sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | t-coffee 12.00.7fb08c2-4 (arm64) Mon, 11 Nov 2019 20:33:19 +0000 | +==============================================================================+ Package: t-coffee Version: 12.00.7fb08c2-4 Source Version: 12.00.7fb08c2-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-3a84e6da-0fd2-4801-86bc-a9a57442cf65' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-viut4e/resolver-yhrbAo' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [139 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-11-0825.46.pdiff [8691 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-11-1416.22.pdiff [44.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-11-1416.22.pdiff [44.9 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-11-0825.46.pdiff [9103 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-11-1416.22.pdiff [45.2 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main arm64 Packages [8055 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-11-1416.22.pdiff [45.2 kB] Fetched 8357 kB in 2s (4274 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libsystemd0 libudev1 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 507 kB of archives. After this operation, 5120 B of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 libsystemd0 amd64 243-5 [346 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libudev1 amd64 243-5 [161 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 507 kB in 0s (8792 kB/s) (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 ... 14997 files and directories currently installed.) Preparing to unpack .../libsystemd0_243-5_amd64.deb ... Unpacking libsystemd0:amd64 (243-5) over (242-8) ... Setting up libsystemd0:amd64 (243-5) ... (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 ... 14997 files and directories currently installed.) Preparing to unpack .../libudev1_243-5_amd64.deb ... Unpacking libudev1:amd64 (243-5) over (242-8) ... Setting up libudev1:amd64 (243-5) ... Processing triggers for libc-bin (2.29-3) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 't-coffee' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/t-coffee.git Please use: git clone https://salsa.debian.org/med-team/t-coffee.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3538 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main t-coffee 12.00.7fb08c2-4 (dsc) [2157 B] Get:2 http://debian.oregonstate.edu/debian unstable/main t-coffee 12.00.7fb08c2-4 (tar) [3521 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main t-coffee 12.00.7fb08c2-4 (diff) [14.8 kB] Fetched 3538 kB in 0s (44.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/t-coffee-viut4e/t-coffee-12.00.7fb08c2' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-viut4e' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 12~), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper (>= 12~), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [401 B] Get:5 copy:/<>/apt_archive ./ Packages [489 B] Fetched 1847 B in 0s (85.2 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdmainutils cpp-9-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-9-aarch64-linux-gnu gcc-9-aarch64-linux-gnu-base gcc-9-base:arm64 gcc-9-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:arm64 libasan5-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbsd0 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:arm64 libgcc-9-dev-arm64-cross libgcc1:arm64 libgcc1-arm64-cross libglib2.0-0 libgomp1:arm64 libgomp1-arm64-cross libicu63 libio-string-perl libitm1:arm64 libitm1-arm64-cross liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:arm64 libstdc++-9-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtool libtsan0:arm64 libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch gcc-9-doc libstdc++6-9-dbg-arm64-cross libgcc1-dbg-arm64-cross libgomp1-dbg-arm64-cross libitm1-dbg-arm64-cross libatomic1-dbg-arm64-cross libasan5-dbg-arm64-cross liblsan0-dbg-arm64-cross libtsan0-dbg-arm64-cross libubsan1-dbg-arm64-cross libquadmath0-dbg-arm64-cross manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:arm64 libc-l10n:arm64 locales:arm64 manpages-dev:arm64 libstdc++-9-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:arm64 libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdmainutils cpp-9-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-9-aarch64-linux-gnu gcc-9-aarch64-linux-gnu-base gcc-9-base:arm64 gcc-9-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:arm64 libasan5-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbsd0 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:arm64 libgcc-9-dev-arm64-cross libgcc1:arm64 libgcc1-arm64-cross libglib2.0-0 libgomp1:arm64 libgomp1-arm64-cross libicu63 libio-string-perl libitm1:arm64 libitm1-arm64-cross liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:arm64 libstdc++-9-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtool libtsan0:arm64 libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:arm64 sensible-utils ucf 0 upgraded, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 62.8 MB of archives. After this operation, 262 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.0-1 [1307 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-9-base arm64 9.2.1-19 [194 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-6 [253 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-6 [119 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-6 [67.2 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.33.1-2 [2775 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-aarch64-linux-gnu-base amd64 9.2.1-19cross1 [194 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-aarch64-linux-gnu amd64 9.2.1-19cross1 [6540 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:9.2.1-3.1 [16.7 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-19cross1 [190 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-arm64-cross all 2.29-1cross7 [1253 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-arm64-cross all 1:9.2.1-19cross1 [34.0 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-arm64-cross all 9.2.1-19cross1 [76.6 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-arm64-cross all 9.2.1-19cross1 [24.2 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-arm64-cross all 9.2.1-19cross1 [8656 B] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-arm64-cross all 9.2.1-19cross1 [347 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-arm64-cross all 9.2.1-19cross1 [121 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-arm64-cross all 9.2.1-19cross1 [267 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-arm64-cross all 9.2.1-19cross1 [416 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-arm64-cross all 9.2.1-19cross1 [117 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-arm64-cross all 9.2.1-19cross1 [885 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-aarch64-linux-gnu amd64 9.2.1-19cross1 [6907 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:9.2.1-3.1 [1460 B] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-arm64-cross all 5.2.9-2cross7 [1310 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-arm64-cross all 2.29-1cross7 [2273 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-arm64-cross all 9.2.1-19cross1 [1635 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-aarch64-linux-gnu amd64 9.2.1-19cross1 [7118 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:9.2.1-3.1 [1180 B] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-arm64 all 12.8 [6644 B] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-11 [547 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.7.1 [173 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.2-1 [23.6 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.2-1 [14.6 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-2 [145 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.2-3 [1318 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20191019-1 [102 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.7.1 [997 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc1 arm64 1:9.2.1-19 [34.1 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main arm64 libc6 arm64 2.29-3 [2464 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main arm64 libasan5 arm64 9.2.1-19 [354 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main arm64 libatomic1 arm64 9.2.1-19 [8824 B] Get:82 http://debian.oregonstate.edu/debian unstable/main arm64 linux-libc-dev arm64 5.3.9-1 [983 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main arm64 libc6-dev arm64 2.29-3 [2286 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main arm64 libgomp1 arm64 9.2.1-19 [78.5 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main arm64 libitm1 arm64 9.2.1-19 [24.7 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main arm64 liblsan0 arm64 9.2.1-19 [122 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main arm64 libtsan0 arm64 9.2.1-19 [274 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++6 arm64 9.2.1-19 [454 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main arm64 libubsan1 arm64 9.2.1-19 [118 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-9-dev arm64 9.2.1-19 [885 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++-9-dev arm64 9.2.1-19 [1655 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.8 MB in 1s (74.2 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 14997 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.0-1_amd64.deb ... Unpacking man-db (2.9.0-1) ... 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Setting up libfile-which-perl (1.23-1) ... Setting up libmagic-mgc (1:5.37-6) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:amd64 (2.62.2-3) ... No schema files found: doing nothing. Setting up gcc-9-aarch64-linux-gnu-base:amd64 (9.2.1-19cross1) ... Setting up libdebhelper-perl (12.7.1) ... Setting up libmagic1:amd64 (1:5.37-6) ... Setting up linux-libc-dev:arm64 (5.3.9-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up binutils-aarch64-linux-gnu (2.33.1-2) ... Setting up cpp-9-aarch64-linux-gnu (9.2.1-19cross1) ... Setting up file (1:5.37-6) ... Setting up libyaml-perl (1.29-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cpp-aarch64-linux-gnu (4:9.2.1-3.1) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libncurses6:amd64 (6.1+20191019-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libc6-arm64-cross (2.29-1cross7) ... Setting up autopoint (0.19.8.1-9) ... Setting up gcc-9-cross-base (9.2.1-19cross1) ... Setting up linux-libc-dev-arm64-cross (5.2.9-2cross7) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:arm64 (9.2.1-19) ... Setting up libatomic1-arm64-cross (9.2.1-19cross1) ... Setting up libgcc1-arm64-cross (1:9.2.1-19cross1) ... Setting up libfile-stripnondeterminism-perl (1.6.2-1) ... Setting up liblsan0-arm64-cross (9.2.1-19cross1) ... Setting up libgomp1-arm64-cross (9.2.1-19cross1) ... Setting up libtool (2.4.6-11) ... Setting up libtsan0-arm64-cross (9.2.1-19cross1) ... Setting up m4 (1.4.18-4) ... Setting up libc6-dev-arm64-cross (2.29-1cross7) ... Setting up libasan5-arm64-cross (9.2.1-19cross1) ... Setting up libstdc++6-arm64-cross (9.2.1-19cross1) ... Setting up bsdmainutils (11.1.2+b1) ... 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 libcroco3:amd64 (0.6.13-1) ... Setting up libitm1-arm64-cross (9.2.1-19cross1) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dh-strip-nondeterminism (1.6.2-1) ... Setting up dwz (0.13-2) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libubsan1-arm64-cross (9.2.1-19cross1) ... Setting up libgcc-9-dev-arm64-cross (9.2.1-19cross1) ... Setting up man-db (2.9.