sbuild (Debian sbuild) 0.81.2+deb11u1 (31 August 2022) on debian-ci-siliconvalley +==============================================================================+ | t-coffee 13.41.0.28bdc39+dfsg-4 (armhf) Wed, 14 Sep 2022 16:40:43 +0000 | +==============================================================================+ Package: t-coffee Version: 13.41.0.28bdc39+dfsg-4 Source Version: 13.41.0.28bdc39+dfsg-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-16b06c1b-0fc5-42dd-86bf-d29d6e4ec442' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-VRrJEC/resolver-0atGCN' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [192 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2022-09-14-0803.07-F-2022-09-14-0206.30.pdiff [12.4 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2022-09-14-0803.07-F-2022-09-14-0206.30.pdiff [15.3 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2022-09-14-0803.07-F-2022-09-14-0206.30.pdiff [12.4 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2022-09-14-0803.07-F-2022-09-14-0206.30.pdiff [15.3 kB] Get:6 http://localhost:3142/debian sid/main armhf Packages [8959 kB] Fetched 9306 kB in 3s (3575 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... 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 3249 kB of source archives. Get:1 http://localhost:3142/debian sid/main t-coffee 13.41.0.28bdc39+dfsg-4 (dsc) [2196 B] Get:2 http://localhost:3142/debian sid/main t-coffee 13.41.0.28bdc39+dfsg-4 (tar) [3230 kB] Get:3 http://localhost:3142/debian sid/main t-coffee 13.41.0.28bdc39+dfsg-4 (diff) [17.1 kB] Fetched 3249 kB in 12s (282 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/t-coffee-VRrJEC/t-coffee-13.41.0.28bdc39+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-VRrJEC' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper-compat (= 12), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf 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 [404 B] Get:5 copy:/<>/apt_archive ./ Packages [490 B] Fetched 1851 B in 0s (0 B/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-arm-linux-gnueabihf bsdextrautils cpp-12-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-11-base:armhf gcc-12-arm-linux-gnueabihf gcc-12-arm-linux-gnueabihf-base gcc-12-base:armhf gcc-12-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:armhf libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libcom-err2:armhf libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armhf libcrypt1:armhf libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:armhf libgcc-12-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libgomp1:armhf libgomp1-armhf-cross libgssapi-krb5-2:armhf libicu71 libio-string-perl libk5crypto3:armhf libkeyutils1:armhf libkrb5-3:armhf libkrb5support0:armhf liblocale-gettext-perl libmagic-mgc libmagic1 libnsl-dev:armhf libnsl2:armhf libpipeline1 libssl3:armhf libstdc++-11-dev:armhf libstdc++-12-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtirpc-dev:armhf libtirpc3:armhf libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-12-locales cpp-12-doc cpp-doc dh-make binutils-multiarch gcc-12-doc manpages-dev flex bison gdb-arm-linux-gnueabihf gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armhf libc-l10n:armhf locales:armhf libnss-nis:armhf libnss-nisplus:armhf manpages-dev:armhf krb5-doc:armhf krb5-user:armhf libstdc++-11-doc:armhf 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:armhf libarchive-cpio-perl krb5-locales:armhf 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-arm-linux-gnueabihf bsdextrautils cpp-12-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-11-base:armhf gcc-12-arm-linux-gnueabihf gcc-12-arm-linux-gnueabihf-base gcc-12-base:armhf gcc-12-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:armhf libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libcom-err2:armhf libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armhf libcrypt1:armhf libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:armhf libgcc-12-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libgomp1:armhf libgomp1-armhf-cross libgssapi-krb5-2:armhf libicu71 libio-string-perl libk5crypto3:armhf libkeyutils1:armhf libkrb5-3:armhf libkrb5support0:armhf liblocale-gettext-perl libmagic-mgc libmagic1 libnsl-dev:armhf libnsl2:armhf libpipeline1 libssl3:armhf libstdc++-11-dev:armhf libstdc++-12-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtirpc-dev:armhf libtirpc3:armhf libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:armhf sensible-utils ucf 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 84.4 MB of archives. After this operation, 329 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-4+b2 [19.2 kB] Get:3 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:4 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.41-4 [295 kB] Get:5 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.41-4 [129 kB] Get:6 http://localhost:3142/debian sid/main amd64 file amd64 1:5.41-4 [67.0 kB] Get:7 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-9 [175 kB] Get:8 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:9 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.22.4-8 [936 kB] Get:10 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.38.1-1 [145 kB] Get:11 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.6-2 [39.4 kB] Get:12 http://localhost:3142/debian sid/main amd64 man-db amd64 2.10.2-3 [1413 kB] Get:13 http://localhost:3142/debian sid/main amd64 ucf all 3.0043 [74.0 kB] Get:14 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-1 [291 kB] Get:15 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-2 [343 kB] Get:16 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:17 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:18 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-9 [510 kB] Get:19 http://localhost:3142/debian sid/main amd64 binutils-arm-linux-gnueabihf amd64 2.38.90.20220713-2 [3174 kB] Get:20 http://localhost:3142/debian sid/main amd64 gcc-12-arm-linux-gnueabihf-base amd64 12.2.0-2cross2 [208 kB] Get:21 http://localhost:3142/debian sid/main amd64 cpp-12-arm-linux-gnueabihf amd64 12.2.0-2cross2 [8665 kB] Get:22 http://localhost:3142/debian sid/main amd64 cpp-arm-linux-gnueabihf amd64 4:12.2.0-1 [17.2 kB] Get:23 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:24 http://localhost:3142/debian sid/main amd64 gcc-12-cross-base all 12.2.0-2cross2 [204 kB] Get:25 http://localhost:3142/debian sid/main amd64 libc6-armhf-cross all 2.34-3cross1 [1073 kB] Get:26 http://localhost:3142/debian sid/main amd64 libgcc-s1-armhf-cross all 12.2.0-2cross2 [36.6 kB] Get:27 http://localhost:3142/debian sid/main amd64 libgomp1-armhf-cross all 12.2.0-2cross2 [94.8 kB] Get:28 http://localhost:3142/debian sid/main amd64 libatomic1-armhf-cross all 12.2.0-2cross2 [6780 B] Get:29 http://localhost:3142/debian sid/main amd64 libasan8-armhf-cross all 12.2.0-2cross2 [2114 kB] Get:30 http://localhost:3142/debian sid/main amd64 libstdc++6-armhf-cross all 12.2.0-2cross2 [476 kB] Get:31 http://localhost:3142/debian sid/main amd64 libubsan1-armhf-cross all 12.2.0-2cross2 [855 kB] Get:32 http://localhost:3142/debian sid/main amd64 libgcc-12-dev-armhf-cross all 12.2.0-2cross2 [743 kB] Get:33 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libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:54 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:55 http://localhost:3142/debian sid/main amd64 crossbuild-essential-armhf all 12.9 [6708 B] Get:56 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.9.1 [196 kB] Get:57 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-4 [526 kB] Get:58 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:59 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:60 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-3 [10.4 kB] Get:61 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB] Get:62 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB] Get:63 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.187-2 [179 kB] Get:64 http://localhost:3142/debian sid/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:65 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-9 [1315 kB] Get:66 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:67 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:68 http://localhost:3142/debian sid/main amd64 debhelper all 13.9.1 [1071 kB] Get:69 http://localhost:3142/debian sid/main armhf gcc-11-base armhf 11.3.0-6 [209 kB] Get:70 http://localhost:3142/debian sid/main armhf gcc-12-base armhf 12.2.0-2 [208 kB] Get:71 http://localhost:3142/debian sid/main armhf libgcc-s1 armhf 12.2.0-2 [36.6 kB] Get:72 http://localhost:3142/debian sid/main armhf libc6 armhf 2.34-8 [2388 kB] Get:73 http://localhost:3142/debian sid/main armhf libasan6 armhf 11.3.0-6 [1970 kB] Get:74 http://localhost:3142/debian sid/main armhf libatomic1 armhf 12.2.0-2 [6992 B] Get:75 http://localhost:3142/debian sid/main armhf linux-libc-dev armhf 5.19.6-1 [1591 kB] Get:76 http://localhost:3142/debian sid/main armhf libcrypt1 armhf 1:4.4.28-2 [96.2 kB] Get:77 http://localhost:3142/debian sid/main armhf libcrypt-dev armhf 1:4.4.28-2 [125 kB] Get:78 http://localhost:3142/debian sid/main armhf libcom-err2 armhf 1.46.6~rc1-1 [75.1 kB] Get:79 http://localhost:3142/debian sid/main armhf libkrb5support0 armhf 1.20-1 [62.8 kB] Get:80 http://localhost:3142/debian sid/main armhf libk5crypto3 armhf 1.20-1 [108 kB] Get:81 http://localhost:3142/debian sid/main armhf libkeyutils1 armhf 1.6.3-1 [14.7 kB] Get:82 http://localhost:3142/debian sid/main armhf libssl3 armhf 3.0.5-2 [1678 kB] Get:83 http://localhost:3142/debian sid/main armhf libkrb5-3 armhf 1.20-1 [320 kB] Get:84 http://localhost:3142/debian sid/main armhf libgssapi-krb5-2 armhf 1.20-1 [144 kB] Get:85 http://localhost:3142/debian sid/main armhf libtirpc3 armhf 1.3.3+ds-1 [72.9 kB] Get:86 http://localhost:3142/debian sid/main armhf libnsl2 armhf 1.3.0-2 [33.9 kB] Get:87 http://localhost:3142/debian sid/main armhf libtirpc-dev armhf 1.3.3+ds-1 [182 kB] Get:88 http://localhost:3142/debian sid/main armhf libnsl-dev armhf 1.3.0-2 [62.1 kB] Get:89 http://localhost:3142/debian sid/main armhf libc6-dev armhf 2.34-8 [1446 kB] Get:90 http://localhost:3142/debian sid/main armhf libgomp1 armhf 12.2.0-2 [97.0 kB] Get:91 http://localhost:3142/debian sid/main armhf libstdc++6 armhf 12.2.0-2 [519 kB] Get:92 http://localhost:3142/debian sid/main armhf libubsan1 armhf 12.2.0-2 [856 kB] Get:93 http://localhost:3142/debian sid/main armhf libgcc-11-dev armhf 11.3.0-6 [708 kB] Get:94 http://localhost:3142/debian sid/main armhf libstdc++-11-dev armhf 11.3.0-6 [1981 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 84.4 MB in 0s (182 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 13611 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-4+b2_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.41-4_amd64.