sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | t-coffee 12.00.7fb08c2-1 (s390x) Sun, 03 Feb 2019 16:44:06 +0000 | +==============================================================================+ Package: t-coffee Version: 12.00.7fb08c2-1 Source Version: 12.00.7fb08c2-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: s390x Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-7764c21a-b0b1-4168-82cb-e488af2c9c7f' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [243 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-02-03-0812.15.pdiff [2254 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-02-03-1415.37.pdiff [20.7 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-02-03-1415.37.pdiff [20.7 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-02-03-0812.15.pdiff [1167 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-02-03-1415.37.pdiff [10.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-02-03-1415.37.pdiff [10.2 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main s390x Packages [8010 kB] Fetched 8343 kB in 2s (4558 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 3537 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main t-coffee 12.00.7fb08c2-1 (dsc) [2157 B] Get:2 http://debian.oregonstate.edu/debian unstable/main t-coffee 12.00.7fb08c2-1 (tar) [3521 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main t-coffee 12.00.7fb08c2-1 (diff) [14.2 kB] Fetched 3537 kB in 0s (10.1 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/t-coffee-bqzx0V/t-coffee-12.00.7fb08c2' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-bqzx0V' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-s390x:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-s390x:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-njrUeC/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-njrUeC/apt_archive ./ InRelease Get:2 copy:/<>/resolver-njrUeC/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-njrUeC/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-njrUeC/apt_archive ./ Sources [361 B] Get:5 copy:/<>/resolver-njrUeC/apt_archive ./ Packages [452 B] Fetched 1770 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: binutils-s390x-linux-gnu cpp-8-s390x-linux-gnu cpp-s390x-linux-gnu cross-config crossbuild-essential-s390x dpkg-cross file g++-8-s390x-linux-gnu g++-s390x-linux-gnu gcc-8-cross-base gcc-8-s390x-linux-gnu gcc-8-s390x-linux-gnu-base gcc-s390x-linux-gnu libasan5-s390x-cross libatomic1-s390x-cross libc6-dev-s390x-cross libc6-s390x-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-s390x-cross libgcc1-s390x-cross libgomp1-s390x-cross libicu63 libio-string-perl libitm1-s390x-cross liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-s390x-cross libstdc++6-s390x-cross libubsan1-s390x-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-s390x-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch g++-8-multilib-s390x-linux-gnu gcc-8-doc libstdc++6-8-dbg-s390x-cross gcc-8-multilib-s390x-linux-gnu libgcc1-dbg-s390x-cross libgomp1-dbg-s390x-cross libitm1-dbg-s390x-cross libatomic1-dbg-s390x-cross libasan5-dbg-s390x-cross liblsan0-dbg-s390x-cross libtsan0-dbg-s390x-cross libubsan1-dbg-s390x-cross libmpx2-dbg-s390x-cross libquadmath0-dbg-s390x-cross manpages-dev autoconf automake libtool flex bison gdb-s390x-linux-gnu gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-s390x-linux-gnu cpp-8-s390x-linux-gnu cpp-s390x-linux-gnu cross-config crossbuild-essential-s390x dpkg-cross file g++-8-s390x-linux-gnu g++-s390x-linux-gnu gcc-8-cross-base gcc-8-s390x-linux-gnu gcc-8-s390x-linux-gnu-base gcc-s390x-linux-gnu libasan5-s390x-cross libatomic1-s390x-cross libc6-dev-s390x-cross libc6-s390x-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-s390x-cross libgcc1-s390x-cross libgomp1-s390x-cross libicu63 libio-string-perl libitm1-s390x-cross liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-s390x-cross libstdc++6-s390x-cross libubsan1-s390x-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-s390x-cross sbuild-build-depends-core-dummy:s390x sensible-utils ucf 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 39.5 MB of archives. After this operation, 145 MB of additional disk space will be used. Get:1 copy:/<>/resolver-njrUeC/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [876 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-2 [242 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.35-2 [117 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-2 [66.1 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-s390x-linux-gnu amd64 2.31.1-11 [2127 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-s390x-linux-gnu-base amd64 8.2.0-11cross1 [188 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-s390x-linux-gnu amd64 8.2.0-11cross1 [5934 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-s390x-linux-gnu amd64 4:8.2.0-2 [16.4 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-2 [39.