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up intltool-debian (0.35.0+20060710.5) ... Setting up gcc-9-aarch64-linux-gnu (9.2.1-19cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-9-dev-arm64-cross (9.2.1-19cross1) ... Setting up gcc-aarch64-linux-gnu (4:9.2.1-3.1) ... Setting up po-debconf (1.0.21) ... Setting up g++-9-aarch64-linux-gnu (9.2.1-19cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-aarch64-linux-gnu (4:9.2.1-3.1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-arm64 (12.8) ... Setting up libc6:arm64 (2.29-3) ... Setting up libc6-dev:arm64 (2.29-3) ... Setting up libitm1:arm64 (9.2.1-19) ... Setting up libgcc1:arm64 (1:9.2.1-19) ... Setting up libgomp1:arm64 (9.2.1-19) ... Setting up dh-autoreconf (19) ... Setting up libasan5:arm64 (9.2.1-19) ... Setting up libatomic1:arm64 (9.2.1-19) ... Setting up libstdc++6:arm64 (9.2.1-19) ... Setting up liblsan0:arm64 (9.2.1-19) ... Setting up libtsan0:arm64 (9.2.1-19) ... Setting up debhelper (12.7.1) ... Setting up libubsan1:arm64 (9.2.1-19) ... Setting up libgcc-9-dev:arm64 (9.2.1-19) ... Setting up libstdc++-9-dev:arm64 (9.2.1-19) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.29-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.33.1-2 dpkg-dev_1.19.7 g++-8_8.3.0-24 g++-9_9.2.1-19 gcc-8_8.3.0-24 gcc-9_9.2.1-19 libc6-dev_2.29-3 libstdc++-8-dev_8.3.0-24 libstdc++-9-dev_9.2.1-19 libstdc++-9-dev-arm64-cross_9.2.1-19cross1 libstdc++6_9.2.1-19 libstdc++6-arm64-cross_9.2.1-19cross1 linux-libc-dev_5.3.9-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 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MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: t-coffee Binary: t-coffee, t-coffee-examples Architecture: any all Version: 12.00.7fb08c2-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/t-coffee Vcs-Git: https://salsa.debian.org/med-team/t-coffee.git Testsuite: autopkgtest Build-Depends: debhelper (>= 12~) Package-List: t-coffee deb science optional arch=any t-coffee-examples deb science optional arch=all Checksums-Sha1: a6b5eb9a423b3497087105473ff4bfe106e7584b 3520829 t-coffee_12.00.7fb08c2.orig.tar.gz 949d3cc1e4694ec852f9a3920d746035d8bc691c 14812 t-coffee_12.00.7fb08c2-4.debian.tar.xz Checksums-Sha256: 6119514a0e36da4b4de88741b8c12f9c8ab653772b3952a011d4cb373beee44f 3520829 t-coffee_12.00.7fb08c2.orig.tar.gz 6774a081517f7bbe95e16e728b78545b5339b3966c9dde5af9a907dd7869fcb5 14812 t-coffee_12.00.7fb08c2-4.debian.tar.xz Files: c7eb2c67634a3a9b35d114fb6211f34d 3520829 t-coffee_12.00.7fb08c2.orig.tar.gz 0b1d876c508b0362e8aae3762be187fc 14812 t-coffee_12.00.7fb08c2-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxmYHsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHcPQ/9HyhnIuXpNsJsFt7lnrZb+SXXiWx6ws0+ KQ6arSbuUXCG6uuIOfTlsZ7rWU+wlg73MS5GLIda3csoL76sAmNKulYAmzcHK34l J1m3LUWSDotXxJq90x1nLo0lak10Ug+5lq6SVFafDVNQ+blf2g6v6i1wdQKxGlOl Vxvq0PIBd9PWrU+WXllJYHwRdhMIqRsKeIMJ2ckIFyh3flXttDy3kkI8VIcCkB8U N1ElsZysC+oYiY/J6qSkUYDTulFAz5N/8VMRPt2bhWZnc8dw2ady68PAWC2xsfD9 9DXFQp72HKT5HDI/ARy3ys1hDZz3Ot9BcFZnpxOVvN2rCJUP4PmALwNDsUb0jaK6 H9GqmhTR1BB8F1pTObllW7Fi3PuCzSsFpjeNl4iNLxb6cvyiWew46fwlwH+8rFfQ 7VJlb6P7PsZLTf6wb4SYbRT/MAkHwE6e4Rr+Rbx0XDsUb4Euiebsu6EPn3xvhO8y 9cN8JghCcWHeYJ0BPxGdDnO4gBywGDLH47n9fJTfHVYfGpINSXuMPrT3mfZ5Z5lQ 8oovBniuemv2/tM8SlJ0qQTpDDgTOKAxvWFg4A1ER5wSOhEOxffKyqVqK6VINN2T KYObCgmsOd4XukDyimffRlmfsB8QVkl25Q/bbf844/ip98Vo9aMya+13S7i0gtNY APTfIZ2vpQo= =pc4G -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Feb 15 06:47:23 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./t-coffee_12.00.7fb08c2-4.dsc dpkg-source: info: extracting t-coffee in /<> dpkg-source: info: unpacking t-coffee_12.00.7fb08c2.orig.tar.gz dpkg-source: info: unpacking t-coffee_12.00.7fb08c2-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying ncbi-blast++_has_dropped_pl_extension.patch dpkg-source: info: applying use_debian_packaged_TMalign.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying set_proper_dir_permissions.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying stable-linking-inputs.patch dpkg-source: info: applying clustalw2.patch dpkg-source: info: applying fix_tempfile_name_sharing.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut 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=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-3a84e6da-0fd2-4801-86bc-a9a57442cf65 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 12.00.7fb08c2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/t_coffee.log bin/t_coffee rm -rf t_coffee_source/TMalign find . -name "*.o" -delete find . -name "*.deps" -delete chmod 644 example/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules build-arch dh build-arch --sourcedirectory=t_coffee_source dh_update_autotools_config -a -O--sourcedirectory=t_coffee_source dh_autoreconf -a -O--sourcedirectory=t_coffee_source dh_auto_configure -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" 'CC=$(CXX)' all cd t_coffee_source && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc USER_BIN=../bin/ "FCC=gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" CC=\$\(CXX\) all make[2]: Entering directory '/<>/t_coffee_source' CC dev_lib/dev1.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dev_lib/dev1.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dev_lib/dev1.c: In function ‘void aln2hitMat(Alignment*, char*)’: dev_lib/dev1.c:89:19: warning: too many arguments for format [-Wformat-extra-args] 89 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ CC dp_lib/CUSTOM_evaluate_for_struc.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/evaluate.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/evaluate.c: In function ‘Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)’: dp_lib/evaluate.c:2956:53: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘int’ [-Wformat=] 2956 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~~~^ ~~~ | | | | double int | %3.2d dp_lib/evaluate.c:2956:67: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘double’ [-Wformat=] 2956 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~^ ~~~~~~~ | | | | int double | %3f dp_lib/evaluate.c:2956:79: warning: format ‘%f’ expects argument of type ‘double’, but argument 6 has type ‘int’ [-Wformat=] 2956 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~~^ ~~~~~~~~ | | | | double int | %.3d dp_lib/evaluate.c:2956:95: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘double’ [-Wformat=] 2956 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~^ ~~~~~~ | | | | int double | %3f dp_lib/evaluate.c: In function ‘Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)’: dp_lib/evaluate.c:809:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 809 | fscanf (fp, "%d ", &res); | ~~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:814:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 814 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:819:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 819 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c: In function ‘float** initialise_aa_physico_chemical_property_table(int*)’: dp_lib/evaluate.c:7511:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 7511 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/evaluate_dirichlet.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_dirichlet.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/evaluate_dirichlet.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/evaluate_dirichlet.c: In function ‘Mixture* read_dirichlet(char*)’: dp_lib/evaluate_dirichlet.c:317:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 317 | fscanf(fp, "%f\n", &f); | ~~~~~~^~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 319 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 323 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 326 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ CC dp_lib/evaluate_for_domain.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_for_domain.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_domain.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/evaluate_for_struc.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_for_struc.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/fsa_dp.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/fsa_dp.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/pavie_dp.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/pavie_dp.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/pavie_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/pavie_dp.c: In function ‘double** pavie_seq2pavie_aln(Sequence*, char*, char*)’: dp_lib/pavie_dp.c:127:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 127 | fscanf (fp, "%s\n",mat_list[nch++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’: dp_lib/pavie_dp.c:1079:15: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1079 | system (command); | ~~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c:1081:14: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1081 | system (command); | ~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c: In function ‘Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)’: dp_lib/pavie_dp.c:1365:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1365 | fscanf (fp, "%s", mat); | ~~~~~~~^~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’: dp_lib/pavie_dp.c:1078:33: warning: ‘%s’ directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); | ^~ ~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from dp_lib/pavie_dp.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 1004) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c:1080:30: warning: ‘%s’ directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] 1080 | sprintf ( command, "cp %s %s", latest, current); | ^~ ~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from dp_lib/pavie_dp.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 2003 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/showpair.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/showpair.c:32: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/showpair.c:32: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_domain_dp.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_domain_dp.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_domain_dp_drivers.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_domain_dp_drivers.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_cdna_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_clean_maln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_clean_maln.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_clean_maln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_drivers.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_drivers.