=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:149:23: warning: when type is in parentheses, array cannot have dynamic size bMM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:150:23: warning: when type is in parentheses, array cannot have dynamic size bMI[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:151:23: warning: when type is in parentheses, array cannot have dynamic size bIM[i]=new(char[Nt]);:2430:28 : ~ ^~ ~ warning : ./hhhit.Cwhen type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ~ ^~~~~~~~~~ ~:152 : 23./hhalignment.C: warning: when type is in parentheses, array cannot have dynamic size: bGD[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:153:23: warning: when type is in parentheses, array cannot have dynamic size bDG[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:154:28: warning: when type is in parentheses, array cannot have dynamic size cell_off[i]=new(char[Nt]); ~ ^~ ~ 926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:2442:23./hhalignment.C:: warning: when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ 928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C:923:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]);:192:20: ~ ^~~~~~~~~~~~~~~~~~~~ ~warning : when type is in parentheses, array cannot have dynamic size F_MM=new(double*[Nq]);./hhalignment.C:./hhalignment.C949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ~ ^~ ~ ./hhhit.C:199:20: warning./hhalignment.C:972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ : when type is in parentheses, array cannot have dynamic size scale=new(double[Nq+1]); // need Nq+3?:926: 21 ~ ^~~~ ~ : warning./hhhit.C: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1598:37: warning: ./hhalignment.Cwhen type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ :202:28: warning: ./hhalignment.Cwhen type is in parentheses, array cannot have dynamic size F_MM[i] = new(double[Nt]); ~ ^~ ~ :1031:21: warning: when type is in parentheses, array cannot have dynamic size 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 ~ ^~~~~~ ~ ./hhhit.C:928:./hhalignment.C35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ::16051032::4023:: warningwarning: : when type is in parentheses, array cannot have dynamic sizewhen type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ~ ^~~~~~ ~ ./hhalignment.C:./hhalignment.C:1609:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ 252:20: warning: when type is in parentheses, array cannot have dynamic size B_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C:261:28: warning: when type is in parentheses, array cannot have dynamic size B_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit.C:2574:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~./hhalignment.C ./hhalignment.C:./hhalignment.C1033:21: warning: when type is in parentheses, array cannot have dynamic size : int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ~ ^~~ ~ ./hhalignment.C:1034:25: warning: when type is in parentheses, array cannot have dynamic size972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment.C:1035:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C./hhalignment.C:1036:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ :2587:26: warning:: 291when type is in parentheses, array cannot have dynamic size: 15 seq[N_in]=new(char[h]);: warning: ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1065:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ when type is in parentheses, array cannot have dynamic size ~ ^ ~ i = new(int[len]); ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C./hhalignment.C ~ ^~~ ~ ./hhhit.C:292:15: warning: when type is in parentheses, array cannot have dynamic size j = new(int[len]); ~ ^~~ ~ ::2590:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ 1095./hhalignment.C:2592:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ :21: warning./hhalignment.C: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ :2594:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1031:21: warning: when type is in parentheses, array cannot have dynamic size 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:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1033:21: warning:: 2625when type is in parentheses, array cannot have dynamic size: 20 int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax): warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ~ ^~~ ~ ./hhalignment.C ./hhalignment.C:1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1034:./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ 25: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment.C:1035:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C:1036:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C:2663:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k:2665:24:./hhalignment.C ~ ^~~~ ~ ./hhalignment.C:1065:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ :1764:16: warning:: 1303when type is in parentheses, array cannot have dynamic size: 30./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ n = new(int*[L+2]);: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:1095:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~ ~ warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2667:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~ ~ ./hhalignment.C ~ ^~~~ ~ ./hhalignment.C:1312:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1313:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1326:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ./hhalignment.C:2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C ~ ^~~~ ~ ./hhalignment.C:2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ In file included from ./hhalignment.C:1826:57: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2047:55: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1598:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ :1326:20: warning: ./hhalignment.Cwhen type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ :972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ ./hhalignment.C:1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:1609:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1031:21: warning: when type is in parentheses, array cannot have dynamic size 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:2173:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~~~~ ~ ~ ^~~ ~./hhalignment.C ./hhalignment.C./hhalignment.C:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1033:21: warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ~ ^~~ ~ ./hhalignment.C:1034:25: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment.C:1035:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C:1036:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C:1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1598:37: :warning1147: :when type is in parentheses, array cannot have dynamic size./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ 21 q->seq[q->ncons]=new(char[L+2]);: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~ ~ ~ ^~~~~~~~ ~./hhalignment.C ./hhhit.C:1148:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhalignment.C:2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhhit.C:1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1065:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1095:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ :1609:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1764:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ./hhalignment.C:1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ~ ^~~ ~ ./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C:1487:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ./hhalignment.C:2430:28: warning: when type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ~ ^~~~~~~~ ~ ./hhhit.C:1826:57: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0;:./hhalignment.C2574:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ :1795:21: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:2587:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ longname=new(char[strlen(t->longname)+1]); ./hhalignment.C:2590:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2592:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment.C:2594:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1796:21: warning: when type is in parentheses, array cannot have dynamic size name =new(char[strlen(t->name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2625:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhhit.C:1797:21: warning: when type is in parentheses, array cannot have dynamic size file =new(char[strlen(t->file)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ : ./hhalignment.C ^ ./hhhit.C1980:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]);./hhalignment.C:2173:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2663:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1598:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2665:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~:2667 : 38./hhalignment.C: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ~ ^~~ ~ ./hhalignment.C:1609:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1808:22: warning: when type is in parentheses, array cannot have dynamic size this->i = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1809:22: warning: when type is in parentheses, array cannot have dynamic size this->j = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1810:23: warning: when type is in parentheses, array cannot have dynamic size states = new( char[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:./hhalignment.C1813:19: warning: when type is in parentheses, array cannot have dynamic size sname=new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1814:19: warning: when type is in parentheses, array cannot have dynamic size seq =new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ :2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~./hhhit.C:1833:24: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(t->sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1834:24: warning: when type is in parentheses, array cannot have dynamic size seq[k] = new(char[strlen(t->seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ 2047:55: warning: add explicit braces to avoid dangling else [-Wdangling-else]./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:1840:20: warning: when type is in parentheses, array cannot have dynamic size dbfile = new(char[strlen(ptr)+1]); ~ ^~~~~~~~~~~~~ ~ ::2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ 2173:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2243In file included from :58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ :1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.Chhsearch.C:114: ./hhhit.C:66:15: error: inline declaration of '_mm_flog2_ps' follows non-inline definition inline __m128 _mm_flog2_ps(__m128 X); // Fast SSE2 log2 for four floats ^ ./util.C:129:8: note: previous definition is here __m128 _mm_flog2_ps(__m128 X) ^ In file included from hhsearch.C:114: ./hhhit.C:141:17: warning: when type is in parentheses, array cannot have dynamic size bMM=new(char*[Nq]); ~ ^~ ~ : 1764./hhhit.C:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]);:142: 17 ~ ^~~ ~: warning In file included from ./hhalignment.C: when type is in parentheses, array cannot have dynamic size bMI=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:143:17: warning: when type is in parentheses, array cannot have dynamic size bIM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:144:17: warning: when type is in parentheses, array cannot have dynamic size bDG=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:145:17: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C