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.41-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.41-4) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.41-4_amd64.deb ... Unpacking file (1:5.41-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-9_amd64.deb ... Unpacking gettext-base (0.21-9) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libgcc-s1-armhf-cross (12.2.0-2cross2) ... Setting up libdebhelper-perl (13.9.1) ... Setting up libmagic1:amd64 (1:5.41-4) ... Setting up linux-libc-dev:armhf (5.19.6-1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-9) ... Setting up m4 (1.4.19-1) ... Setting up file (1:5.41-4) ... Setting up libatomic1-armhf-cross (12.2.0-2cross2) ... Setting up libyaml-perl (1.30-1) ... Setting up gcc-12-base:armhf (12.2.0-2) ... Setting up libxml-sax-base-perl (1.09-2) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up libstdc++6-armhf-cross (12.2.0-2cross2) ... Setting up gcc-12-arm-linux-gnueabihf-base:amd64 (12.2.0-2cross2) ... Setting up linux-libc-dev-armhf-cross (5.18.16-1cross1) ... Setting up autopoint (0.21-9) ... Setting up libubsan1-armhf-cross (12.2.0-2cross2) ... Setting up autoconf (2.71-2) ... Setting up sensible-utils (0.0.17) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-3) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up binutils-arm-linux-gnueabihf (2.38.90.20220713-2) ... Setting up libelf1:amd64 (0.187-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1+b1) ... Setting up liblocale-gettext-perl (1.07-4+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgomp1-armhf-cross (12.2.0-2cross2) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libasan8-armhf-cross (12.2.0-2cross2) ... Setting up gettext (0.21-9) ... Setting up libtool (2.4.7-4) ... Setting up libc6-dev-armhf-cross (2.34-3cross1) ... Setting up cpp-12-arm-linux-gnueabihf (12.2.0-2cross2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up dh-autoreconf (20) ... Setting up ucf (3.0043) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1) ... Setting up libgcc-12-dev-armhf-cross (12.2.0-2cross2) ... Setting up groff-base (1.22.4-8) ... Setting up cpp-arm-linux-gnueabihf (4:12.2.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.10.2-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... 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... grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / Setting up libstdc++-12-dev-armhf-cross (12.2.0-2cross2) ... Setting up gcc-12-arm-linux-gnueabihf (12.2.0-2cross2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1) ... 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... grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / Setting up gcc-arm-linux-gnueabihf (4:12.2.0-1) ... Setting up g++-12-arm-linux-gnueabihf (12.2.0-2cross2) ... Setting up debhelper (13.9.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-arm-linux-gnueabihf (4:12.2.0-1) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up crossbuild-essential-armhf (12.9) ... Setting up libgcc-s1:armhf (12.2.0-2) ... Setting up libc6:armhf (2.34-8) ... Setting up libstdc++6:armhf (12.2.0-2) ... Setting up libkeyutils1:armhf (1.6.3-1) ... Setting up libssl3:armhf (3.0.5-2) ... Setting up libcrypt1:armhf (1:4.4.28-2) ... Setting up libcom-err2:armhf (1.46.6~rc1-1) ... Setting up libgomp1:armhf (12.2.0-2) ... Setting up libasan6:armhf (11.3.0-6) ... Setting up libkrb5support0:armhf (1.20-1) ... Setting up libatomic1:armhf (12.2.0-2) ... Setting up libk5crypto3:armhf (1.20-1) ... Setting up libubsan1:armhf (12.2.0-2) ... Setting up libgcc-11-dev:armhf (11.3.0-6) ... Setting up libcrypt-dev:armhf (1:4.4.28-2) ... Setting up libkrb5-3:armhf (1.20-1) ... Setting up libgssapi-krb5-2:armhf (1.20-1) ... Setting up libtirpc3:armhf (1.3.3+ds-1) ... Setting up libtirpc-dev:armhf (1.3.3+ds-1) ... Setting up libnsl2:armhf (1.3.0-2) ... Setting up libnsl-dev:armhf (1.3.0-2) ... Setting up libc6-dev:armhf (2.34-8) ... Setting up libstdc++-11-dev:armhf (11.3.0-6) ... Setting up sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.34-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) amd64 (x86_64) Toolchain package versions: binutils_2.38.90.20220713-2 dpkg-dev_1.21.9 g++-11_11.3.0-6 g++-12_12.2.0-2 gcc-11_11.3.0-6 gcc-12_12.2.0-2 libc6-dev_2.34-8 libstdc++-11-dev_11.3.0-6 libstdc++-12-dev_12.2.0-2 libstdc++-12-dev-armhf-cross_12.2.0-2cross2 libstdc++6_12.2.0-2 libstdc++6-armhf-cross_12.2.0-2cross2 linux-libc-dev_5.19.6-1 Package versions: adduser_3.129 apt_2.5.2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: t-coffee Binary: t-coffee, t-coffee-examples Architecture: any all Version: 13.41.0.28bdc39+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://www.tcoffee.org/Projects/tcoffee/index.html Standards-Version: 4.5.0 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-compat (= 12) Package-List: t-coffee deb science optional arch=any t-coffee-examples deb science optional arch=all Checksums-Sha1: fab3dbecabca6c0248a8c8a0336f5995be3b4e3f 3229824 t-coffee_13.41.0.28bdc39+dfsg.orig.tar.xz 40c1a9f0ea7b599343d3a16f965b32e0ef77faec 17124 t-coffee_13.41.0.28bdc39+dfsg-4.debian.tar.xz Checksums-Sha256: a1b37c67caba574ccf53c38279863dffa67d62232e017317754b5eb29db60746 3229824 t-coffee_13.41.0.28bdc39+dfsg.orig.tar.xz 36b1a1da7837f2206d5892bca66d9a9257a349cedadb7124302bd2f1491c4a00 17124 t-coffee_13.41.0.28bdc39+dfsg-4.debian.tar.xz Files: 74a867b32054875c3ce5f2a11767d610 3229824 t-coffee_13.41.0.28bdc39+dfsg.orig.tar.xz f284e548233a1d9726e0a0a0baedb510 17124 t-coffee_13.41.0.28bdc39+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl7qcV0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHNaQ//bgReo0RgFiZiS7+jiL6sZz3j8nI+n9gU g2tKwflXxBbo0COzy9lBqIimUOiTtX4rXx8gCPWoz8YmAWUy/5T2LuXrKO5Pt4Ks HRfyNNjucPMD1zEB1SgaCBvMfee+i20aQmxl2TFFSSohNf1V/IrYZH/Dd2PEUzc2 D+3c5aCFirl5WZyv4KprhCF2TzGuSICsbE4TZlwcp5T5T7uM/QJsUMLokUAmn1ye mv/sVETbsyxIADtKyfdXOuoZH1okbA9jdBGLooGbrNQCVeCGHrqo23S/kTMpXYQM nvJaIhDS5vfobvvrFSbX6ZkqQGxW/RiuKRq4PlAzCkeBQ+ulpQJcVufRgaBfkRQM 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patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying bypass_legacy_blast.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 verbose_build dpkg-source: info: applying increase_max_pid.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.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-16b06c1b-0fc5-42dd-86bf-d29d6e4ec442 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 13.41.0.28bdc39+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Etienne Mollier dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf 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 armhf 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/ph_tree_scan.txt 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 binary-arch dh binary-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 -ffile-prefix-map=/<>=. -fstack-protector-strong" 'CC=$(CXX)' all cd t_coffee_source && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong" CC=\$\(CXX\) all make[2]: Entering directory '/<>/t_coffee_source' CC dev_lib/dev1.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c 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:89:26: warning: too many arguments for format [-Wformat-extra-args] 89 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ CC dp_lib/CUSTOM_evaluate_for_struc.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c 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:3070:67: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘int’ [-Wformat=] 3070 | 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:3070:81: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘double’ [-Wformat=] 3070 | 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:3070:93: warning: format ‘%f’ expects argument of type ‘double’, but argument 6 has type ‘int’ [-Wformat=] 3070 | 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:3070:109: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘double’ [-Wformat=] 3070 | 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:809:26: 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:814:26: 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:819:18: 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:7626:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/evaluate_dirichlet.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c 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:317:23: 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:319:23: 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:323:31: 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:326:23: 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c 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:127:18: 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/arm-linux-gnueabihf/include/stdio.h:888, from dp_lib/pavie_dp.c:27: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’ at dp_lib/pavie_dp.c:1078:15: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 1004) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’: 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 function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’ at dp_lib/pavie_dp.c:1080:15: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 2003 bytes into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC dp_lib/showpair.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c 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 ‘Constraint_list* sap_pair(char*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2051 | register int a; | ^ 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:1080:17: 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:1108:17: 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:1149:15: 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:1160:23: 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:1161:23: 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:1164:23: 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:1211:17: 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:1280:13: 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:1363:28: 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:1717:15: 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:1774:15: 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:1906:15: 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:1981:15: 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:2073:17: 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:2121:24: 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:2122:23: 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:2142:23: 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:2256:13: 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:382:31: 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/arm-linux-gnueabihf/include/stdio.h:888, from dp_lib/util_dp_drivers.c:27: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Constraint_list* method2pw_cl(TC_method*, Constraint_list*)’ at dp_lib/util_dp_drivers.c:382:16: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* method2pw_cl(TC_method*, Constraint_list*)’: dp_lib/util_dp_drivers.c:373:30: 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 function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Constraint_list* method2pw_cl(TC_method*, Constraint_list*)’ at dp_lib/util_dp_drivers.c:373:15: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* method2pw_cl(TC_method*, Constraint_list*)’: 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 function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Constraint_list* method2pw_cl(TC_method*, Constraint_list*)’ at dp_lib/util_dp_drivers.c:386:33: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Alignment* realign_block(Alignment*, int, int, char*)’: dp_lib/util_dp_drivers.c:921:25: warning: ‘ -infile=’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); | ^~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Alignment* realign_block(Alignment*, int, int, char*)’ at dp_lib/util_dp_drivers.c:921:11: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 38 or more bytes (assuming 1037) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __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 function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)’ at dp_lib/util_dp_drivers.c:1854:11: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 71 or more bytes (assuming 5068) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __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 function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)’ at dp_lib/util_dp_drivers.c:3717:13: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_est.