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_drivers.c: In function ‘char* seq_file2msa_file(char*, char*, char*)’: dp_lib/util_dp_drivers.c:1014:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1014 | chdir (dir); | ~~~~~~^~~~~ dp_lib/util_dp_drivers.c:1028:16: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1028 | chdir (cdir); | ~~~~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* align_pdb_pair_2(char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1080:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1080 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* align_pdb_pair(char*, char*, char*, char*, Constraint_list*, Job_TC*)’: dp_lib/util_dp_drivers.c:1108:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1108 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* hh_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1149:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1149 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1160:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] 1160 | tmpnam(aln1); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1161:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] 1161 | tmpnam(aln2); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1164:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] 1164 | tmpnam(hhfile); | ~~~~~~^~~~~~~~ dp_lib/util_dp_drivers.c:1211:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1211 | fgets (buf2, 10000, fp); | ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1280:6: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1280 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1363:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1363 | fscanf (fp, "%s", bufname); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_pair_decomposed(TC_method*, char*, Constraint_list*, char*)’: dp_lib/util_dp_drivers.c:1445:7: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1445 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_subset_pair_old(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1581:7: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1581 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* pdbid_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1717:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1717 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* pdb_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1774:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1774 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* thread_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1906:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1906 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* lsqman_pair(char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1981:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1981 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* sap_pair(char*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:2073:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2073 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2121:10: warning: ignoring return value of ‘char* getcwd(char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 2121 | getcwd (cdir, sizeof(char)*1000); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2122:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2122 | chdir (get_cache_dir()); | ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2142:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2142 | chdir (cdir); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* rnapdb_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:2256:6: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2256 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* method2pw_cl(TC_method*, Constraint_list*)’: dp_lib/util_dp_drivers.c:382:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:373:23: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 373 | sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:386:41: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 386 | if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Alignment* realign_block(Alignment*, int, int, char*)’: dp_lib/util_dp_drivers.c:920:25: warning: ‘ -infile=’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 920 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); | ^~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 38 or more bytes (assuming 1037) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1854:80: warning: ‘%s’ directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] 1854 | sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 71 or more bytes (assuming 6067) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)’: dp_lib/util_dp_drivers.c:3717:25: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 3717 | sprintf ( dp_mode, "%s", CL->dp_mode); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_est.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_est.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_est.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_fasta_nw.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_fasta_sw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_fasta_sw.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_sw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_generic_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_generic_fasta_nw.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_gotoh_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_gotoh_nw.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_gotoh_sw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_gotoh_sw.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_sw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_gotoh_sw.c: In function ‘int gotoh_pair_wise_sw(Alignment*, int*, int**, Constraint_list*)’: dp_lib/util_dp_gotoh_sw.c:391:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_mm_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_mm_nw.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_mm_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_sim.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_sim.c:32: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_ssec_pwaln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_ssec_pwaln.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_suboptimal_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_suboptimal_nw.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_dp_suboptimal_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_graph_maln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_graph_maln.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/diagonal.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/diagonal.c:31: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from fastal/diagonal.c:31: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ fastal/diagonal.c: In function ‘int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)’: fastal/diagonal.c:434:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 434 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/diagonal.c:439:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 439 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 440 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 441 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ CC fastal/fastal.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/fastal.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:1924:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1924 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1929:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1929 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1930 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1931 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1976:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1976 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1980:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1980 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1981 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1982 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:2115:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2115 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:2262:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2262 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)’: fastal/fastal.c:3201:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3201 | fgets (line, LINE_LENGTH , seq_file); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)’: fastal/fastal.c:3323:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3323 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3326:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3326 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3329 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3331 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3333 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3352 | fgets(line, LINE_LENGTH , profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)’: fastal/fastal.c:3502:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3502 | fgets (line, LINE_LENGTH , sequence_file); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)’: fastal/fastal.c:3575:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3575 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3577 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3579 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3581 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/fastal_opt_parsing.c CC fastal/iteration.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/iteration.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from fastal/iteration.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ fastal/iteration.c: In function ‘void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)’: fastal/iteration.c:185:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 185 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function ‘void iterate(Fastal_param*, void*, char*, char*, int)’: fastal/iteration.c:310:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 310 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 435 | system(command); | ~~~~~~^~~~~~~~~ fastal/iteration.c: In function ‘void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)’: fastal/iteration.c:501:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:535:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function ‘void edit2seq_pattern(FILE*, char*, char*)’: fastal/iteration.c:563:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 563 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 565 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 567 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 569 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/parttree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/parttree.c:36: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ fastal/parttree.c: In function ‘int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)’: fastal/parttree.c:695:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 695 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c:701:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 701 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘void get_table(short int*, FILE*, long int)’: fastal/parttree.c:848:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 848 | fgets(line, LINE_LENGTH, tables_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:859:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 859 | fgets(line, LINE_LENGTH, tables_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘int euclidean_dist(FILE*, long int, long int, short int*, short int*, int)’: fastal/parttree.c:891:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 891 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 903 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 906 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 912 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘int euclidean_dist_half(FILE*, long int, short int*, short int*, int)’: fastal/parttree.c:951:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 951 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/scoring.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/scoring.c:37: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from fastal/scoring.