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.2.0-11cross1 [183 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-s390x-cross all 2.28-4cross1 [1308 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-s390x-cross all 1:8.2.0-11cross1 [24.8 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-s390x-cross all 8.2.0-11cross1 [67.2 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-s390x-cross all 8.2.0-11cross1 [26.4 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-s390x-cross all 8.2.0-11cross1 [8096 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-s390x-cross all 8.2.0-11cross1 [352 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-s390x-cross all 8.2.0-11cross1 [312 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-s390x-cross all 8.2.0-11cross1 [112 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-s390x-cross all 8.2.0-11cross1 [638 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-s390x-linux-gnu amd64 8.2.0-11cross1 [6354 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-s390x-linux-gnu amd64 4:8.2.0-2 [1452 B] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-s390x-cross all 4.19.13-1cross1 [1211 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-s390x-cross all 2.28-4cross1 [2254 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-s390x-cross all 8.2.0-11cross1 [1473 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-s390x-linux-gnu amd64 8.2.0-11cross1 [6511 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 g++-s390x-linux-gnu amd64 4:8.2.0-2 [1176 B] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.1-6 [8292 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0132+dfsg-2+b1 [344 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-2 [38.5 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-2 [49.3 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-s390x all 12.5 [6540 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.5 MB in 1s (68.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11800 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-2) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-2_amd64.deb ... Unpacking file (1:5.35-2) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... 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Selecting previously unselected package crossbuild-essential-s390x. Preparing to unpack .../43-crossbuild-essential-s390x_12.5_all.deb ... Unpacking crossbuild-essential-s390x (12.5) ... Selecting previously unselected package sbuild-build-depends-core-dummy:s390x. Preparing to unpack .../44-sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy:s390x (0.invalid.0) ... Setting up libc6-s390x-cross (2.28-4cross1) ... Setting up gcc-8-cross-base (8.2.0-11cross1) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up gcc-8-s390x-linux-gnu-base:amd64 (8.2.0-11cross1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up libicu63:amd64 (63.1-6) ... Setting up libfile-which-perl (1.23-1) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up binutils-s390x-linux-gnu (2.31.1-11) ... Setting up libatomic1-s390x-cross (8.2.0-11cross1) ... Setting up libyaml-perl (1.27-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up libmagic-mgc (1:5.35-2) ... Setting up libmagic1:amd64 (1:5.35-2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up sensible-utils (0.0.12) ... Setting up linux-libc-dev-s390x-cross (4.19.13-1cross1) ... Setting up cross-config (2.6.15-2) ... Setting up libio-string-perl (1.08-3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libgomp1-s390x-cross (8.2.0-11cross1) ... Setting up libgcc1-s390x-cross (1:8.2.0-11cross1) ... Setting up libitm1-s390x-cross (8.2.0-11cross1) ... Setting up libstdc++6-s390x-cross (8.2.0-11cross1) ... Setting up cpp-8-s390x-linux-gnu (8.2.0-11cross1) ... Setting up cpp-s390x-linux-gnu (4:8.2.0-2) ... Setting up libasan5-s390x-cross (8.2.0-11cross1) ... Setting up libc6-dev-s390x-cross (2.28-4cross1) ... Setting up file (1:5.35-2) ... Setting up ucf (3.0038+nmu1) ... Setting up libubsan1-s390x-cross (8.2.0-11cross1) ... Setting up libxml-sax-perl (1.00+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-8-dev-s390x-cross (8.2.0-11cross1) ... Setting up libstdc++-8-dev-s390x-cross (8.2.0-11cross1) ... Setting up gcc-8-s390x-linux-gnu (8.2.0-11cross1) ... Setting up libxml-libxml-perl (2.0132+dfsg-2+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up g++-8-s390x-linux-gnu (8.2.0-11cross1) ... Setting up gcc-s390x-linux-gnu (4:8.2.0-2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-2) ... Setting up g++-s390x-linux-gnu (4:8.2.0-2) ... Setting up dpkg-cross (2.6.15-2) ... Setting up crossbuild-essential-s390x (12.5) ... Setting up sbuild-build-depends-core-dummy:s390x (0.invalid.0) ... Processing triggers for libc-bin (2.28-5) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any all) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-njrUeC/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-njrUeC/apt_archive ./ InRelease Get:2 copy:/<>/resolver-njrUeC/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-njrUeC/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-njrUeC/apt_archive ./ Sources [483 B] Get:5 copy:/<>/resolver-njrUeC/apt_archive ./ Packages [570 B] Fetched 2016 B in 0s (0 B/s) Reading package lists... Reading package lists... Install essential build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-essential-dummy:s390x 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 840 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-njrUeC/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [840 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 840 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:s390x. (Reading database ... 