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c 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 | ^~~~~~~ dp_lib/util_dp_fasta_nw.c: In function ‘int* makepointtable(int*, int*, int)’: dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 157 | register int *p; | ^ CC dp_lib/util_dp_fasta_sw.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c 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:391:42: 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c 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 | ^~~~~~~ dp_lib/util_dp_sim.c: In function ‘int addnode(int, int, int, int, int, int, int)’: dp_lib/util_dp_sim.c:173:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 173 | register int d; | ^ dp_lib/util_dp_sim.c: In function ‘int sim_pair_wise_lalign(Alignment*, int*, int**, Constraint_list*)’: dp_lib/util_dp_sim.c:248:20: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 248 | vertexptr findmax(); /* return the largest score node */ | ^~ dp_lib/util_dp_sim.c:248:20: note: remove parentheses to default-initialize a variable 248 | vertexptr findmax(); /* return the largest score node */ | ^~ | -- dp_lib/util_dp_sim.c:248:20: note: or replace parentheses with braces to value-initialize a variable dp_lib/util_dp_sim.c: In function ‘int big_pass(int*, int*, int, int, int, int)’: dp_lib/util_dp_sim.c:481:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:481:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:482:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 482 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:483:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 483 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:484:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 484 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:485:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 485 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:486:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:486:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:487:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:487:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:488:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:488:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:489:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:489:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function ‘int locate(int*, int*, int)’: dp_lib/util_dp_sim.c:562:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:562:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:563:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 563 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:564:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 564 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:565:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 565 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:566:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 566 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:567:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:567:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:568:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:568:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:569:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:569:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:570:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:570:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:572:16: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 572 | int addnode(); /* function for inserting a node */ | ^~ dp_lib/util_dp_sim.c:572:16: note: remove parentheses to default-initialize a variable 572 | int addnode(); /* function for inserting a node */ | ^~ | -- dp_lib/util_dp_sim.c:572:16: note: or replace parentheses with braces to value-initialize a variable dp_lib/util_dp_sim.c: In function ‘int small_pass(int*, int*, int, int)’: dp_lib/util_dp_sim.c:786:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:786:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:787:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 787 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:788:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 788 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:789:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 789 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:790:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 790 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:791:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:791:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:792:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:792:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:793:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:793:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:794:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:794:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function ‘SIM_NODE* findmax()’: dp_lib/util_dp_sim.c:864:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c:864:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c: In function ‘int no_cross()’: dp_lib/util_dp_sim.c:883:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 883 | register int i; | ^ dp_lib/util_dp_sim.c: In function ‘int diff_sim(int*, int*, int, int, int, int)’: dp_lib/util_dp_sim.c:911:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:911:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:912:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ CC dp_lib/util_dp_ssec_pwaln.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c 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:434:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 434 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/diagonal.c:439:14: 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:440:14: 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:441:14: 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c 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:1924:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1924 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1929:14: 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:1930:14: 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:1931:14: 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:1976:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1976 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1980:22: 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:1981:22: 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:1982:22: 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:2115:15: 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:2262:15: 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:3201:15: 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:3323:14: 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:3326:14: 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:3329:14: 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:3331:14: 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:3333:14: 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:3352:22: 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:3502:15: 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:3575:14: 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:3577:14: 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:3579:14: 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:3581:14: 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:3643:14: 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c CC fastal/iteration.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c 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:185:14: 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:310:22: 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:435:15: 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:501:22: 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:504:22: 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:535:38: 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:563:14: 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:565:14: 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:567:14: 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:569:14: 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c 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 ‘void makepointtable_fast(int*, int, int, int)’: fastal/parttree.c:757:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 757 | register int *p; | ^ fastal/parttree.c: In function ‘int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)’: fastal/parttree.c:695:22: 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:701:30: 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:848:14: 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:859:22: 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:891:14: 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:903:22: 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:906:14: 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:912:22: 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:951:14: 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:962:22: 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c 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:76:22: 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:78:14: 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:82:22: 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:384:30: 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:398:23: 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:488:22: 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:502:15: 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:583:14: 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:584:14: 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:585:14: 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:624:49: 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/arm-linux-gnueabihf/include/stdio.h:888, from fastal/scoring.c:28: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int complete_agreement_score(char*, const char*)’ at fastal/scoring.c:624:11: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 756 bytes into a destination of size 200 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC fastal/tree.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c 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:511:30: 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:971:29: 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c 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* ckalloc(size_t)’: io_lib/pb_util_read_seq_util.c:68:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 68 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function ‘void* ckvrealloc(void*, size_t)’: io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 91 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function ‘char* rtrim(char*)’: io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 191 | register int p; | ^ io_lib/pb_util_read_seq_util.c: In function ‘char* upstr(char*)’: io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 240 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function ‘char* lowstr(char*)’: io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 258 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function ‘void get_path(char*, char*)’: io_lib/pb_util_read_seq_util.c:356:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 356 | register int i; | ^ io_lib/pb_util_read_seq_util.c: In function ‘void getstr(char*, char*)’: io_lib/pb_util_read_seq_util.c:269:14: 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:280:22: 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:305:22: 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c 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 fill_chartab()’: io_lib/pb_util_read_sequence.c:79:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 79 | register int i; | ^ io_lib/pb_util_read_sequence.c:80:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 80 | register int c; | ^ 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:144:14: 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:149:51: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 149 | for(i=1;i>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c In file included from ./io_lib_header.h:33, from io_lib/tree_util.