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ fastal/scoring.c: In function ‘double calculate_sum_of_pairs_score_affine(char*, int**, double, double)’: fastal/scoring.c:76:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 76 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 78 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 82 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function ‘void compute_ref_alignments(char*, char*, int, int)’: fastal/scoring.c:384:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 384 | fgets(line, LINE_LENGTH, seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 398 | system(aln_command); | ~~~~~~^~~~~~~~~~~~~ fastal/scoring.c: In function ‘void make_ref_alignment(char*, char*, char*, int)’: fastal/scoring.c:488:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 488 | fgets(line, LINE_LENGTH, seq_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 502 | system(command); | ~~~~~~^~~~~~~~~ fastal/scoring.c: In function ‘double agreement_score(char*, char*)’: fastal/scoring.c:583:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 583 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 584 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function ‘int complete_agreement_score(char*, const char*)’: fastal/scoring.c:624:28: warning: ‘%s’ directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); | ^~ ~~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from fastal/scoring.c:28: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 756 bytes into a destination of size 200 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/tree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/tree.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from fastal/tree.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC io_lib/io_func.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/io_func.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from io_lib/io_func.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ io_lib/io_func.c: In function ‘int output_raw_score(Alignment*, Alignment*, char*)’: io_lib/io_func.c:1235:17: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 1235 | if (!A)return NULL; | ^~~~ io_lib/io_func.c: In function ‘int aln2compressed_ps(Alignment*, char*)’: io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] 2076 | } | ^ io_lib/io_func.c: In function ‘int** read_matrice(char*)’: io_lib/io_func.c:511:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 511 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ io_lib/io_func.c: In function ‘void get_rgb_values(int, Color*)’: io_lib/io_func.c:971:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 971 | fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC io_lib/pb_util_read_seq_util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/pb_util_read_seq_util.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_seq_util.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘void getstr(char*, char*)’: io_lib/pb_util_read_seq_util.c:269:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 269 | fgets(outstr, 100, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘double getreal(char*, double, double, double)’: io_lib/pb_util_read_seq_util.c:280:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 280 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘int getint(char*, int, int, int)’: io_lib/pb_util_read_seq_util.c:305:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 305 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ CC io_lib/pb_util_read_sequence.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/pb_util_read_sequence.c:35: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_sequence.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ io_lib/pb_util_read_sequence.c: In function ‘void get_clustal_seq(char*, char*, int*, char*, int)’: io_lib/pb_util_read_sequence.c:144:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 144 | fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ | ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_sequence.c:149:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 149 | for(i=1;iname, b,split_format); | ^~ ~~~~~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from t_coffee_lib/t_coffee.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 10 or more bytes (assuming 1018) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/aln_compare.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/aln_compare.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/aln_convertion_util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/aln_convertion_util.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/aln_convertion_util.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2conservation(Alignment*, int, char*)’: util_lib/aln_convertion_util.c:4446:1: warning: no return statement in function returning non-void [-Wreturn-type] 4446 | } | ^ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2N_replicate(Alignment*, char*, char*)’: util_lib/aln_convertion_util.c:7697:1: warning: no return statement in function returning non-void [-Wreturn-type] 7697 | } | ^ util_lib/aln_convertion_util.c: In function ‘Alignment* extract_aln3(Alignment*, char*)’: util_lib/aln_convertion_util.c:7459:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 7459 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7478:31: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 7478 | if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7482:13: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 7482 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function ‘float** get_weight(Alignment*, Sequence*, char*)’: util_lib/aln_convertion_util.c:12082:32: warning: ‘ -w ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12082 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); | ^~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/aln_convertion_util.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 1005) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:12076:32: warning: ‘ -i ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12076 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); | ^~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/aln_convertion_util.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 10 or more bytes (assuming 1009) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/hsearch.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/hsearch.c:35: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/hsearch.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/random.c CC util_lib/reformat.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/reformat.c:35: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/reformat.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat.c: In function ‘int output_suchard_aln(char*, Alignment*)’: util_lib/reformat.c:7441:1: warning: no return statement in function returning non-void [-Wreturn-type] 7441 | } | ^ util_lib/reformat.c: In function ‘void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’: util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11290:35: note: in expansion of macro ‘ATOI_ACTION’ 11290 | (D1->A)=aln2bootstrap (D1->A, ATOI_ACTION (1)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11296:32: note: in expansion of macro ‘ATOI_ACTION’ 11296 | (D1->A)=aln2sample (D1->A, ATOI_ACTION (1)); | ^~~~~~~~~~~ util_lib/reformat.c:11529:41: warning: null argument where non-null required (argument 1) [-Wnonnull] 11529 | if (ACTION (3))D=atof (ACTION(3)); | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11563:38: note: in expansion of macro ‘ATOI_ACTION’ 11563 | else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11662:38: note: in expansion of macro ‘ATOI_ACTION’ 11662 | else TS=treelist2sub_seq((D1->S),ATOI_ACTION(2)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11663:34: note: in expansion of macro ‘ATOI_ACTION’ 11663 | treelist2lti (D1->S,TS, (int)ATOI_ACTION(1), stdout ); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11670:38: note: in expansion of macro ‘ATOI_ACTION’ 11670 | else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11677:35: note: in expansion of macro ‘ATOI_ACTION’ 11677 | D1->S=treelist2sub_seq (D1->S,ATOI_ACTION(1)); | ^~~~~~~~~~~ util_lib/reformat.c:11705:27: warning: null argument where non-null required (argument 1) [-Wnonnull] 11705 | ng=atoi(ACTION (2))+1; | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11733:31: note: in expansion of macro ‘ATOI_ACTION’ 11733 | tree2bucket (D2->T, D1->S,ATOI_ACTION(1), ACTION(2)); | ^~~~~~~~~~~ util_lib/reformat.c:11743:29: warning: null argument where non-null required (argument 1) [-Wnonnull] 11743 | int shuf=atoi (ACTION(1)); | ^ util_lib/reformat.c:11754:29: warning: null argument where non-null required (argument 1) [-Wnonnull] 11754 | int shuf=atoi (ACTION(1)); | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11880:44: note: in expansion of macro ‘ATOI_ACTION’ 11880 | D1->T= aln2km_tree(D1->A, (ACTION(1)), ATOI_ACTION(2)); | ^~~~~~~~~~~ util_lib/reformat.c:11963:32: warning: null argument where non-null required (argument 1) [-Wnonnull] 11963 | else max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:11966:32: warning: null argument where non-null required (argument 1) [-Wnonnull] 11966 | else enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:11978:77: warning: null argument where non-null required (argument 1) [-Wnonnull] 11978 | if (ACTION(na+1)&& !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:11979:77: warning: null argument where non-null required (argument 1) [-Wnonnull] 11979 | if (ACTION(na+2)&& !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:11987:78: warning: null argument where non-null required (argument 1) [-Wnonnull] 11987 | if (ACTION(na+1) && !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:11988:78: warning: null argument where non-null required (argument 1) [-Wnonnull] 11988 | if (ACTION(na+2) && !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:12022:30: warning: null argument where non-null required (argument 1) [-Wnonnull] 12022 | radius=atof(ACTION(1)); | ^ util_lib/reformat.c:12030:33: warning: null argument where non-null required (argument 1) [-Wnonnull] 12030 | threshold=atof(ACTION(2)); | ^ util_lib/reformat.c:12037:27: warning: null argument where non-null required (argument 1) [-Wnonnull] 12037 | min=atoi(ACTION(3)); | ^ util_lib/reformat.c:12073:32: warning: null argument where non-null required (argument 1) [-Wnonnull] 12073 | else max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:12076:32: warning: null argument where non-null required (argument 1) [-Wnonnull] 12076 | else enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:12088:77: warning: null argument where non-null required (argument 1) [-Wnonnull] 12088 | if (ACTION(na+1)&& !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:12089:77: warning: null argument where non-null required (argument 1) [-Wnonnull] 12089 | if (ACTION(na+2)&& !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:12097:78: warning: null argument where non-null required (argument 1) [-Wnonnull] 12097 | if (ACTION(na+1) && !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:12098:78: warning: null argument where non-null required (argument 1) [-Wnonnull] 12098 | if (ACTION(na+2) && !