14897 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-essential-dummy:s390x (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:s390x (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~) Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~) dpkg-deb: building package 'sbuild-build-depends-t-coffee-dummy' in '/<>/resolver-njrUeC/apt_archive/sbuild-build-depends-t-coffee-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-t-coffee-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-njrUeC/apt_archive ./ InRelease Get:2 copy:/<>/resolver-njrUeC/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-njrUeC/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-njrUeC/apt_archive ./ Sources [632 B] Get:5 copy:/<>/resolver-njrUeC/apt_archive ./ Packages [712 B] Fetched 2307 B in 0s (136 kB/s) Reading package lists... Reading package lists... Install t-coffee 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 bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:s390x gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:s390x libatomic1:s390x libbsd0 libc6:s390x libc6-dev:s390x libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:s390x libgcc1:s390x libglib2.0-0 libgomp1:s390x libitm1:s390x libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:s390x libstdc++6:s390x libtool libubsan1:s390x libuchardet0 linux-libc-dev:s390x m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:s390x libc-l10n:s390x locales:s390x manpages-dev:s390x libstdc++-8-doc:s390x libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:s390x libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:s390x gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:s390x libatomic1:s390x libbsd0 libc6:s390x libc6-dev:s390x libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:s390x libgcc1:s390x libglib2.0-0 libgomp1:s390x libitm1:s390x libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:s390x libstdc++6:s390x libtool libubsan1:s390x libuchardet0 linux-libc-dev:s390x m4 man-db po-debconf sbuild-build-depends-t-coffee-dummy:s390x 0 upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After this operation, 88.8 MB of additional disk space will be used. Get:1 copy:/<>/resolver-njrUeC/apt_archive ./ sbuild-build-depends-t-coffee-dummy 0.invalid.0 [876 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-1 [99.3 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-2 [917 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-1 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.5-1 [1274 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-9 [547 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.1.0-1 [19.5 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.0-1 [12.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.175-2 [160 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.58.2-4 [1257 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-1 [102 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12 [1002 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main s390x gcc-8-base s390x 8.2.0-16 [189 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main s390x libgcc1 s390x 1:8.2.0-16 [24.7 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main s390x libc6 s390x 2.28-5 [2500 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main s390x libstdc++6 s390x 8.2.0-16 [390 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main s390x libasan5 s390x 8.2.0-16 [319 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main s390x libatomic1 s390x 8.2.0-16 [8188 B] Get:35 http://debian.oregonstate.edu/debian unstable/main s390x linux-libc-dev s390x 4.19.16-1 [1127 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main s390x libc6-dev s390x 2.28-5 [2268 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main s390x libgomp1 s390x 8.2.0-16 [68.8 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main s390x libitm1 s390x 8.2.0-16 [26.7 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main s390x libubsan1 s390x 8.2.0-16 [113 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main s390x libgcc-8-dev s390x 8.2.0-16 [640 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main s390x libstdc++-8-dev s390x 8.2.0-16 [1495 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.7 MB in 0s (58.7 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 14897 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-2_amd64.deb ... Unpacking groff-base (1.22.4-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-1_amd64.deb ... Unpacking man-db (2.8.5-1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../07-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../08-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../09-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../10-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../11-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../12-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../13-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../14-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../15-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../16-libfile-stripnondeterminism-perl_1.1.