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ io_lib/tree_util.c: In function ‘tnode* tree_scan(Alignment*, NT_node, char*, char*)’: io_lib/tree_util.c:836:26: warning: too many arguments for format [-Wformat-extra-args] 836 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: In function ‘Alignment* phylotrim(Alignment*, NT_node, char*, char*, char*)’: io_lib/tree_util.c:1299:1: warning: no return statement in function returning non-void [-Wreturn-type] 1299 | } | ^ io_lib/tree_util.c: In function ‘tnode* no_rec_free_tree(NT_node)’: io_lib/tree_util.c:2317:1: warning: no return statement in function returning non-void [-Wreturn-type] 2317 | } | ^ io_lib/tree_util.c: In function ‘int node_sort(char*, NT_node)’: io_lib/tree_util.c:6273:1: warning: no return statement in function returning non-void [-Wreturn-type] 6273 | } | ^ io_lib/tree_util.c: In function ‘int treelist2leafgroup(Sequence*, Sequence*, char*)’: io_lib/tree_util.c:6566:1: warning: no return statement in function returning non-void [-Wreturn-type] 6566 | } | ^ io_lib/tree_util.c: In function ‘int count_tree_groups(Sequence*, char*)’: io_lib/tree_util.c:6669:1: warning: no return statement in function returning non-void [-Wreturn-type] 6669 | } | ^ io_lib/tree_util.c: In function ‘int treelist2splits(Sequence*, Sequence*)’: io_lib/tree_util.c:7047:1: warning: no return statement in function returning non-void [-Wreturn-type] 7047 | } | ^ io_lib/tree_util.c: In function ‘int treelist2splits_old(Sequence*, Sequence*)’: io_lib/tree_util.c:7131:1: warning: no return statement in function returning non-void [-Wreturn-type] 7131 | } | ^ io_lib/tree_util.c: In function ‘int treelist2frame(Sequence*, Sequence*)’: io_lib/tree_util.c:7204:1: warning: no return statement in function returning non-void [-Wreturn-type] 7204 | } | ^ io_lib/tree_util.c: In function ‘char* graph2cons_d(long unsigned int, int)’: io_lib/tree_util.c:10163:27: warning: NULL used in arithmetic [-Wpointer-arith] 10163 | while ((c=rn_c(s))!=NULL) | ^~~~ io_lib/tree_util.c: In function ‘long unsigned int insert_gap_in_graph_d(long unsigned int)’: io_lib/tree_util.c:10181:20: warning: converting to non-pointer type ‘long unsigned int’ from NULL [-Wconversion-null] 10181 | unsigned long pn=NULL; | ^~~~ io_lib/tree_util.c:10183:22: warning: converting to non-pointer type ‘long unsigned int’ from NULL [-Wconversion-null] 10183 | if (!start) return NULL; | ^~~~ io_lib/tree_util.c:10196:14: warning: passing NULL to non-pointer argument 2 of ‘void wn_c(long unsigned int, long unsigned int)’ [-Wconversion-null] 10196 | wn_c(n,NULL); | ^~~~ io_lib/tree_util.c:9947:46: note: declared here 9947 | void wn_c (unsigned long n, unsigned long t); | ~~~~~~~~~~~~~~^ io_lib/tree_util.c: In function ‘FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)’: io_lib/tree_util.c:3973:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3973 | fscanf(fp,"%f",&dist); | ~~~~~~^~~~~~~~~~~~~~~ io_lib/tree_util.c:3981:19: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3981 | fscanf(fp,"%f",&bootstrap); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: In function ‘int check_node(ALN_node, char*)’: io_lib/tree_util.c:9772:1: warning: control reaches end of non-void function [-Wreturn-type] 9772 | } | ^ io_lib/tree_util.c: In function ‘Sequence* get_nexus(char*)’: io_lib/tree_util.c:4597:40: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 4597 | sprintf (index, "%d", i); | ^~ io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] 4597 | sprintf (index, "%d", i); | ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:888, from io_lib/tree_util.c:27: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Sequence* get_nexus(char*)’ at io_lib/tree_util.c:4597:17: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 5 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC km_coffee/Stack.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c CC km_coffee/Vector.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c CC km_coffee/classes.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c CC km_coffee/km_coffee.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c In file included from ./io_lib_header.h:33, from km_coffee/km_coffee.c:43: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ km_coffee/km_coffee.c: In function ‘void traverse_km_tree(KM_node*, int*, const SeqSet*, char*, int, int, int, char*)’: km_coffee/km_coffee.c:148:53: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 148 | sprintf(command, "%li",current->id); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:157:73: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 157 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:157:104: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 157 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:159:73: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 159 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %s -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:169:53: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 169 | sprintf(command, "%li",current->id); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:172:73: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 172 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:172:104: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 172 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:174:73: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 174 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %s -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:185:53: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 185 | sprintf(command, "%li.fa",current->id); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:195:115: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 195 | sprintf(command, "t_coffee -output fasta_aln -method %s -quiet -outfile %li.fa -n_core %i -gapopen %i -profile FILE::prf.fa ", method, current->id,n_cores, gapopen); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:201:59: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 201 | fprintf(prf_F, "%li.fa\n", current->children[j]->id); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c: In function ‘int km_coffee_align3(char*, int, int, char*, char*, int, int, int, char*)’: km_coffee/km_coffee.c:491:14: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 491 | chdir(km_tmp_dir); | ~~~~~^~~~~~~~~~~~ CC km_coffee/km_util.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c km_coffee/km_util.c: In function ‘void* my_malloc(size_t)’: km_coffee/km_util.c:49:76: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 49 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); | ~~^ ~~~~ | | | | | size_t {aka unsigned int} | long int | %i km_coffee/km_util.c: In function ‘void* my_calloc(size_t, size_t)’: km_coffee/km_util.c:61:76: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 61 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size*num); | ~~^ ~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_util.c: In function ‘void* my_realloc(void*, size_t)’: km_coffee/km_util.c:74:76: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 74 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); | ~~^ ~~~~ | | | | | size_t {aka unsigned int} | long int | %i km_coffee/km_util.c: In function ‘char* my_make_temp_dir(char*, char*)’: km_coffee/km_util.c:96:69: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=] 96 | fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); | ~^ | | | char* CC km_coffee/kmeans.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c CC t_coffee_lib/t_coffee.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c In file included from ./io_lib_header.h:33, from t_coffee_lib/t_coffee.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ t_coffee_lib/t_coffee.c: In function ‘char** km_coffee(int, char**)’: t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] 6577 | } | ^ t_coffee_lib/t_coffee.c: In function ‘Alignment* t_coffee_dpa(int, char**)’: t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function ‘int run_other_pg(int, char**)’: t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function ‘Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)’: t_coffee_lib/t_coffee.c:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/string.h:519, from t_coffee_lib/t_coffee.c:32: In function ‘char* strcpy(char*, const char*)’, inlined from ‘char** km_coffee(int, char**)’ at t_coffee_lib/t_coffee.c:6543:14: /usr/arm-linux-gnueabihf/include/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/bits/string_fortified.h:79:33: note: in a call to built-in function ‘void* __builtin_memcpy(void*, const void*, unsigned int)’ In function ‘char* strcpy(char*, const char*)’, inlined from ‘char** km_coffee(int, char**)’ at t_coffee_lib/t_coffee.c:6545:14: /usr/arm-linux-gnueabihf/include/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/bits/string_fortified.h:79:33: note: in a call to built-in function ‘void* __builtin_memcpy(void*, const void*, unsigned int)’ t_coffee_lib/t_coffee.c: In function ‘int batch_main(int, char**)’: t_coffee_lib/t_coffee.c:5662:66: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); | ^~ ~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:888, from t_coffee_lib/t_coffee.c:27: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int batch_main(int, char**)’ at t_coffee_lib/t_coffee.c:5662:18: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 10 or more bytes (assuming 1018) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC util_lib/aln_compare.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c 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 ‘int trim_aln_file(char*, char*, char*, char*)’: util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) | ^~~~ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2conservation(Alignment*, int, char*)’: util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] 4511 | } | ^ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2N_replicate(Alignment*, char*, char*)’: util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] 7762 | } | ^ util_lib/aln_convertion_util.c: In function ‘Alignment* extract_aln3(Alignment*, char*)’: util_lib/aln_convertion_util.c:7524:16: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7524 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7543:38: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7543 | if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7547:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7547 | 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:12147:32: warning: ‘ -w ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); | ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:888, from util_lib/aln_convertion_util.c:27: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘float** get_weight(Alignment*, Sequence*, char*)’ at util_lib/aln_convertion_util.c:12147:15: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 1005) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function ‘float** get_weight(Alignment*, Sequence*, char*)’: util_lib/aln_convertion_util.c:12141:32: warning: ‘ -i ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘float** get_weight(Alignment*, Sequence*, char*)’ at util_lib/aln_convertion_util.c:12141:15: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 10 or more bytes (assuming 1009) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC util_lib/hsearch.