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12146:44: note: in expansion of macro ‘ATOI_ACTION’ 12146 | float results=shuff (D1->S, ACTION (1),ATOI_ACTION(2)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12266:37: note: in expansion of macro ‘ATOI_ACTION’ 12266 | D1->A=aln2conservation ( D1->A, ATOI_ACTION (1), ACTION (2)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12390:31: note: in expansion of macro ‘ATOI_ACTION’ 12390 | D1->A=shuffle_aln (D1->A, ATOI_ACTION(1), ACTION(2), ACTION (3)); | ^~~~~~~~~~~ util_lib/reformat.c:12901:36: warning: null argument where non-null required (argument 1) [-Wnonnull] 12901 | else if (strstr (ACTION(1), "h")) | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12908:10: note: in expansion of macro ‘ATOI_ACTION’ 12908 | F->t=ATOI_ACTION(2); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12909:10: note: in expansion of macro ‘ATOI_ACTION’ 12909 | F->f=ATOI_ACTION(3); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12910:11: note: in expansion of macro ‘ATOI_ACTION’ 12910 | F->p1=ATOI_ACTION(4); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12911:11: note: in expansion of macro ‘ATOI_ACTION’ 12911 | F->p2=ATOI_ACTION(5); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12912:11: note: in expansion of macro ‘ATOI_ACTION’ 12912 | F->p3=ATOI_ACTION(6); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12913:11: note: in expansion of macro ‘ATOI_ACTION’ 12913 | F->p3=ATOI_ACTION(7); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12936:34: note: in expansion of macro ‘ATOI_ACTION’ 12936 | D1->A=unalign_aln (D1->A,SA, ATOI_ACTION(1)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13076:10: note: in expansion of macro ‘ATOI_ACTION’ 13076 | if (!ATOI_ACTION(1))myexit(fprintf_error (stderr,"-kmeans ")); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13077:19: note: in expansion of macro ‘ATOI_ACTION’ 13077 | km_seq (D1->A,ATOI_ACTION (1),ACTION(2),ACTION(3)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13081:27: note: in expansion of macro ‘ATOI_ACTION’ 13081 | D1->A=gap_trim (D1->A,ATOI_ACTION(1)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13088:34: note: in expansion of macro ‘ATOI_ACTION’ 13088 | D1->A=trim_RNA(D1->A, D2->S, ATOI_ACTION(1)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13616:7: note: in expansion of macro ‘ATOI_ACTION’ 13616 | t=ATOI_ACTION(1); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13617:7: note: in expansion of macro ‘ATOI_ACTION’ 13617 | f=ATOI_ACTION(2); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13618:8: note: in expansion of macro ‘ATOI_ACTION’ 13618 | p1=ATOI_ACTION(3); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13619:8: note: in expansion of macro ‘ATOI_ACTION’ 13619 | p2=ATOI_ACTION(4); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13620:8: note: in expansion of macro ‘ATOI_ACTION’ 13620 | p3=ATOI_ACTION(5); | ^~~~~~~~~~~ util_lib/reformat.c: In function ‘int output_header_mat(int**, char*)’: util_lib/reformat.c:14324:1: warning: no return statement in function returning non-void [-Wreturn-type] 14324 | } | ^ util_lib/reformat.c: In function ‘Sequence* quick_read_seq(char*)’: util_lib/reformat.c:1321:1: warning: control reaches end of non-void function [-Wreturn-type] 1321 | } | ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln_static(char*)’: util_lib/reformat.c:1360:1: warning: control reaches end of non-void function [-Wreturn-type] 1360 | } | ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln(char*)’: util_lib/reformat.c:1402:1: warning: control reaches end of non-void function [-Wreturn-type] 1402 | } | ^ util_lib/reformat.c: In function ‘int read_nameseq(char*, char***, char***, char***)’: util_lib/reformat.c:1416:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1416 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1417:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1417 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1427:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1427 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1430:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1430 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1435:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1435 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1437:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1437 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int read_nameseq_old(char*, char***, char***, char***)’: util_lib/reformat.c:1461:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1461 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1462:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1462 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1472:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1472 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1475:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1475 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1480:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1480 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1482:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1482 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int is_pdb_name(char*)’: util_lib/reformat.c:1779:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1779 | fscanf ( fp, "%d", &result); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘char* get_pdb_id(char*)’: util_lib/reformat.c:1817:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1817 | fscanf ( fp, "\n%s\n", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fast_format_determination(char*)’: util_lib/reformat.c:2486:1: warning: control reaches end of non-void function [-Wreturn-type] 2486 | } | ^ util_lib/reformat.c: In function ‘Weights* get_amps_sd_scores(char*)’: util_lib/reformat.c:3926:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3926 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3933:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3933 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3942:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3942 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3948:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3948 | fscanf ( fp, "%s",W->seq_name[a]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3950:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3950 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3961:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3961 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ util_lib/reformat.c: In function ‘Structure* read_rna_struc_number(Alignment*, char*)’: util_lib/reformat.c:4234:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4234 | fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4237:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4237 | fscanf ( fp, "%d %d %d %c %c %f\n", &(ST)->list[a][0],&(ST)->list[a][1],&(ST)->list[a][2], &x, &y, &f); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_struc_gor(char*)’: util_lib/reformat.c:4464:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4464 | fscanf ( fp, "%s %d", name, &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4485:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4485 | fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4490:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4490 | fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_sequence_dali(char*)’: util_lib/reformat.c:4527:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4527 | fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_dialign_sequence(char*)’: util_lib/reformat.c:4602:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4602 | {fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fscanf_seq_name(FILE*, char*)’: util_lib/reformat.c:5636:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 5636 | fscanf (fp, "%s", name); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int get_amps_seq_name(char**, char*)’: util_lib/reformat.c:5989:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 5989 | {fscanf (fp, "%*d >%s", name[nseq++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* read_gotoh_aln(char*, Alignment*)’: util_lib/reformat.c:6038:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 6038 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6060:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 6060 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘float output_maln_pval(char*, Alignment*)’: util_lib/reformat.c:6258:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 6258 | fscanf ( fp, "%s",string); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* similarities_file2aln(char*)’: util_lib/reformat.c:6423:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 6423 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix(char*)’: util_lib/reformat.c:14165:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14165 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14178:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14178 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14203:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14203 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix_old(char*)’: util_lib/reformat.c:14228:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 14228 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14245:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14245 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14258:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14258 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14285:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14285 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_pavie_matrix(char*)’: util_lib/reformat.c:14396:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 14396 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’: util_lib/reformat.c:13510:27: warning: ‘ -method ’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 13510 | sprintf ( command, "%s -method %s -aln %s -tree %s -dmatrix %s -weightfile %s %s",method_4_msa_weights, action_list[1],aln_name, tree_name, dist_matrix_name,weight_name, TO_NULL_DEVICE); | ^~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/reformat.c:27: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 64 or more bytes (assuming 3059) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’ at util_lib/reformat.c:11528:17: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/reformat_struc.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/reformat_struc.c:34: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/reformat_struc.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat_struc.c: In function ‘void bfactor2x_in_pdb(char*, char*, float*)’: util_lib/reformat_struc.c:125:18: warning: too many arguments for format [-Wformat-extra-args] 125 | fprintf (out, "ATOM ", lw[1]);//ATOM | ^~~~~~~~ util_lib/reformat_struc.c: In function ‘Ca_trace* simple_read_ca_trace(char*)’: util_lib/reformat_struc.c:370:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 370 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:372:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 372 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:378:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 378 | fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:405:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 405 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:407:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 407 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:416:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 416 | fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util.c:52: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/util.c:52: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util.c: In function ‘int cherry(int, char**)’: util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] 1009 | } | ^ util_lib/util.c: In function ‘int dump_nfc(char*, char*)’: util_lib/util.c:4455:1: warning: no return statement in function returning non-void [-Wreturn-type] 4455 | } | ^ util_lib/util.c: In function ‘int set_nproc(int)’: util_lib/util.c:5488:1: warning: no return statement in function returning non-void [-Wreturn-type] 5488 | } | ^ util_lib/util.c: In function ‘char* vremove3(char*, char*)’: util_lib/util.c:6920:1: warning: no return statement in function returning non-void [-Wreturn-type] 6920 | } | ^ util_lib/util.c: In function ‘FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))’: util_lib/util.c:281:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 281 | fread( rra, size, len,fp); /*rra=ra[--l]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:286:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 286 | fread( rra, size, len,fp); /*rra=ra[ir]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:289:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 289 | fread( rrb, size, len,fp); /*rrb=ra[0]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:306:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 306 | fread (ra_j, size, len, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:311:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 311 | fread (ra_j_1, size, len, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))’: util_lib/util.c:420:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 420 | fread ( key2, el_size, entry_len,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* get_number_list_in_file(FILE*, int*, int*, int*)’: util_lib/util.c:847:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 847 | fscanf ( fp, "%d",&list[n[0]++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int quantile(int, char**)’: util_lib/util.c:1321:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1321 | fscanf ( fp, "%s %s\n", s1, s2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** input_array_int(char*)’: util_lib/util.c:1805:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1805 | fscanf (fp, "%d\n", &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1809:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1809 | fscanf(fp, "%d ", &len2); | ~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1812:8: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1812 | fscanf(fp, "%d ", &array[a][b]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1813:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1813 | fscanf (fp, "\n"); | ~~~~~~~^~~~~~~~~~ util_lib/util.c: In function ‘int perl_strstr(char*, char*)’: util_lib/util.c:2468:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2468 | fscanf (fp, "%d", &r); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int printf_system_direct_check(char*, ...)’: util_lib/util.c:4439:19: warning: control reaches end of non-void function [-Wreturn-type] 4439 | printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* count_strings_in_file(char*, char*)’: util_lib/util.c:5760:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 5760 | fscanf (fp, "%s\n",list[n]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stderr(char*)’: util_lib/util.c:6300:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 6300 | freopen(stderr_file, "w", stderr); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stdout(char*)’: util_lib/util.c:6343:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 6343 | freopen(stdout_file, "w", stdout); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)’: util_lib/util.c:7554:2: warning: second parameter of ‘va_start’ not last named argument [-Wvarargs] 7554 | va_start (ap, usage); | ^~~~~~~~ util_lib/util.c: In function ‘char** get_parameter(char*, int*, char*)’: util_lib/util.c:7821:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 7821 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* set_fp_id(FILE*, char*)’: util_lib/util.c:7841:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 7841 | fscanf ( fp, "%s", string); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** get_file_block_pattern(char*, int*, int)’: util_lib/util.c:8228:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 8228 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:8258:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 8258 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_for_update(char*)’: util_lib/util.c:8345:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 8345 | fscanf ( fp, "Version_%f", &new_version); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_internet_connection(int)’: util_lib/util.c:8437:10: warning: control reaches end of non-void function [-Wreturn-type] 8437 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int km_main(int, char**)’: util_lib/util.c:10370:1: warning: control reaches end of non-void function [-Wreturn-type] 10370 | } | ^ util_lib/util.c: In function ‘char* get_cache_4_tcoffee()’: util_lib/util.c:5392:42: warning: ‘/cache/’ directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5392 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 8 and 1007 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_plugins_4_tcoffee()’: util_lib/util.c:5434:43: warning: ‘/plugins/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5434 | else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); | ^~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 11 and 1109 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* long_tmpnam_2(char*)’: util_lib/util.c:6808:22: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] 6808 | sprintf (buf, "%s/%s%d%s",tmpdir,root2, file++,set_file2remove_extension (NULL, GET)); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 3 or more bytes (assuming 10101) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* ultrashort_tmpnam_2(char*)’: util_lib/util.c:6840:22: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] 6840 | sprintf (buf, "%s/%s%d%s",tmpdir,root2, file++,set_file2remove_extension (NULL, GET)); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 3 or more bytes (assuming 10101) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* short_tmpnam_2(char*)’: util_lib/util.c:6871:22: warning: ‘%s’ directive writing up to 99 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] 6871 | sprintf (buf, "%s%d%s",root2, file++,set_file2remove_extension (NULL, GET)); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10110 bytes into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_methods_4_tcoffee()’: util_lib/util.c:5420:44: warning: ‘/methods/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5420 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_mcoffee_4_tcoffee()’: util_lib/util.c:5407:44: warning: ‘/mcoffee/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5407 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_cache_4_tcoffee()’: util_lib/util.c:5392:42: warning: ‘/cache/’ directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5392 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 8 and 1007 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char** standard_initialisation(char**, int*)’: util_lib/util.c:5407:44: warning: ‘/mcoffee/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5407 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:5420:44: warning: ‘/methods/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5420 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util.c:32: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_aln_analyze.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_aln_analyze.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/util_aln_analyze.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_aln_analyze.c: In function ‘Alignment* sar_analyze(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] 713 | } | ^ util_lib/util_aln_analyze.c: In function ‘Alignment* or_scan(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] 4480 | } | ^ CC util_lib/util_analyse_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_analyse_constraints_list.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/util_analyse_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_constraints_list.c:37: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/util_constraints_list.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* unfreeze_constraint_list(Constraint_list*)’: util_lib/util_constraints_list.c:1312:1: warning: no return statement in function returning non-void [-Wreturn-type] 1312 | } | ^ util_lib/util_constraints_list.c: In function ‘Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)’: util_lib/util_constraints_list.c:2225:28: warning: too many arguments for format [-Wformat-extra-args] 2225 | fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* read_constraint_list_file(Constraint_list*, char*)’: util_lib/util_constraints_list.c:2852:19: warning: too many arguments for format [-Wformat-extra-args] 2852 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); | ^~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Job_TC* submit_lib_job(Job_TC*)’: util_lib/util_constraints_list.c:582:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 582 | chdir (tdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c:585:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 585 | chdir (cdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function ‘char* method_file_tag2value(char*, char*)’: util_lib/util_constraints_list.c:1151:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1151 | fgets ( line,LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘TC_method* method_file2TC_method(char*)’: util_lib/util_constraints_list.c:1194:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1194 | fgets ( line,LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘int read_cpu_in_list(char*)’: util_lib/util_constraints_list.c:2600:20: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2600 | if ( c=='C')fscanf( fp, "PU %d\n", &cpu); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)’: util_lib/util_constraints_list.c:2918:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2918 | fscanf (fp, "%d\n", &max_nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2923:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2923 | fscanf (fp, "%*s %d %*s\n", &l); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2955:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2955 | fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2980:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 2980 | fgets (line , 200 , fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)’: util_lib/util_constraints_list.c:4054:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4054 | fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘char* make_aln_command(TC_method*, char*, char*)’: util_lib/util_constraints_list.c:1287:21: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1287 | sprintf ( buf, "%s %s %s%s %s %s%s %s", m->executable, m->param1, m->in_flag, seq,m->param2, m->out_flag,aln, m->param); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)’: util_lib/util_constraints_list.c:4923:19: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4923 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:4924:23: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4924 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)’: util_lib/util_constraints_list.c:695:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 695 | sprintf ( aln_mode, "%s", method->aln_mode); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:696:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 696 | sprintf ( out_mode, "%s", method->out_mode); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/aarch64-linux-gnu/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_declare.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_declare.c:37: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/util_declare.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_domain_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_domain_constraints_list.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/util_domain_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_dps.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_dps.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/util_dps.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_job_handling.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_job_handling.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/util_job_handling.