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../17-dh-strip-nondeterminism_1.1.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../18-libelf1_0.175-2_amd64.deb ... Unpacking libelf1:amd64 (0.175-2) ... Selecting previously unselected package dwz. Preparing to unpack .../19-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../20-libglib2.0-0_2.58.2-4_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.2-4) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../21-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../22-libncurses6_6.1+20181013-1_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-1) ... Selecting previously unselected package gettext. Preparing to unpack .../23-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../24-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../25-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../26-debhelper_12_all.deb ... Unpacking debhelper (12) ... Selecting previously unselected package gcc-8-base:s390x. Preparing to unpack .../27-gcc-8-base_8.2.0-16_s390x.deb ... Unpacking gcc-8-base:s390x (8.2.0-16) ... Selecting previously unselected package libgcc1:s390x. Preparing to unpack .../28-libgcc1_1%3a8.2.0-16_s390x.deb ... Unpacking libgcc1:s390x (1:8.2.0-16) ... Selecting previously unselected package libc6:s390x. Preparing to unpack .../29-libc6_2.28-5_s390x.deb ... Unpacking libc6:s390x (2.28-5) ... Selecting previously unselected package libstdc++6:s390x. Preparing to unpack .../30-libstdc++6_8.2.0-16_s390x.deb ... Unpacking libstdc++6:s390x (8.2.0-16) ... Selecting previously unselected package libasan5:s390x. Preparing to unpack .../31-libasan5_8.2.0-16_s390x.deb ... Unpacking libasan5:s390x (8.2.0-16) ... Selecting previously unselected package libatomic1:s390x. Preparing to unpack .../32-libatomic1_8.2.0-16_s390x.deb ... Unpacking libatomic1:s390x (8.2.0-16) ... Selecting previously unselected package linux-libc-dev:s390x. Preparing to unpack .../33-linux-libc-dev_4.19.16-1_s390x.deb ... Unpacking linux-libc-dev:s390x (4.19.16-1) ... Selecting previously unselected package libc6-dev:s390x. Preparing to unpack .../34-libc6-dev_2.28-5_s390x.deb ... Unpacking libc6-dev:s390x (2.28-5) ... Selecting previously unselected package libgomp1:s390x. Preparing to unpack .../35-libgomp1_8.2.0-16_s390x.deb ... Unpacking libgomp1:s390x (8.2.0-16) ... Selecting previously unselected package libitm1:s390x. Preparing to unpack .../36-libitm1_8.2.0-16_s390x.deb ... Unpacking libitm1:s390x (8.2.0-16) ... Selecting previously unselected package libubsan1:s390x. Preparing to unpack .../37-libubsan1_8.2.0-16_s390x.deb ... Unpacking libubsan1:s390x (8.2.0-16) ... Selecting previously unselected package libgcc-8-dev:s390x. Preparing to unpack .../38-libgcc-8-dev_8.2.0-16_s390x.deb ... Unpacking libgcc-8-dev:s390x (8.2.0-16) ... Selecting previously unselected package libstdc++-8-dev:s390x. Preparing to unpack .../39-libstdc++-8-dev_8.2.0-16_s390x.deb ... Unpacking libstdc++-8-dev:s390x (8.2.0-16) ... Selecting previously unselected package sbuild-build-depends-t-coffee-dummy:s390x. Preparing to unpack .../40-sbuild-build-depends-t-coffee-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-t-coffee-dummy:s390x (0.invalid.0) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libelf1:amd64 (0.175-2) ... Setting up libglib2.0-0:amd64 (2.58.2-4) ... No schema files found: doing nothing. Setting up linux-libc-dev:s390x (4.19.16-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libpipeline1:amd64 (1.5.1-1) ... Setting up m4 (1.4.18-2) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up gcc-8-base:s390x (8.2.0-16) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libncurses6:amd64 (6.1+20181013-1) ... Setting up autopoint (0.19.8.1-9) ... Setting up libfile-stripnondeterminism-perl (1.1.0-1) ... Setting up libtool (2.4.6-9) ... Setting up gettext (0.19.8.1-9) ... Setting up groff-base (1.22.4-2) ... Setting up autoconf (2.69-11) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up po-debconf (1.0.21) ... Setting up libc6:s390x (2.28-5) ... Setting up libc6-dev:s390x (2.28-5) ... Setting up libitm1:s390x (8.2.0-16) ... Setting up libgcc1:s390x (1:8.2.0-16) ... Setting up libgomp1:s390x (8.2.0-16) ... Setting up libatomic1:s390x (8.2.0-16) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.0-1) ... Setting up libstdc++6:s390x (8.2.0-16) ... Setting up libasan5:s390x (8.2.0-16) ... Setting up libubsan1:s390x (8.2.0-16) ... Setting up debhelper (12) ... Setting up libgcc-8-dev:s390x (8.2.0-16) ... Setting up libstdc++-8-dev:s390x (8.2.0-16) ... Setting up sbuild-build-depends-t-coffee-dummy:s390x (0.invalid.0) ... Processing triggers for libc-bin (2.28-5) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-11 dpkg-dev_1.19.4 g++-8_8.2.0-16 gcc-8_8.2.0-16 libc6-dev_2.28-5 libstdc++-8-dev_8.2.0-16 libstdc++-8-dev-s390x-cross_8.2.0-11cross1 libstdc++6_8.2.0-16 libstdc++6-s390x-cross_8.2.0-11cross1 linux-libc-dev_4.19.16-1 Package versions: adduser_3.118 apt_1.8.0~beta1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_5.0-2 binutils_2.31.1-11 binutils-common_2.31.1-11 binutils-s390x-linux-gnu_2.31.1-11 binutils-x86-64-linux-gnu_2.31.1-11 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 coreutils_8.30-1 cpp_4:8.2.0-2 cpp-8_8.2.0-16 cpp-8-s390x-linux-gnu_8.2.0-11cross1 cpp-s390x-linux-gnu_4:8.2.0-2 cross-config_2.6.15-2 crossbuild-essential-s390x_12.5 dash_0.5.10.2-5 debconf_1.5.70 debhelper_12 debian-archive-keyring_2018.