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c CC util_lib/reformat.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c 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:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] 7551 | } | ^ util_lib/reformat.c: In function ‘int output_header_mat(int**, char*)’: util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } | ^ util_lib/reformat.c: In function ‘Sequence* quick_read_seq(char*)’: util_lib/reformat.c:1332:1: warning: control reaches end of non-void function [-Wreturn-type] 1332 | } | ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln_static(char*)’: util_lib/reformat.c:1371:1: warning: control reaches end of non-void function [-Wreturn-type] 1371 | } | ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln(char*)’: util_lib/reformat.c:1413:1: warning: control reaches end of non-void function [-Wreturn-type] 1413 | } | ^ util_lib/reformat.c: In function ‘int read_nameseq(char*, char***, char***, char***)’: util_lib/reformat.c:1427:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1427 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1428:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1428 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1438:22: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1438 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1441:22: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1441 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1446:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1446 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1448:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1448 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int read_nameseq_old(char*, char***, char***, char***)’: util_lib/reformat.c:1472:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1472 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1473:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1473 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1483:22: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1483 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1486:22: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1486 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1491:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1491 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1493:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1493 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int is_pdb_name(char*)’: util_lib/reformat.c:1788:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1788 | fscanf ( fp, "%d", &result); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘char* get_pdb_id(char*)’: util_lib/reformat.c:1826:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1826 | fscanf ( fp, "\n%s\n", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fast_format_determination(char*)’: util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] 2507 | } | ^ util_lib/reformat.c: In function ‘Weights* get_amps_sd_scores(char*)’: util_lib/reformat.c:3948:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3948 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3955:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3955 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3964:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3964 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3970:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3970 | fscanf ( fp, "%s",W->seq_name[a]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3972:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3972 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3983:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3983 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ util_lib/reformat.c: In function ‘Structure* read_rna_struc_number(Alignment*, char*)’: util_lib/reformat.c:4256:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4256 | fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4259:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4259 | 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:4486:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4486 | fscanf ( fp, "%s %d", name, &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4507:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4507 | fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4512:28: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4512 | 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:4549:32: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4549 | fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_dialign_sequence(char*)’: util_lib/reformat.c:4624:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4624 | {fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int get_next_fasta_sequence(FILE*, char**, char**, char**)’: util_lib/reformat.c:5264:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5264 | fgets (line, ml,fp); | ~~~~~~^~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fscanf_seq_name(FILE*, char*)’: util_lib/reformat.c:5724:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5724 | fscanf (fp, "%s", name); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int get_amps_seq_name(char**, char*)’: util_lib/reformat.c:6077:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6077 | {fscanf (fp, "%*d >%s", name[nseq++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* read_gotoh_aln(char*, Alignment*)’: util_lib/reformat.c:6126:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6126 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6148:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6148 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘float output_maln_pval(char*, Alignment*)’: util_lib/reformat.c:6346:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6346 | fscanf ( fp, "%s",string); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* similarities_file2aln(char*)’: util_lib/reformat.c:6511:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix(char*)’: util_lib/reformat.c:14294:20: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14294 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14307:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14307 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14332:19: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14332 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix_old(char*)’: util_lib/reformat.c:14357:19: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14357 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14374:20: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14374 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14387:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14387 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14414:19: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14414 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_pavie_matrix(char*)’: util_lib/reformat.c:14525:19: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14525 | 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:13639:34: warning: ‘ -method ’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 13639 | 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/arm-linux-gnueabihf/include/stdio.h:888, from util_lib/reformat.c:27: 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:13639:13: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 64 or more bytes (assuming 3059) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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:11638:32: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 11638 | sprintf (type, "%s", ACTION (2)); | ^~ CC util_lib/reformat_struc.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c 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:125:25: 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:378:23: 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:416:23: 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c 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:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] 4456 | } | ^ util_lib/util.c: In function ‘int set_nproc(int)’: util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] 5489 | } | ^ util_lib/util.c: In function ‘char* vremove3(char*, char*)’: util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] 6938 | } | ^ 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:281:18: 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:286:18: 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:289:18: 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:306:22: 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:311:25: 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:420:20: 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:847:32: 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:1812:15: 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:4440:19: warning: control reaches end of non-void function [-Wreturn-type] 4440 | 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:5761:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5761 | fscanf (fp, "%s\n",list[n]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stderr(char*)’: util_lib/util.c:6301:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6301 | freopen(stderr_file, "w", stderr); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stdout(char*)’: util_lib/util.c:6344:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6344 | 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:7645:9: warning: second parameter of ‘va_start’ not last named argument [-Wvarargs] 7645 | va_start (ap, usage); | ^~~~~~~~ util_lib/util.c: In function ‘char** get_parameter(char*, int*, char*)’: util_lib/util.c:7912:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7912 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* set_fp_id(FILE*, char*)’: util_lib/util.c:7932:32: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7932 | fscanf ( fp, "%s", string); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** get_file_block_pattern(char*, int*, int)’: util_lib/util.c:8319:25: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8319 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:8349:25: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8349 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_for_update(char*)’: util_lib/util.c:8436:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8436 | fscanf ( fp, "Version_%f", &new_version); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_internet_connection(int)’: util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int km_main(int, char**)’: util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] 10533 | } | ^ util_lib/util.c: In function ‘char* get_cache_4_tcoffee()’: util_lib/util.c:5385:42: warning: ‘/cache/’ directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:888, from