bGD=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:146:22: warning: when type is in parentheses, array cannot have dynamic size cell_off=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:149:23: warning: when type is in parentheses, array cannot have dynamic size bMM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:150:23: warning: when type is in parentheses, array cannot have dynamic size hhblits.C:145: ./hhhalfalignment.C:46:15: warning: when type is in parentheses, array cannot have dynamic size h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written bMI[i]=new(char[Nt]); ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:47:17: warning: when type is in parentheses, array cannot have dynamic size : s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:48:16: warning: when type is in parentheses, array cannot have dynamic size 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:49:16: warning: when type is in parentheses, array cannot have dynamic size m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ~ ^~~~~~~~~ ~ 1826 ~ ^~ ~: 57 : ./hhhit.Cwarning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:2625:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2663:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2665:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2667:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2173:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size :2625:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ I[N_in]=new(short unsigned int[L+2]);./hhalignment.C:2663:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2665:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ~ ^~~ ~ ./hhalignment.C:2667:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C./hhalignment.C:2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ :2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ :2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ In file included from hhalign.C:97: ./hhhit.C:66:15: error: inline declaration of '_mm_flog2_ps' follows non-inline definition inline __m128 _mm_flog2_ps(__m128 X); // Fast SSE2 log2 for four floats ^ ./util.C:129:8: note: previous definition is here __m128 _mm_flog2_ps(__m128 X) ^ In file included from hhalign.C:97: ./hhhit.C:141:17: warning: when type is in parentheses, array cannot have dynamic size bMM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:142:17: warning: when type is in parentheses, array cannot have dynamic size bMI=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:143:17: warning: when type is in parentheses, array cannot have dynamic size bIM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:144:17: warning: when type is in parentheses, array cannot have dynamic size bDG=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:145:17: warning: when type is in parentheses, array cannot have dynamic size bGD=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:146:22: warning: when type is in parentheses, array cannot have dynamic size cell_off=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:149:23: warning: when type is in parentheses, array cannot have dynamic size bMM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:150:23: warning: ./hhalignment.C:2430:28: warning: when type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ~ ^~~~~~~~~~ ~ ./hhalignment.C:2442:23: warning: when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ ./hhhit.Cwhen type is in parentheses, array cannot have dynamic size bMI[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:151:23: warning: when type is in parentheses, array cannot have dynamic size bIM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:152:23: warning: when type is in parentheses, array cannot have dynamic size bGD[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:153:23: warning: when type is in parentheses, array cannot have dynamic size bDG[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:154:28: warning: when type is in parentheses, array cannot have dynamic size cell_off[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:192:20: warning: when type is in parentheses, array cannot have dynamic size F_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C:199:20: warning: when type is in parentheses, array cannot have dynamic size scale=new(double[Nq+1]); // need Nq+3? ~ ^~~~ ~ ./hhhit.C:202:28: warning: when type is in parentheses, array cannot have dynamic size F_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit.C:252:20: warning: when type is in parentheses, array cannot have dynamic size B_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C::261:28: warning: when type is in parentheses, array cannot have dynamic size B_MM[i] = new(double[Nt]); ~ ^~ ~ 1147:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C./hhhit.C:291:15: warning: when type is in parentheses, array cannot have dynamic size i = new(int[len]); ~ ^~~ ~ ./hhhit.C:292:15: warning: when type is in parentheses, array cannot have dynamic size j = new(int[len]); ~ ^~~ ~ ./hhalignment.C:2574:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ :1148:21: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:2587:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ S_ss = new( float[nsteps+1]); ./hhalignment.C:2590:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ~ ^~~~~~~~ ~./hhalignment.C :2592:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment.C:2594:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2625:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhhit.C:1487:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1488:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1489:28: warning: when type is in parentheses, array cannot have dynamic size P_posterior = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C./hhalignment.C:2663:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2665:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2667:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ :1795:21: warning: when type is in parentheses, array cannot have dynamic size longname=new(char[strlen(t->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1796:21: warning: when type is in parentheses, array cannot have dynamic size name =new(char[strlen(t->name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1797:21: warning: when type is in parentheses, array cannot have dynamic size file =new(char[strlen(t->file)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1808:22: warning: when type is in parentheses, array cannot have dynamic size this->i = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1809:22: warning: when type is in parentheses, array cannot have dynamic size this->j = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1810:23: warning: when type is in parentheses, array cannot have dynamic size states = new( char[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1813:19: warning: when type is in parentheses, array cannot have dynamic size sname=new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1814:19: warning: when type is in parentheses, array cannot have dynamic size seq =new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1833:24: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(t->sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1834:24: warning: when type is in parentheses, array cannot have dynamic size seq[k] = new(char[strlen(t->seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1840:20: warning: when type is in parentheses, array cannot have dynamic size dbfile = new(char[strlen(ptr)+1]); ~ ^~~~~~~~~~~~~ ~ In file included from hhsearch.C:115: ./hhhalfalignment.C:46:15: warning: when type is in parentheses, array cannot have dynamic size./hhhit.C h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:47:17: warning: when type is in parentheses, array cannot have dynamic size s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:48:16: warning: when type is in parentheses, array cannot have dynamic size 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:49:16: warning: when type is in parentheses, array cannot have dynamic size m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ~ ^~~~~~~~~ ~ In file included from hhblits.C:147: ./hhhitlist.C:542:10: warning: address of array 'q->fam' will always evaluate to 'true' [-Wpointer-bool-conversion] if (q->fam && q->fam[0]>='a' && q->fam[0]<='k' && q->fam[1]=='.') ~~~^~~ ~~ :1147:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1148:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1487:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1488:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1489:28: warning: when type is in parentheses, array cannot have dynamic size P_posterior = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C103 warnings and 1 error generated. :1795:21: warning: when type is in parentheses, array cannot have dynamic size longname=new(char[strlen(t->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1796:21: warning: when type is in parentheses, array cannot have dynamic size name =new(char[strlen(t->name)+1]); 99 ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.Cmake[3]: *** [hhconsensus] Error 1 :1797Makefile:128: recipe for target 'hhconsensus' failed :21: warning: when type is in parentheses, array cannot have dynamic size file =new(char[strlen(t->file)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1808:22: warning: when type is in parentheses, array cannot have dynamic size this->i = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1809:22: warning: when type is in parentheses, array cannot have dynamic size this->j = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1810:23: warning: when type is in parentheses, array cannot have dynamic size states = new( char[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C warnings and 1 error generated. :1813:make[3]: *** [hhfilter] Error 1 Makefile:119: recipe for target 'hhfilter' failed 19: warning: when type is in parentheses, array cannot have dynamic size sname=new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1814:19: warning: when type is in parentheses, array cannot have dynamic size seq =new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1833:24: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(t->sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1834:24: warning: when type is in parentheses, array cannot have dynamic size seq[k] = new(char[strlen(t->seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1840:20: warning: when type is in parentheses, array cannot have dynamic size dbfile = new(char[strlen(ptr)+1]); ~ ^~~~~~~~~~~~~ ~ In file included from hhalign.C:98: ./hhhalfalignment.C:46:15: warning: when type is in parentheses, array cannot have dynamic size h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:47:17: warning: when type is in parentheses, array cannot have dynamic size s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:48:16: warning: when type is in parentheses, array cannot have dynamic size 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:49:16: warning: when type is in parentheses, array cannot have dynamic size m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ~ ^~~~~~~~~ ~ In file included from hhsearch.C:117: ./hhhitlist.C:542:10: warning: address of array 'q->fam' will always evaluate to 'true' [-Wpointer-bool-conversion] if (q->fam && q->fam[0]>='a' && q->fam[0]<='k' && q->fam[1]=='.') ~~~^~~ ~~ In file included from hhblits.C:262: ./hhprefilter.C:794:34: warning: when type is in parentheses, array cannot have dynamic size dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhprefilter.C99:846:30: warning: when type is in parentheses, array