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dpkg_1.19.4 dpkg-cross_2.6.15-2 dpkg-dev_1.19.4 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2 g++-8_8.2.0-16 g++-8-s390x-linux-gnu_8.2.0-11cross1 g++-s390x-linux-gnu_4:8.2.0-2 gcc_4:8.2.0-2 gcc-8_8.2.0-16 gcc-8-base_8.2.0-16 gcc-8-cross-base_8.2.0-11cross1 gcc-8-s390x-linux-gnu_8.2.0-11cross1 gcc-8-s390x-linux-gnu-base_8.2.0-11cross1 gcc-s390x-linux-gnu_4:8.2.0-2 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.12-1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.8.0~beta1 libarchive-zip-perl_1.64-1 libasan5_8.2.0-16 libasan5-s390x-cross_8.2.0-11cross1 libatomic1_8.2.0-16 libatomic1-s390x-cross_8.2.0-11cross1 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-11 libblkid1_2.33.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-5 libc-dev-bin_2.28-5 libc6_2.28-5 libc6-dev_2.28-5 libc6-dev-s390x-cross_2.28-4cross1 libc6-s390x-cross_2.28-4cross1 libcap-ng0_0.7.9-2 libcc1-0_8.2.0-16 libcom-err2_1.44.5-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.3 libdebconfclient0_0.246 libdebian-dpkgcross-perl_2.6.15-2 libdpkg-perl_1.19.4 libelf1_0.175-2 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.1.0-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.2.0-16 libgcc-8-dev-s390x-cross_8.2.0-11cross1 libgcc1_1:8.2.0-16 libgcc1-s390x-cross_1:8.2.0-11cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-2 libgdbm6_1.18.1-2 libglib2.0-0_2.58.2-4 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.2.0-16 libgomp1-s390x-cross_8.2.0-11cross1 libgpg-error0_1.33-3 libhogweed4_3.4.1-1 libicu63_63.1-6 libidn2-0_2.0.5-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.2.0-16 libitm1-s390x-cross_8.2.0-11cross1 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.2.0-16 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.2.0-16 libncurses6_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam0g_1.1.8-4 libpcre3_2:8.39-11 libperl5.28_5.28.1-4 libpipeline1_1.5.1-1 libquadmath0_8.2.0-16 libseccomp2_2.3.3-3 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libss2_1.44.5-1 libstdc++-8-dev_8.2.0-16 libstdc++-8-dev-s390x-cross_8.2.0-11cross1 libstdc++6_8.2.0-16 libstdc++6-s390x-cross_8.2.0-11cross1 libsystemd0_240-5 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-1 libtool_2.4.6-9 libtsan0_8.2.0-16 libubsan1_8.2.0-16 libubsan1-s390x-cross_8.2.0-11cross1 libuchardet0_0.0.6-3 libudev1_240-5 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml-libxml-perl_2.0132+dfsg-2+b1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.16-1 linux-libc-dev-s390x-cross_4.19.13-1cross1 login_1:4.5-1.1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.28_5.28.1-4 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-t-coffee-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-6 tar_1.30+dfsg-4 tzdata_2018i-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Dec 17 14:42:20 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./t-coffee_12.00.7fb08c2-1.dsc dpkg-source: info: extracting t-coffee in /<> dpkg-source: info: unpacking t-coffee_12.00.7fb08c2.orig.tar.gz dpkg-source: info: unpacking t-coffee_12.00.7fb08c2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying ncbi-blast++_has_dropped_pl_extension.patch dpkg-source: info: applying use_debian_packaged_TMalign.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying set_proper_dir_permissions.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying stable-linking-inputs.patch dpkg-source: info: applying clustalw2.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.s390x DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-7764c21a-b0b1-4168-82cb-e488af2c9c7f SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 12.00.7fb08c2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type s390x-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/t_coffee.log bin/t_coffee rm -rf t_coffee_source/TMalign find . -name "*.o" -delete find . -name "*.deps" -delete chmod 644 example/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules build-arch dh build-arch --sourcedirectory=t_coffee_source dh_update_autotools_config -a -O--sourcedirectory=t_coffee_source dh_autoreconf -a -O--sourcedirectory=t_coffee_source dh_auto_configure -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- -i USER_BIN=../bin/ FCC="gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" all cd t_coffee_source && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=s390x-linux-gnu-pkg-config CXX=s390x-linux-gnu-g\+\+ CC=s390x-linux-gnu-gcc -i USER_BIN=../bin/ "FCC=gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" all make[2]: Entering directory '/<>/t_coffee_source' CC dev_lib/dev1.