util_lib/util.c:32: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* get_cache_4_tcoffee()’ at util_lib/util.c:5385:20: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 8 and 1007 bytes into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_plugins_4_tcoffee()’: util_lib/util.c:5435:43: warning: ‘/plugins/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5435 | else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); | ^~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* get_plugins_4_tcoffee()’ at util_lib/util.c:5435:20, inlined from ‘char* get_plugins_4_tcoffee()’ at util_lib/util.c:5419:7: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 11 and 1109 bytes into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_methods_4_tcoffee()’: util_lib/util.c:5413:44: warning: ‘/methods/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* get_methods_4_tcoffee()’ at util_lib/util.c:5413:20, inlined from ‘char* get_methods_4_tcoffee()’ at util_lib/util.c:5405:7: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_mcoffee_4_tcoffee()’: util_lib/util.c:5400:44: warning: ‘/mcoffee/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* get_mcoffee_4_tcoffee()’ at util_lib/util.c:5400:20, inlined from ‘char* get_mcoffee_4_tcoffee()’ at util_lib/util.c:5392:7: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_cache_4_tcoffee()’: util_lib/util.c:5385:42: warning: ‘/cache/’ directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* get_cache_4_tcoffee()’ at util_lib/util.c:5385:20, inlined from ‘char* get_cache_4_tcoffee()’ at util_lib/util.c:5376:7: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 8 and 1007 bytes into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* display_output_filename(FILE*, char*, char*, char*, int)’: util_lib/util.c:8658:68: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); | ^~ util_lib/util.c: In function ‘char** _Z23standard_initialisationPPcPi.part.0(char**, int*)’: util_lib/util.c:5400:44: warning: ‘/mcoffee/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* get_mcoffee_4_tcoffee()’ at util_lib/util.c:5400:20, inlined from ‘char* get_mcoffee_4_tcoffee()’ at util_lib/util.c:5392:7, inlined from ‘char** _Z23standard_initialisationPPcPi.part.0(char**, int*)’ at util_lib/util.c:10018:11: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char** _Z23standard_initialisationPPcPi.part.0(char**, int*)’: util_lib/util.c:5413:44: warning: ‘/methods/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* get_methods_4_tcoffee()’ at util_lib/util.c:5413:20, inlined from ‘char* get_methods_4_tcoffee()’ at util_lib/util.c:5405:7, inlined from ‘char** _Z23standard_initialisationPPcPi.part.0(char**, int*)’ at util_lib/util.c:10019:11: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC util_lib/util_aln_analyze.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c 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 | } | ^ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:888, from util_lib/util_aln_analyze.c:27: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)’ at util_lib/util_aln_analyze.c:4598:11, inlined from ‘Alignment* or_sar(Alignment*, Alignment*, char*, int)’ at util_lib/util_aln_analyze.c:4560:29: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: warning: null destination pointer [-Wformat-overflow=] 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_aln_analyze.c: In function ‘Alignment* or_sar(Alignment*, Alignment*, char*, int)’: util_lib/util_aln_analyze.c:4599:23: warning: ‘COMBINED’ directive writing 8 bytes into a region of size 0 [-Wformat-overflow=] 4599 | sprintf ( N->mode, "COMBINED"); | ^~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)’ at util_lib/util_aln_analyze.c:4599:11, inlined from ‘Alignment* or_sar(Alignment*, Alignment*, char*, int)’ at util_lib/util_aln_analyze.c:4560:29: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin_sprintf’ output 9 bytes into a destination of size 0 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC util_lib/util_analyse_constraints_list.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c 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:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] 1311 | } | ^ 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:2224:49: warning: too many arguments for format [-Wformat-extra-args] 2224 | 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:2851:40: warning: too many arguments for format [-Wformat-extra-args] 2851 | 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:582:19: 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:585:19: 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:1150:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1150 | 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:1193:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1193 | 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:2599:27: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2599 | 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:2917:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2917 | fscanf (fp, "%d\n", &max_nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2922:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2922 | fscanf (fp, "%*s %d %*s\n", &l); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2954:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2954 | fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2979:31: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2979 | 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:4053:40: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4053 | 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:1286:28: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1286 | 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/arm-linux-gnueabihf/include/stdio.h:888, from util_lib/util_constraints_list.c:29: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘char* make_aln_command(TC_method*, char*, char*)’ at util_lib/util_constraints_list.c:1286:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __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:4922:26: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)’ at util_lib/util_constraints_list.c:4922:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __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:4923:30: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)’ at util_lib/util_constraints_list.c:4923:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __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:694:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 694 | sprintf ( aln_mode, "%s", method->aln_mode); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)’ at util_lib/util_constraints_list.c:694:11: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __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 ( out_mode, "%s", method->out_mode); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)’ at util_lib/util_constraints_list.c:695:11: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC util_lib/util_declare.c arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c 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 arm-linux-gnueabihf-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c 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 ‘void fast_nj_tree(char**)’: util_lib/util_make_tree.c:853:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 853 | register int i; | ^ 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:160:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 160 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* seq2cw_aln_file(char*, char*)’: util_lib/util_make_tree.c:190:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:192:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 192 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* prf_pair2cw_aln_file(char*, char*, char*)’: util_lib/util_make_tree.c:223:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 223 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:226:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 226 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns1_dnd(Sequence*)’: util_lib/util_make_tree.c:1855:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1855 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1868:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1868 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns2_dnd(Sequence*)’: util_lib/util_make_tree.c:1884:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1884 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1897:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2mafft_dnd(Sequence*)’: util_lib/util_make_tree.c:1913:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1913 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1926:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1926 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2parttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1943:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1943 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1956:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1956 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2dpparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1973:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1973 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1988:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1988 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fastparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:2006:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2006 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2019:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2019 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cwquick_dnd(Sequence*)’: util_lib/util_make_tree.c:2035:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2035 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2043:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2043 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_dnd(Sequence*)’: util_lib/util_make_tree.c:2060:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2060 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2068:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2068 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* aln2cw_tree(Alignment*)’: util_lib/util_make_tree.c:2088:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2088 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2095:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2095 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_tree(Sequence*)’: util_lib/util_make_tree.c:2110:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2110 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2119:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2119 | chdir (cdir); | ~~~~~~~~~^~~~~~ Linking... arm-linux-gnueabihf-g++ dev_lib/dev1.o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/evaluate.o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_struc.o dp_lib/fsa_dp.o dp_lib/pavie_dp.o dp_lib/showpair.o dp_lib/util_domain_dp.o dp_lib/util_domain_dp_drivers.o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_drivers.o dp_lib/util_dp_est.o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_sim.o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_graph_maln.o fastal/diagonal.o fastal/fastal.o fastal/fastal_opt_parsing.o fastal/iteration.o fastal/parttree.o fastal/scoring.o fastal/tree.o io_lib/io_func.o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_sequence.o io_lib/tree_util.o km_coffee/Stack.o km_coffee/Vector.o km_coffee/classes.o km_coffee/km_coffee.o km_coffee/km_util.o km_coffee/kmeans.o t_coffee_lib/t_coffee.o util_lib/aln_compare.o util_lib/aln_convertion_util.o util_lib/hsearch.o util_lib/random.o util_lib/reformat.o util_lib/reformat_struc.o util_lib/util.o util_lib/util_aln_analyze.o util_lib/util_analyse_constraints_list.o util_lib/util_constraints_list.o util_lib/util_declare.o util_lib/util_domain_constraints_list.o util_lib/util_dps.o util_lib/util_job_handling.o util_lib/util_make_tree.o -o t_coffee -lm -Wl,-z,relro -Wl,-z,now /usr/lib/gcc-cross/arm-linux-gnueabihf/12/../../../../arm-linux-gnueabihf/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 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 for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/share/doc/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done 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_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 dpkg-shlibdeps: warning: debian/t-coffee/usr/bin/t_coffee contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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_13.41.0.28bdc39+dfsg-4_armhf.deb'. dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.deb'. dpkg-genbuildinfo --build=any -O../t-coffee_13.41.0.28bdc39+dfsg-4_armhf.buildinfo dpkg-genchanges --build=any -O../t-coffee_13.41.0.28bdc39+dfsg-4_armhf.