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_make_tree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_make_tree.c:33: ./programmes_define.h:379:9: warning: ISO C++11 requires whitespace after the macro name 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ^~~~~ ./programmes_define.h:380:9: warning: ISO C++11 requires whitespace after the macro name 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ^~~~~ ./programmes_define.h:380: warning: "x3dna" redefined 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:379: note: this is the location of the previous definition 379 | #define x3dna-ssr_4_TCOFFEE "x3dna" | ./programmes_define.h:381:9: warning: ISO C++11 requires whitespace after the macro name 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ^~~~~ ./programmes_define.h:381: warning: "x3dna" redefined 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:380: note: this is the location of the previous definition 380 | #define x3dna-ssr_type "RNA_secondarystructure_predictor" | ./programmes_define.h:382:9: warning: ISO C++11 requires whitespace after the macro name 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ^~~~~ ./programmes_define.h:382: warning: "x3dna" redefined 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:381: note: this is the location of the previous definition 381 | #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" | ./programmes_define.h:383:9: warning: ISO C++11 requires whitespace after the macro name 383 | #define x3dna-ssr_mode "saracoffee" | ^~~~~ ./programmes_define.h:383: warning: "x3dna" redefined 383 | #define x3dna-ssr_mode "saracoffee" | ./programmes_define.h:382: note: this is the location of the previous definition 382 | #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" | ./programmes_define.h:384:9: warning: ISO C++11 requires whitespace after the macro name 384 | #define x3dna-ssr_update_action "never" | ^~~~~ ./programmes_define.h:384: warning: "x3dna" redefined 384 | #define x3dna-ssr_update_action "never" | ./programmes_define.h:383: note: this is the location of the previous definition 383 | #define x3dna-ssr_mode "saracoffee" | In file included from ./io_lib_header.h:33, from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_make_tree.c: In function ‘tnode* redundate(Sequence*, NT_node, char*, char*)’: util_lib/util_make_tree.c:66:1: warning: no return statement in function returning non-void [-Wreturn-type] 66 | } | ^ util_lib/util_make_tree.c: In function ‘char* seq2co_aln_file(char*, char*)’: util_lib/util_make_tree.c:124:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 124 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:127:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 127 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* seq2mafft_aln_file(char*, char*)’: util_lib/util_make_tree.c:157:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 157 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:159:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 159 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* seq2cw_aln_file(char*, char*)’: util_lib/util_make_tree.c:189:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 189 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:191:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 191 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* prf_pair2cw_aln_file(char*, char*, char*)’: util_lib/util_make_tree.c:222:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 222 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:225:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 225 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns1_dnd(Sequence*)’: util_lib/util_make_tree.c:1854:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1854 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1867:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1867 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns2_dnd(Sequence*)’: util_lib/util_make_tree.c:1883:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1883 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1896:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1896 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2mafft_dnd(Sequence*)’: util_lib/util_make_tree.c:1912:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1912 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1925:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1925 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2parttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1942:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1942 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1955:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1955 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2dpparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1972:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1972 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1987:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1987 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fastparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:2005:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2005 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2018:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2018 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cwquick_dnd(Sequence*)’: util_lib/util_make_tree.c:2034:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2034 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2042:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2042 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_dnd(Sequence*)’: util_lib/util_make_tree.c:2059:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2059 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2067:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2067 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* aln2cw_tree(Alignment*)’: util_lib/util_make_tree.c:2087:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2087 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2094:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2094 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_tree(Sequence*)’: util_lib/util_make_tree.c:2109:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2109 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2118:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2118 | chdir (cdir); | ~~~~~~~~~^~~~~~ Linking... /usr/lib/gcc-cross/aarch64-linux-gnu/9/../../../../aarch64-linux-gnu/bin/ld: dp_lib/util_dp_drivers.o: in function `hh_pair(TC_method*, char*, Constraint_list*)': ./t_coffee_source/dp_lib/util_dp_drivers.c:1160: warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/<>/t_coffee_source' make[1]: Leaving directory '/<>' dh_auto_test -a -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --sourcedirectory=t_coffee_source dh_testroot -a -O--sourcedirectory=t_coffee_source dh_prep -a -O--sourcedirectory=t_coffee_source dh_auto_install -a -O--sourcedirectory=t_coffee_source dh_install -a -O--sourcedirectory=t_coffee_source dh_installdocs -a -O--sourcedirectory=t_coffee_source dh_installchangelogs -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples mkdir -p /<>/debian/t-coffee/usr/share/doc/t-coffee/examples; cp -aR example/* /<>/debian/t-coffee/usr/share/doc/t-coffee/examples/; make[1]: Leaving directory '/<>' dh_installman -a -O--sourcedirectory=t_coffee_source dh_installinit -a -O--sourcedirectory=t_coffee_source dh_installsystemduser -a -O--sourcedirectory=t_coffee_source dh_perl -a -O--sourcedirectory=t_coffee_source dh_perl: /usr/lib/aarch64-linux-gnu/perl/cross-config-5.30.0/Config.pm does not exist (missing build dependency on perl-xs-dev?) dh_link -a -O--sourcedirectory=t_coffee_source dh_strip_nondeterminism -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_compress make[1]: Entering directory '/<>' #Compressing most of the files in examples/ makes them unusable dh_compress -Xt-coffee-examples ( cd debian/t-coffee-examples/ && \ chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \ gzip -9 -n usr/share/doc/t-coffee-examples/changelog.Debian ) || true /bin/sh: 1: cd: can't cd to debian/t-coffee-examples/ make[1]: Leaving directory '/<>' dh_fixperms -a -O--sourcedirectory=t_coffee_source dh_missing -a -O--sourcedirectory=t_coffee_source dh_dwz -a -O--sourcedirectory=t_coffee_source dh_strip -a -O--sourcedirectory=t_coffee_source dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -O--sourcedirectory=t_coffee_source dh_installdeb -a -O--sourcedirectory=t_coffee_source dh_gencontrol -a -O--sourcedirectory=t_coffee_source dh_md5sums -a -O--sourcedirectory=t_coffee_source dh_builddeb -a -O--sourcedirectory=t_coffee_source dpkg-deb: building package 't-coffee' in '../t-coffee_12.00.7fb08c2-4_arm64.deb'. dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_12.00.7fb08c2-4_arm64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../t-coffee_12.00.7fb08c2-4_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-11-11T20:36:04Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ t-coffee_12.00.7fb08c2-4_arm64.changes: --------------------------------------- Format: 1.8 Date: Fri, 15 Feb 2019 07:43:22 +0100 Source: t-coffee Binary: t-coffee t-coffee-dbgsym Built-For-Profiles: cross nocheck Architecture: arm64 Version: 12.00.7fb08c2-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: t-coffee - Multiple Sequence Alignment Closes: 922196 Changes: t-coffee (12.00.7fb08c2-4) unstable; urgency=medium . [ Helmut Grohne ] * Fix FTCBFS: Pass C++ compiler as CC. Closes: #922196 Checksums-Sha1: ad8f39dab752597c08c6d1c1128db31c1c098df8 2845068 t-coffee-dbgsym_12.00.7fb08c2-4_arm64.deb 09a23b470593bf996f3c3a6917f3d5c1dd242cca 4725 t-coffee_12.00.7fb08c2-4_arm64.buildinfo 4fd0fb008c87b786249f7b5b51951183bb6515d1 1409324 t-coffee_12.00.7fb08c2-4_arm64.deb Checksums-Sha256: 9fa0ff093711578e110600b8e255a4d07aa7b9fd6a9422fd0184ac75a3afa3af 2845068 t-coffee-dbgsym_12.00.7fb08c2-4_arm64.deb a4e688afb95e36f65fe038ed31f7d9084fac81951307c92993a35a8e7f06521f 4725 t-coffee_12.00.7fb08c2-4_arm64.buildinfo 72db48a1afd376ca370ae1d0af5eb3992dfa8a15fa309dffd9ea8750e55f302b 1409324 t-coffee_12.00.7fb08c2-4_arm64.deb Files: e06c2a68315d7c1bb4db6fc3900c4b4b 2845068 debug optional t-coffee-dbgsym_12.00.7fb08c2-4_arm64.deb a4c7566a90fcfad33737216211136e2f 4725 science optional t-coffee_12.00.7fb08c2-4_arm64.buildinfo 63d60a29027ffee9448bc032c0e38ae9 1409324 science optional t-coffee_12.00.7fb08c2-4_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: arm64 Version: 12.00.7fb08c2-4 Checksums-Md5: e06c2a68315d7c1bb4db6fc3900c4b4b 2845068 t-coffee-dbgsym_12.00.7fb08c2-4_arm64.deb 63d60a29027ffee9448bc032c0e38ae9 1409324 t-coffee_12.00.7fb08c2-4_arm64.deb Checksums-Sha1: ad8f39dab752597c08c6d1c1128db31c1c098df8 2845068 t-coffee-dbgsym_12.00.7fb08c2-4_arm64.deb 4fd0fb008c87b786249f7b5b51951183bb6515d1 1409324 t-coffee_12.00.7fb08c2-4_arm64.deb Checksums-Sha256: 9fa0ff093711578e110600b8e255a4d07aa7b9fd6a9422fd0184ac75a3afa3af 2845068 t-coffee-dbgsym_12.00.7fb08c2-4_arm64.deb 72db48a1afd376ca370ae1d0af5eb3992dfa8a15fa309dffd9ea8750e55f302b 1409324 t-coffee_12.00.7fb08c2-4_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 11 Nov 2019 20:36:03 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.46), bash (= 5.0-5), binutils (= 2.33.1-2), binutils-common (= 2.33.1-2), binutils-x86-64-linux-gnu (= 2.33.1-2), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.8), bzip2 (= 1.0.8-2), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-8 (= 8.3.0-24), cpp-9 (= 9.2.1-19), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.7.1), debianutils (= 4.9), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.2-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-2), fdisk (= 2.34-0.1), file (= 1:5.37-6), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.2.1-19), gcc (= 4:9.2.1-3.1), gcc-8 (= 8.3.0-24), gcc-8-base (= 8.3.0-24), gcc-9 (= 9.2.1-19), gcc-9-base (= 9.2.1-19), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3+b1), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-5), libarchive-zip-perl (= 1.67-1), libasan5 (= 9.2.1-19), libatomic1 (= 9.2.1-19), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2), libbinutils (= 2.33.1-2), libblkid1 (= 2.34-0.