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dev_lib/dev1.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dev_lib/dev1.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dev_lib/dev1.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dev_lib/dev1.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dev_lib/dev1.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ dev_lib/dev1.c: In function 'aln2hitMat': dev_lib/dev1.c:89:19: warning: too many arguments for format [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ^~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: dev_lib/dev1.o] Error 1 (ignored) CC dp_lib/CUSTOM_evaluate_for_struc.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/CUSTOM_evaluate_for_struc.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/CUSTOM_evaluate_for_struc.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/CUSTOM_evaluate_for_struc.o] Error 1 (ignored) CC dp_lib/evaluate.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/evaluate.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./util_lib_header.h:41, from dp_lib/evaluate.c:35: ./util_lib/hsearch.h:70:10: error: conflicting types for 'hcreate' HaschT * hcreate ( int n_elements,struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) ); ^~~~~~~ In file included from dp_lib/evaluate.c:33: /usr/s390x-linux-gnu/include/search.h:90:12: note: previous declaration of 'hcreate' was here extern int hcreate (size_t __nel) __THROW; ^~~~~~~ In file included from ./util_lib_header.h:41, from dp_lib/evaluate.c:35: ./util_lib/hsearch.h:71:9: error: conflicting types for 'hdestroy' HaschT *hdestroy (HaschT *T,struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) ); ^~~~~~~~ In file included from dp_lib/evaluate.c:33: /usr/s390x-linux-gnu/include/search.h:93:13: note: previous declaration of 'hdestroy' was here extern void hdestroy (void) __THROW; ^~~~~~~~ In file included from ./util_lib_header.h:41, from dp_lib/evaluate.c:35: ./util_lib/hsearch.h:72:14: error: conflicting types for 'hsearch' Hasch_entry* hsearch (HaschT *T, int k, int action, struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) ); ^~~~~~~ In file included from dp_lib/evaluate.c:33: /usr/s390x-linux-gnu/include/search.h:87:15: note: previous declaration of 'hsearch' was here extern ENTRY *hsearch (ENTRY __item, ACTION __action) __THROW; ^~~~~~~ In file included from ./dp_lib_header.h:49, from dp_lib/evaluate.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/evaluate.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ dp_lib/evaluate.c: In function 'msa_list2struc_evaluate4tcoffee': dp_lib/evaluate.c:1122:20: error: initializer element is not constant static char *tmp=vtmpnam (NULL); ^~~~~~~ dp_lib/evaluate.c: In function 'shuff': dp_lib/evaluate.c:1246:20: error: initializer element is not constant static char *seq=vtmpnam(NULL); ^~~~~~~ dp_lib/evaluate.c:1247:20: error: initializer element is not constant static char *aln=vtmpnam(NULL); ^~~~~~~ dp_lib/evaluate.c: In function 'hotnode2aln': dp_lib/evaluate.c:1472:21: error: initializer element is not constant static char *seq0=vtmpnam (NULL); ^~~~~~~ dp_lib/evaluate.c:1473:21: error: initializer element is not constant static char *seq1=vtmpnam (NULL); ^~~~~~~ dp_lib/evaluate.c:1474:21: error: initializer element is not constant static char *aln0=vtmpnam (NULL); ^~~~~~~ dp_lib/evaluate.c:1475:21: error: initializer element is not constant static char *aln1=vtmpnam (NULL); ^~~~~~~ dp_lib/evaluate.c:1476:21: error: initializer element is not constant static char *aln2=vtmpnam (NULL); ^~~~~~~ dp_lib/evaluate.c: In function 'struc_evaluate4tcoffee': dp_lib/evaluate.c:1969:25: warning: assignment to 'int *' from incompatible pointer type 'Alignment *' {aka 'struct Alignment *'} [-Wincompatible-pointer-types] if (!A->Tree)T=A->Tree=declare_aln2(ntrees,0); ^ dp_lib/evaluate.c:1969:17: warning: assignment to 'Alignment *' {aka 'struct Alignment *'} from incompatible pointer type 'int *' [-Wincompatible-pointer-types] if (!A->Tree)T=A->Tree=declare_aln2(ntrees,0); ^ dp_lib/evaluate.c:2134:36: error: initializer element is not constant static int distance_mode=atoigetenv ("THREED_TREE_MODE"); ^~~~~~~~~~ dp_lib/evaluate.c:2135:38: error: initializer element is not constant static double distance_modeE=atofgetenv ("THREED_TREE_MODE_EXP"); ^~~~~~~~~~ dp_lib/evaluate.c:2278:25: error: initializer element is not constant static char *treeF=vtmpnam (NULL); ^~~~~~~ dp_lib/evaluate.c: In function 'msa2distances': dp_lib/evaluate.c:2956:53: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] 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); ~~~~^ ~~~ %3.2d dp_lib/evaluate.c:2956:67: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] 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); ~~^ ~~~~~~~ %3f dp_lib/evaluate.c:2956:79: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] 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); ~~~^ ~~~~~~~~ %.3d dp_lib/evaluate.c:2956:95: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] 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); ~~^ ~~~~~~ %3f dp_lib/evaluate.c: In function 'treealn_evaluate4tcoffee': dp_lib/evaluate.c:3027:4: warning: assignment