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 2022-09-14T16:42:42Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ t-coffee_13.41.0.28bdc39+dfsg-4_armhf.changes: ---------------------------------------------- Format: 1.8 Date: Wed, 17 Jun 2020 20:34:34 +0200 Source: t-coffee Binary: t-coffee t-coffee-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 13.41.0.28bdc39+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Etienne Mollier Description: t-coffee - Multiple Sequence Alignment Closes: 962974 Changes: t-coffee (13.41.0.28bdc39+dfsg-4) unstable; urgency=medium . * Team upload. * Increase MAX_N_PID to 4194304. (Closes: #962974) * Updated the homepage, following permanent redirection. 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/<>/t-coffee_13.41.0.28bdc39+dfsg-4_armhf.changes.new could not be renamed to /<>/t-coffee_13.41.0.28bdc39+dfsg-4_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: t-coffee Binary: t-coffee t-coffee-dbgsym Architecture: armhf Version: 13.41.0.28bdc39+dfsg-4 Checksums-Md5: 9bf25082eeebc664e2f2073922f3b654 2775484 t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.deb 36ae18da21520ba854f97ce12738cb98 877492 t-coffee_13.41.0.28bdc39+dfsg-4_armhf.deb Checksums-Sha1: a207f3bab4b30d1bf5001482bf84e08089f7e9c1 2775484 t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.deb 6354499f7a9ed98e205bc787256e816991586052 877492 t-coffee_13.41.0.28bdc39+dfsg-4_armhf.deb Checksums-Sha256: 9e5967461dc041c34bb623dc4b6cb4f25d283aaa406b769ce74bc2c26d45305c 2775484 t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.deb 29b0bd6d333e1d4880955a745b770c788db8c93f3d608185157be5d2ba278f3a 877492 t-coffee_13.41.0.28bdc39+dfsg-4_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 14 Sep 2022 16:42:42 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-9), autotools-dev (= 20220109.1), base-files (= 12.2), base-passwd (= 3.6.0), bash (= 5.2~rc2-2), binutils (= 2.38.90.20220713-2), binutils-common (= 2.38.90.20220713-2), binutils-x86-64-linux-gnu (= 2.38.90.20220713-2), bsdextrautils (= 2.38.1-1), bsdutils (= 1:2.38.1-1), build-essential (= 12.9), bzip2 (= 1.0.8-5), coreutils (= 8.32-4.1), cpp (= 4:12.2.0-1), cpp-11 (= 11.3.0-6), cpp-12 (= 12.2.0-2), dash (= 0.5.11+git20210903+057cd650a4ed-9), debconf (= 1.5.79), debhelper (= 13.9.1), debianutils (= 5.7-0.3), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-1), dpkg (= 1.21.9), dpkg-dev (= 1.21.9), dwz (= 0.14-1), file (= 1:5.41-4), findutils (= 4.9.0-3), g++ (= 4:12.2.0-1), g++-12 (= 12.2.0-2), gcc (= 4:12.2.0-1), gcc-11 (= 11.3.0-6), gcc-11-base (= 11.3.0-6), gcc-12 (= 12.2.0-2), gcc-12-base (= 12.2.0-2), gettext (= 0.21-9), gettext-base (= 0.21-9), grep (= 3.8-2), groff-base (= 1.22.4-8), gzip (= 1.12-1), hostname (= 3.23), init-system-helpers (= 1.64), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.3.0-6), libasan8 (= 12.2.0-2), libatomic1 (= 12.2.0-2), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.7-1), libaudit1 (= 1:3.0.7-1+b1), libbinutils (= 2.38.90.20220713-2), libblkid1 (= 2.38.1-1), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.34-8), libc-dev-bin (= 2.34-8), libc6 (= 2.34-8), libc6-dev (= 2.34-8), libcap-ng0 (= 0.8.3-1+b1), libcap2 (= 1:2.44-1), libcc1-0 (= 12.2.0-2), libcom-err2 (= 1.46.6~rc1-1), libcrypt-dev (= 1:4.4.28-2), libcrypt1 (= 1:4.4.28-2), libctf-nobfd0 (= 2.38.90.20220713-2), libctf0 (= 2.38.90.20220713-2), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.264), libdebhelper-perl (= 13.9.1), libdpkg-perl (= 1.21.9), libelf1 (= 0.187-2), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-11-dev (= 11.3.0-6), libgcc-12-dev (= 12.2.0-2), libgcc-s1 (= 12.2.0-2), libgcrypt20 (= 1.10.1-2), libgdbm-compat4 (= 1.23-2), libgdbm6 (= 1.23-2), libgmp10 (= 2:6.2.1+dfsg1-1), libgomp1 (= 12.2.0-2), libgpg-error0 (= 1.45-2), libgprofng0 (= 2.38.90.20220713-2), libgssapi-krb5-2 (= 1.20-1), libicu71 (= 71.1-3), libisl23 (= 0.25-1), libitm1 (= 12.2.0-2), libk5crypto3 (= 1.20-1), libkeyutils1 (= 1.6.3-1), libkrb5-3 (= 1.20-1), libkrb5support0 (= 1.20-1), liblsan0 (= 12.2.0-2), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmount1 (= 2.38.1-1), libmpc3 (= 1.2.1-2), libmpfr6 (= 4.1.0-3), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libpam-modules (= 1.5.2-2), libpam-modules-bin (= 1.5.2-2), libpam-runtime (= 1.5.2-2), libpam0g (= 1.5.2-2), libpcre2-8-0 (= 10.40-1), libperl5.34 (= 5.34.0-5), libpipeline1 (= 1.5.6-2), libquadmath0 (= 12.2.0-2), libseccomp2 (= 2.5.4-1+b1), libselinux1 (= 3.4-1+b1), libsmartcols1 (= 2.38.1-1), libssl3 (= 3.0.5-2), libstdc++-12-dev (= 12.2.0-2), libstdc++6 (= 12.2.0-2), libsub-override-perl (= 0.09-3), libsystemd0 (= 251.4-3), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-4), libtsan0 (= 11.3.0-6), libtsan2 (= 12.2.0-2), libubsan1 (= 12.2.0-2), libuchardet0 (= 0.0.7-1), libudev1 (= 251.4-3), libunistring2 (= 1.0-1), libuuid1 (= 2.38.1-1), libxml2 (= 2.9.14+dfsg-1+b1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.19.6-1), login (= 1:4.11.1+dfsg1-2), m4 (= 1.4.19-1), make (= 4.3-4.1), man-db (= 2.10.2-3), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7), perl (= 5.34.0-5), perl-base (= 5.34.0-5), perl-modules-5.34 (= 5.34.0-5), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.05-4), tar (= 1.34+dfsg-1), util-linux (= 2.38.1-1), util-linux-extra (= 2.38.1-1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-4.1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1592418874" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.deb ------------------------------------------------ new Debian package, version 2.0. size 2775484 bytes: control archive=552 bytes. 405 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: t-coffee-dbgsym Source: t-coffee Version: 13.41.0.28bdc39+dfsg-4 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 2952 Depends: t-coffee (= 13.41.0.28bdc39+dfsg-4) Section: debug Priority: optional Description: debug symbols for t-coffee Build-Ids: 4b1081f6e7ec379bec057ff5464f0d622d289b38 drwxr-xr-x root/root 0 2020-06-17 18:34 ./ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/lib/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/lib/debug/.build-id/4b/ -rw-r--r-- root/root 3012156 2020-06-17 18:34 ./usr/lib/debug/.build-id/4b/1081f6e7ec379bec057ff5464f0d622d289b38.debug drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-06-17 18:34 ./usr/share/doc/t-coffee-dbgsym -> t-coffee t-coffee_13.41.0.28bdc39+dfsg-4_armhf.deb ----------------------------------------- new Debian package, version 2.0. size 877492 bytes: control archive=1392 bytes. 1594 bytes, 29 lines control 473 bytes, 7 lines md5sums Package: t-coffee Version: 13.41.0.28bdc39+dfsg-4 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 1932 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), 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/tcoffee/index.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. You can use a subset of your favorite methods if you prefer. drwxr-xr-x root/root 0 2020-06-17 18:34 ./ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/bin/ -rwxr-xr-x root/root 1953148 2020-06-17 18:34 ./usr/bin/t_coffee drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/doc/t-coffee/ -rw-r--r-- root/root 1744 2020-06-17 18:34 ./usr/share/doc/t-coffee/README.Debian -rw-r--r-- root/root 261 2020-06-17 18:34 ./usr/share/doc/t-coffee/README.test -rw-r--r-- root/root 4226 2020-06-17 18:34 ./usr/share/doc/t-coffee/changelog.Debian.gz -rw-r--r-- root/root 1571 2020-06-17 18:34 ./usr/share/doc/t-coffee/copyright -rw-r--r-- root/root 2586 2020-06-17 18:34 ./usr/share/doc/t-coffee/run-unit-test drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/man/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/man/man1/ -rw-r--r-- root/root 1463 2020-06-17 18:34 ./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 [533 B] Get:5 copy:/<>/apt_archive ./ Packages [617 B] Fetched 2113 B in 0s (0 B/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: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:armhf t1utils unzip 0 upgraded, 133 newly installed, 0 to remove and 0 not upgraded. Need to get 14.3 MB of archives. After this operation, 52.0 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://localhost:3142/debian sid/main amd64 netbase all 6.3 [19.9 kB] Get:3 http://localhost:3142/debian sid/main amd64 readline-common all 8.2~rc2-2 [75.8 kB] Get:4 http://localhost:3142/debian sid/main amd64 openssl amd64 3.0.5-2 [1421 kB] Get:5 http://localhost:3142/debian sid/main amd64 ca-certificates all 20211016 [156 kB] Get:6 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.64-1 [36.6 kB] Get:7 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.5-4 [51.3 kB] Get:8 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2~rc2-2 [173 kB] Get:9 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.39-1 [585 kB] Get:10 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.39.3-1 [844 kB] Get:11 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.39-1 [969 kB] Get:12 http://localhost:3142/debian sid/main amd64 iso-codes all 4.11.0-1 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libclass-method-modifiers-perl all 2.13-2 [19.4 kB] Get:34 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4 [37.5 kB] Get:35 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.45-1+b2 [15.5 kB] Get:36 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.28-1 [17.3 kB] Get:37 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-1+b2 [25.7 kB] Get:38 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.928-2 [11.0 kB] Get:39 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:40 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:41 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:42 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.32-1 [130 kB] Get:43 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:44 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:45 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:46 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:47 http://localhost:3142/debian sid/main amd64 libexporter-tiny-perl all 1.004001-1 [38.7 kB] Get:48 http://localhost:3142/debian sid/main amd64 liblist-moreutils-xs-perl amd64 0.430-3 [40.3 kB] Get:49 http://localhost:3142/debian sid/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:50 