cannot have dynamic size dbnames[num_dbs]=new(char[strlen(word)+1]); ~ ^~~~~~~~~~~~~~ ~ ./hhprefilter.C warnings and 1 error generated. make[3]: *** [hhmake] Error 1 Makefile:104: recipe for target 'hhmake' failed :1045:38: warning: when type is in parentheses, array cannot have dynamic size __m128i** workspace = new(__m128i*[cpu]); ~ ^~~ ~ In file included from hhalign.C:100: ./hhhitlist.C:542:10: warning: address of array 'q->fam' will always evaluate to 'true' [-Wpointer-bool-conversion] if (q->fam && q->fam[0]>='a' && q->fam[0]<='k' && q->fam[1]=='.') ~~~^~~ ~~ ./hhprefilter.C:1144:38: warning: when type is in parentheses, array cannot have dynamic size dbfiles_old[ndb_old]=new(char[strlen(db_name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhprefilter.C:1150:38: warning: when type is in parentheses, array cannot have dynamic size dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhsearch.C:375:38: warning: when type is in parentheses, array cannot have dynamic size par.dbfiles = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhsearch.C:445:34: warning: when type is in parentheses, array cannot have dynamic size par.exclstr = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhblits.C:781:32: warning: when type is in parentheses, array cannot have dynamic size Qali.longname = new(char[strlen(q->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:914:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1120:26: warning: when type is in parentheses, array cannot have dynamic size dbfiles[ndb]=new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1406:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhalign.C:442:27: warning: when type is in parentheses, array cannot have dynamic size pngfile = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhalign.C:452:29: warning: when type is in parentheses, array cannot have dynamic size strucfile = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhblits.C:1716:36: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhsearch.C:672:32: warning: when type is in parentheses, array cannot have dynamic size Qali.longname = new(char[strlen(q->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ hhsearch.C:705:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhalign.C:474:26: warning: when type is in parentheses, array cannot have dynamic size tcfile = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhalign.C:491:27: warning: when type is in parentheses, array cannot have dynamic size par.exclstr = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhalign.C:539:28: warning: when type is in parentheses, array cannot have dynamic size dmapfile = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhblits.C:2140:20: warning: when type is in parentheses, array cannot have dynamic size format = new(int[bins]); ~ ^~~~ ~ hhblits.C:2240:33: warning: when type is in parentheses, array cannot have dynamic size dbfiles_new[ndb_new]=new(char[strlen(dbfiles_old[a])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhsearch.C:963:36: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhsearch.C:1268:20: warning: when type is in parentheses, array cannot have dynamic size format = new(int[bins]); ~ ^~~~ ~ hhsearch.C:1304:45: warning: when type is in parentheses, array cannot have dynamic size dbfiles[ndb]=new(char[strlen(dbfile)+1]); ~ ^~~~~~~~~~~~~~~~ ~ hhsearch.C:1317:37: warning: when type is in parentheses, array cannot have dynamic size dbfiles[ndb]=new(char[strlen(dbfile_cur)+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ hhalign.C:916:13: warning: address of array 'par.outfile' will always evaluate to 'true' [-Wpointer-bool-conversion] if (par.outfile && v>=1) fprintf(stderr,"\nWARNING: no output file is written when -index option is used.\n"); ~~~~^~~~~~~ ~~ hhalign.C:943:27: warning: when type is in parentheses, array cannot have dynamic size Pstruc = new(float*[q->L+2]); ~ ^~~~~~ ~ hhalign.C:944:58: warning: when type is in parentheses, array cannot have dynamic size for (int i=0; iL+2; i++) Pstruc[i] = new(float[t->L+2]); ~ ^~~~~~ ~ hhalign.C:945:27: warning: when type is in parentheses, array cannot have dynamic size Sstruc = new(float*[q->L+2]); ~ ^~~~~~ ~ hhalign.C:946:58: warning: when type is in parentheses, array cannot have dynamic size for (int i=0; iL+2; i++) Sstruc[i] = new(float[t->L+2]); ~ ^~~~~~ ~ hhsearch.C:1433:43: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ 149 warnings and 2 errors generated. make[3]: *** [hhalign] Error 1 Makefile:110: recipe for target 'hhalign' failed 151 warnings and 2 errors generated. 148 warnings and 2 errors generated. make[3]: *** [hhblits] Error 1 Makefile:95: recipe for target 'hhblits' failed make[3]: *** [hhsearch] Error 1 Makefile:86: recipe for target 'hhsearch' failed make[3]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: *** [all] Error 2 Makefile:21: recipe for target 'all' failed make[2]: Leaving directory '/«PKGBUILDDIR»' dh_auto_build: make -j10 NO_PNG=1 returned exit code 2 make[1]: *** [override_dh_auto_build] Error 2 debian/rules:43: recipe for target 'override_dh_auto_build' failed make[1]: Leaving directory '/«PKGBUILDDIR»' make: *** [build-arch] Error 2 debian/rules:50: recipe for target 'build-arch' failed dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20150326-0639 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 13032 Build-Time: 13 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 10 Job: hhsuite_2.0.16-5 Machine Architecture: amd64 Package: hhsuite Package-Time: 54 Source-Version: 2.0.16-5 Space: 13032 Status: attempted Version: 2.0.16-5 ──────────────────────────────────────────────────────────────────────────────── Finished at 20150326-0639 Build needed 00:00:54, 13032k disc space DC-Status: Failed 54.89936674s DC-Time-Estimation: 54.89936674 versus expected 597 (r/m: 9.874442374305609 ; m: 54.89936674)