to 'Alignment *' {aka 'struct Alignment *'} from incompatible pointer type 'int *' [-Wincompatible-pointer-types] T=A->Tree; ^ dp_lib/evaluate.c: In function 'evaluate_tree_group': dp_lib/evaluate.c:3112:44: warning: passing argument 1 of 'evaluate_tree_group' from incompatible pointer type [-Wincompatible-pointer-types] if (T->Tree)return evaluate_tree_group (T->Tree, G); ~^~~~~~ dp_lib/evaluate.c:3108:44: note: expected 'Alignment *' {aka 'struct Alignment *'} but argument is of type 'int *' Alignment *evaluate_tree_group (Alignment *T, Sequence *G) ~~~~~~~~~~~^ dp_lib/evaluate.c: In function 'fork_triplet_coffee_evaluate_output': dp_lib/evaluate.c:809:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &res); ^~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:814:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:819:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c: In function 'initialise_aa_physico_chemical_property_table': dp_lib/evaluate.c:7511:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %c %*s",&v1, &c1 ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: dp_lib/evaluate.o] Error 1 (ignored) CC dp_lib/evaluate_dirichlet.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_dirichlet.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/evaluate_dirichlet.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_dirichlet.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/evaluate_dirichlet.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/evaluate_dirichlet.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ dp_lib/evaluate_dirichlet.c:651:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf) ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/evaluate_dirichlet.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ dp_lib/evaluate_dirichlet.c: In function 'read_dirichlet': dp_lib/evaluate_dirichlet.c:317:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f\n", &f); ^~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ^~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ^~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ^~~~~~~~~~~~~~~~ make[2]: [makefile:11: dp_lib/evaluate_dirichlet.o] Error 1 (ignored) CC dp_lib/evaluate_for_domain.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_for_domain.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/evaluate_for_domain.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_domain.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/evaluate_for_domain.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/evaluate_for_domain.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/evaluate_for_domain.o] Error 1 (ignored) CC dp_lib/evaluate_for_struc.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_for_struc.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/evaluate_for_struc.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/evaluate_for_struc.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/evaluate_for_struc.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ dp_lib/evaluate_for_struc.c: In function 'msa2struc_dist': dp_lib/evaluate_for_struc.c:2687:7: error: 'tnode' undeclared (first use in this function) T1=(tnode**)vcalloc (A->len_aln*A->len_aln+1, sizeof (NT_node)); ^~~~~ dp_lib/evaluate_for_struc.c:2687:7: note: each undeclared identifier is reported only once for each function it appears in dp_lib/evaluate_for_struc.c:2687:14: error: expected expression before ')' token T1=(tnode**)vcalloc (A->len_aln*A->len_aln+1, sizeof (NT_node)); ^ dp_lib/evaluate_for_struc.c:2688:14: error: expected expression before ')' token T2=(tnode**)vcalloc (A->len_aln+1, sizeof (NT_node)); ^ dp_lib/evaluate_for_struc.c:2690:14: error: expected expression before ')' token PT=(tnode**)vcalloc (A->len_aln*A->len_aln+1, sizeof (NT_node)); ^ dp_lib/evaluate_for_struc.c:2691:15: error: expected expression before ')' token POS=(tnode**)vcalloc (A->len_aln+1, sizeof (NT_node)); ^ make[2]: [makefile:11: dp_lib/evaluate_for_struc.o] Error 1 (ignored) CC dp_lib/fsa_dp.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/fsa_dp.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/fsa_dp.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/fsa_dp.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/fsa_dp.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/fsa_dp.o] Error 1 (ignored) CC dp_lib/pavie_dp.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/pavie_dp.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/pavie_dp.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/pavie_dp.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/pavie_dp.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/pavie_dp.