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:51 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1 [35.7 kB] Get:52 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-2 [33.7 kB] Get:53 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:54 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:55 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0001-1 [32.2 kB] Get:56 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2 [104 kB] Get:57 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.30-1 [21.0 kB] Get:58 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:59 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2 [25.8 kB] Get:60 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1 [29.1 kB] Get:61 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-2 [13.5 kB] Get:62 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:63 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:64 http://localhost:3142/debian sid/main amd64 libnumber-compare-perl all 0.03-2 [7448 B] Get:65 http://localhost:3142/debian sid/main amd64 libtext-glob-perl all 0.11-2 [8992 B] Get:66 http://localhost:3142/debian sid/main amd64 libfile-find-rule-perl all 0.34-2 [28.4 kB] Get:67 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:68 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get:69 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:70 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:71 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:72 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get:73 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.37-1 [80.9 kB] Get:74 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.10-1 [24.0 kB] Get:75 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-2 [21.6 kB] Get:76 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get:77 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:78 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:79 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:80 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2 [343 kB] Get:81 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.075-1 [220 kB] Get:82 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get:83 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:84 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:85 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.67-1 [194 kB] Get:86 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:87 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:88 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:89 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:90 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:91 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:92 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:93 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-1 [16.1 kB] Get:94 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-4 [42.0 kB] Get:95 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:96 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:97 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-3 [18.8 kB] Get:98 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:99 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:100 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005004-3 [60.5 kB] Get:101 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:102 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:103 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b2 [173 kB] Get:104 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:105 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-2 [11.9 kB] Get:106 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.26-2 [13.7 kB] Get:107 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:108 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.122-1 [56.0 kB] Get:109 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1 [17.5 kB] Get:110 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.009-1+b1 [12.2 kB] Get:111 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.634-1+b1 [46.9 kB] Get:112 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:113 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.001+ds-1 [103 kB] Get:114 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.001+ds-1 [106 kB] Get:115 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-2 [10.7 kB] Get:116 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.25-1 [53.3 kB] Get:117 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.27-1 [28.5 kB] Get:118 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2 [27.2 kB] Get:119 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5 [8656 B] Get:120 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.13-1+b1 [13.6 kB] Get:121 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b1 [197 kB] Get:122 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:123 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2 [73.0 kB] Get:124 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-1+b3 [20.3 kB] Get:125 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.15-1 [120 kB] Get:126 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:127 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.84+ds-1 [36.1 kB] Get:128 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-4 [64.0 kB] Get:129 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:130 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:131 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:132 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-27 [172 kB] Get:133 http://localhost:3142/debian sid/main amd64 lintian all 2.115.3 [1417 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.3 MB in 0s (111 MB/s) Selecting previously unselected package netbase. (Reading database ... 19408 files and directories currently installed.) Preparing to unpack .../000-netbase_6.3_all.deb ... Unpacking netbase (6.3) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2~rc2-2_all.deb ... Unpacking readline-common (8.2~rc2-2) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.5-2_amd64.deb ... Unpacking openssl (3.0.5-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20211016_all.deb ... Unpacking ca-certificates (20211016) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.64-1_amd64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../005-libassuan0_2.5.5-4_amd64.deb ... Unpacking libassuan0:amd64 (2.5.5-4) ... Selecting previously unselected package libreadline8:amd64. 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Unpacking sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b1) ... Setting up liblz1:amd64 (1.13-4) ... Setting up libberkeleydb-perl:amd64 (0.64-1+b2) ... Setting up plzip (1.10-4) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-1+b3) ... Setting up libmouse-perl (2.5.10-1+b2) ... Setting up libdata-messagepack-perl (1.02-1) ... Setting up libdynaloader-functions-perl (0.003-2) ... Setting up libtext-glob-perl (0.11-2) ... Setting up libclass-method-modifiers-perl (2.13-2) ... Setting up liblist-compare-perl (0.55-1) ... Setting up libclone-perl (0.45-1+b2) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-2) ... Setting up libcpanel-json-xs-perl:amd64 (4.32-1) ... Setting up libhtml-tagset-perl (3.20-5) ... Setting up libdevel-size-perl (0.83-2) ... Setting up unzip (6.0-27) ... Setting up libsqlite3-0:amd64 (3.39.3-1) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libyaml-libyaml-perl (0.84+ds-1) ... Setting up libio-interactive-perl (1.023-1) ... Setting up libtry-tiny-perl (0.31-1) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-3) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2) ... Setting up libencode-locale-perl (1.05-2) ... Setting up libassuan0:amd64 (2.5.5-4) ... Setting up libconfig-tiny-perl (2.28-1) ... Setting up libsereal-encoder-perl:amd64 (5.001+ds-1) ... Setting up liblist-utilsby-perl (0.12-1) ... Setting up libnet-netmask-perl (2.0001-1) ... Setting up libsub-install-perl (0.928-2) ... Setting up libnumber-compare-perl (0.03-2) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004003-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.25-1) ... Setting up libfile-find-rule-perl (0.34-2) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libnet-domain-tld-perl (1.75-2) ... Setting up libperlio-utf8-strict-perl (0.009-1+b1) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.64-1) ... Setting up libvariable-magic-perl (0.62-2) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2) ... Setting up liblist-moreutils-xs-perl (0.430-3) ... Setting up libparams-util-perl (1.102-1+b2) ... Setting up libtime-duration-perl (1.21-1) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1+b1) ... Setting up libsub-exporter-progressive-perl (0.001013-2) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libsub-name-perl:amd64 (0.26-2) ... Setting up libsyntax-keyword-try-perl (0.27-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.634-1+b1) ... Setting up libpath-tiny-perl (0.122-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-2) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-2) ... Setting up netbase (6.3) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libclass-xsaccessor-perl (1.19-4) ... Setting up libsort-versions-perl (1.62-2) ... Setting up libexporter-tiny-perl (1.004001-1) ... Setting up libterm-readkey-perl (2.38-2) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.5-2) ... Setting up libtext-levenshteinxs-perl (0.03-5) ... Setting up libperlio-gzip-perl (0.20-1) ... Setting up readline-common (8.2~rc2-2) ... Setting up libhtml-html5-entities-perl (0.004-2) ... Setting up libsereal-decoder-perl (5.001+ds-1) ... Setting up libmarkdown2:amd64 (2.2.7-2) ... Setting up liburi-perl (5.12-1) ... Setting up iso-codes (4.11.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.30-1) ... Setting up libemail-address-xs-perl (1.05-1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libfile-basedir-perl (0.09-1) ... Setting up libfile-listing-perl (6.15-1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libreadline8:amd64 (8.2~rc2-2) ... Setting up libnet-http-perl (6.22-1) ... Setting up libtext-markdown-discount-perl:amd64 (0.13-1+b1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl (0.008-1+b3) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 127 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.78-1) ... Setting up gpgconf (2.2.39-1) ... Setting up libio-socket-ssl-perl (2.075-1) ... Setting up gpg (2.2.39-1) ... Setting up libsub-exporter-perl (0.988-1) ... Setting up libhttp-message-perl (6.37-1) ... Setting up libhtml-form-perl (6.10-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl:amd64 (0.015-2) ... Setting up libcgi-pm-perl (4.54-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblist-someutils-perl (0.58-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.67-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.15-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up lintian (2.115.3) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.34-8) ... Processing triggers for man-db (2.10.2-3) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... 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: 54984 Build-Time: 86 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 10 Job: t-coffee_13.41.0.28bdc39+dfsg-4 Lintian: pass Machine Architecture: amd64 Package: t-coffee Package-Time: 119 Source-Version: 13.41.0.28bdc39+dfsg-4 Space: 54984 Status: successful Version: 13.41.0.28bdc39+dfsg-4 -------------------------------------------------------------------------------- Finished at 2022-09-14T16:42:42Z Build needed 00:01:59, 54984k disk space