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.29-3), libc-dev-bin (= 2.29-3), libc6 (= 2.29-3), libc6-dev (= 2.29-3), libcap-ng0 (= 0.7.9-2.1), libcc1-0 (= 9.2.1-19), libcroco3 (= 0.6.13-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.250), libdebhelper-perl (= 12.7.1), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libfdisk1 (= 2.34-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.6.2-1), libgcc-8-dev (= 8.3.0-24), libgcc-9-dev (= 9.2.1-19), libgcc1 (= 1:9.2.1-19), libgcrypt20 (= 1.8.5-3), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.62.2-3), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 9.2.1-19), libgpg-error0 (= 1.36-7), libicu63 (= 63.2-2), libisl21 (= 0.21-2), libitm1 (= 9.2.1-19), liblsan0 (= 9.2.1-19), liblz4-1 (= 1.9.2-1), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.37-6), libmagic1 (= 1:5.37-6), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-24), libncurses6 (= 6.1+20191019-1), libncursesw6 (= 6.1+20191019-1), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.32-5+b1), libpcre3 (= 2:8.39-12+b1), libperl5.30 (= 5.30.0-9), libpipeline1 (= 1.5.1-2), libquadmath0 (= 9.2.1-19), libseccomp2 (= 2.4.1-2), libselinux1 (= 2.9-2+b2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libstdc++-9-dev (= 9.2.1-19), libstdc++6 (= 9.2.1-19), libsub-override-perl (= 0.09-2), libsystemd0 (= 243-5), libtinfo6 (= 6.1+20191019-1), libtool (= 2.4.6-11), libtsan0 (= 9.2.1-19), libubsan1 (= 9.2.1-19), libuchardet0 (= 0.0.6-3), libudev1 (= 243-5), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 5.3.9-1), login (= 1:4.7-2), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.0-1), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20191019-1), ncurses-bin (= 6.1+20191019-1), patch (= 2.7.6-6), perl (= 5.30.0-9), perl-base (= 5.30.0-9), perl-modules-5.30 (= 5.30.0-9), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.96-1), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-1+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1550213002" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ t-coffee-dbgsym_12.00.7fb08c2-4_arm64.deb ----------------------------------------- new Debian package, version 2.0. size 2845068 bytes: control archive=540 bytes. 391 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: t-coffee-dbgsym Source: t-coffee Version: 12.00.7fb08c2-4 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 3006 Depends: t-coffee (= 12.00.7fb08c2-4) Section: debug Priority: optional Description: debug symbols for t-coffee Build-Ids: d29b64885e1602120df058d763b49413eea0adad drwxr-xr-x root/root 0 2019-02-15 06:43 ./ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/lib/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/lib/debug/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/lib/debug/.build-id/d2/ -rw-r--r-- root/root 3067424 2019-02-15 06:43 ./usr/lib/debug/.build-id/d2/9b64885e1602120df058d763b49413eea0adad.debug drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-02-15 06:43 ./usr/share/doc/t-coffee-dbgsym -> t-coffee t-coffee_12.00.7fb08c2-4_arm64.deb ---------------------------------- new Debian package, version 2.0. size 1409324 bytes: control archive=5728 bytes. 1602 bytes, 29 lines control 16306 bytes, 197 lines md5sums Package: t-coffee Version: 12.00.7fb08c2-4 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 7281 Depends: libc6 (>= 2.29), libgcc1 (>= 1:3.0), libstdc++6 (>= 4.1.1) Recommends: amap-align, clustalo, clustalw, dialign-tx, fsa, kalign, libsoap-lite-perl, libxml-simple-perl, mafft, muscle, mustang, ncbi-blast+, poa, prank, probcons, proda, tm-align Suggests: boxshade, seaview, t-coffee-examples Section: science Priority: optional Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Description: Multiple Sequence Alignment T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. . T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information . T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. 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./usr/share/doc/t-coffee/examples/struc7.pdb -rw-r--r-- root/root 113211 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/struc8.pdb -rw-r--r-- root/root 3876 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/sv.aln -rw-r--r-- root/root 106 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/sv.dnd -rw-r--r-- root/root 1358 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/sv.fasta -rw-r--r-- root/root 3277 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/sv.maln -rw-r--r-- root/root 57 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/template_file.template -rw-r--r-- root/root 85 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/template_file6.template -rw-r--r-- root/root 108 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/template_file7.template -rw-r--r-- root/root 12825 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/test.lib -rw-r--r-- root/root 37563 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/test.tc_lib -rw-r--r-- root/root 12701 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/test_lib.tc_lib -rw-r--r-- root/root 2387 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/three_cdna.fasta -rw-r--r-- root/root 1299 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/three_pdb.aln -rw-r--r-- root/root 51 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/three_pdb.dnd -rw-r--r-- root/root 687 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/three_pdb.fasta -rw-r--r-- root/root 2456 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/three_pdb_two_seq.aln -rw-r--r-- root/root 140 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/three_pdb_two_seq.dnd -rw-r--r-- root/root 1391 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/three_pdb_two_seq.fasta -rw-r--r-- root/root 7699 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/tlara_tRNA_aln10.output -rw-r--r-- root/root 8296 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/tlara_tRNA_aln50.output -rw-r--r-- root/root 8331 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/tlara_tRNA_aln51.output -rw-r--r-- root/root 62 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/two_profiles.template_file -rw-r--r-- root/root 24553 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/x -rw-r--r-- root/root 2662 2019-02-15 06:43 ./usr/share/doc/t-coffee/run-unit-test drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/man/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/man/man1/ -rw-r--r-- root/root 1463 2019-02-15 06:43 ./usr/share/man/man1/t_coffee.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [532 B] Get:5 copy:/<>/apt_archive ./ Packages [619 B] Fetched 2114 B in 0s (94.4 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libfreezethaw-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libpackage-stash-xs-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:arm64 t1utils 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. Need to get 8854 kB of archives. After this operation, 25.0 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-3 [72.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1+b1 [33.6 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.17-3 [524 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.30.1-1 [649 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.17-3 [881 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b2 [71.3 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b2 [11.3 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b1 [15.9 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b2 [25.6 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b2 [46.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.24-1 [18.6 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libberkeleydb-perl amd64 0.62-1+b1 [124 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b4 [105 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.44-1 [223 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:29 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http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.21-1 [95.5 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.20-1 [367 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main 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[33.6 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-2 [101 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libmldbm-perl all 2.05-2 [18.4 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003006-1 [58.7 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.004004-1 [266 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.80+repack-2+b1 [34.8 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.34.0 [1276 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8854 kB in 0s (37.2 MB/s) Selecting previously unselected package readline-common. (Reading database ... 21136 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-3_all.deb ... Unpacking readline-common (8.0-3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-3_amd64.deb ... Unpacking libreadline8:amd64 (8.0-3) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.62-1+b1_amd64.deb ... Unpacking diffstat (1.62-1+b1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.17-3_amd64.deb ... Unpacking gpgconf (2.2.17-3) ... Selecting previously unselected package libsqlite3-0:amd64. 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Setting up libipc-run-perl (20180523.0-2) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsub-name-perl (0.26-1) ... Setting up libpath-tiny-perl (0.108-1) ... Setting up librole-tiny-perl (2.001004-1) ... Setting up netbase (5.6) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b3) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (8.0-3) ... Setting up liburi-perl (1.76-1) ... Setting up libnet-ssleay-perl (1.88-1+b1) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b5) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up libtype-tiny-perl (1.004004-1) ... Setting up libnet-dns-perl (1.20-1) ... Setting up libdevel-callchecker-perl (0.008-1+b1) ... Setting up libio-async-loop-epoll-perl (0.20-1) ... Setting up libhtml-parser-perl (3.72-3+b4) ... Setting up gpgconf (2.2.17-3) ... Setting up libio-socket-ssl-perl (2.066-1) ... Setting up gpg (2.2.17-3) ... Setting up libparams-classify-perl (0.015-1+b2) ... Setting up libcgi-pm-perl (4.44-1) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libmailtools-perl (2.21-1) ... Setting up libmodule-implementation-perl (0.09-1) ... Setting up libemail-valid-perl (1.202-1) ... Setting up libpackage-stash-perl (0.38-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.003006-1) ... Setting up libb-hooks-endofscope-perl (0.24-1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.34.0) ... Setting up sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ... Processing triggers for man-db (2.9.0-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.29-3) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 69444 Build-Time: 134 Distribution: unstable Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 17 Job: t-coffee_12.00.7fb08c2-4 Lintian: pass Machine Architecture: amd64 Package: t-coffee Package-Time: 165 Source-Version: 12.00.7fb08c2-4 Space: 69444 Status: successful Version: 12.00.7fb08c2-4 -------------------------------------------------------------------------------- Finished at 2019-11-11T20:36:04Z Build needed 00:02:45, 69444k disk space