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ dp_lib/pavie_dp.c: In function 'pavie_score': dp_lib/pavie_dp.c:930:28: error: 'const_cast' undeclared (first use in this function); did you mean 'aln_cat'? mat[a]=read_matrice ( const_cast( (mat_file)?mat_file[a]:"idmat" ) ); ^~~~~~~~~~ aln_cat dp_lib/pavie_dp.c:930:28: note: each undeclared identifier is reported only once for each function it appears in dp_lib/pavie_dp.c:930:39: error: expected expression before 'char' mat[a]=read_matrice ( const_cast( (mat_file)?mat_file[a]:"idmat" ) ); ^~~~ dp_lib/pavie_dp.c: In function 'pavie_seq2pavie_aln': dp_lib/pavie_dp.c:127:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",mat_list[nch++]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function 'output_pavie_mat_list': dp_lib/pavie_dp.c:1079:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system (command); ^~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c:1081:7: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system (command); ^~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function 'pavie_seq2pavie_msa': dp_lib/pavie_dp.c:1365:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", mat); ^~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: dp_lib/pavie_dp.o] Error 1 (ignored) CC dp_lib/showpair.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/showpair.c:32: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/showpair.c:32: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/showpair.c:32: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/showpair.c:35: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/showpair.c:35: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/showpair.o] Error 1 (ignored) CC dp_lib/util_domain_dp.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_domain_dp.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_domain_dp.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_domain_dp.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_domain_dp.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_domain_dp.o] Error 1 (ignored) CC dp_lib/util_domain_dp_drivers.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_domain_dp_drivers.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_domain_dp_drivers.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_domain_dp_drivers.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_domain_dp_drivers.o] Error 1 (ignored) CC dp_lib/util_dp_cdna_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_cdna_fasta_nw.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_cdna_fasta_nw.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_cdna_fasta_nw.o] Error 1 (ignored) CC dp_lib/util_dp_clean_maln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_clean_maln.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_clean_maln.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_clean_maln.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_clean_maln.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_clean_maln.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_clean_maln.o] Error 1 (ignored) CC dp_lib/util_dp_drivers.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_drivers.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_drivers.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_drivers.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_drivers.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ dp_lib/util_dp_drivers.c:935:12: error: conflicting types for 'seq2msa' Alignment *seq2msa (char *method,Sequence *S) ^~~~~~~ In file included from ./dp_lib_header.h:44, from dp_lib/util_dp_drivers.c:36: ./dp_lib/util_dp_drivers.h:66:12: note: previous declaration of 'seq2msa' was here Alignment *seq2msa (Sequence *S); ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'profile_pair': dp_lib/util_dp_drivers.c:1353:27: error: initializer element is not constant static char *result2=vtmpnam (NULL); ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'seq_file2msa_file': dp_lib/util_dp_drivers.c:1014:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ dp_lib/util_dp_drivers.c:1028:7: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'align_pdb_pair_2': dp_lib/util_dp_drivers.c:1080:6: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'align_pdb_pair': dp_lib/util_dp_drivers.c:1108:6: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'hh_pair': dp_lib/util_dp_drivers.c:1149:4: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1160:3: warning: ignoring return value of 'tmpnam', declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln1); ^~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1161:3: warning: ignoring return value of 'tmpnam', declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln2); ^~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1164:3: warning: ignoring return value of 'tmpnam', declared with attribute warn_unused_result [-Wunused-result] tmpnam(hhfile); ^~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1211:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets (buf2, 10000, fp); ^~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'profile_pair': dp_lib/util_dp_drivers.c:1280:2: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1363:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", bufname); ^~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'profile_pair_decomposed': dp_lib/util_dp_drivers.c:1445:3: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'profile_subset_pair_old': dp_lib/util_dp_drivers.c:1581:3: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'pdbid_pair': dp_lib/util_dp_drivers.c:1717:4: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'pdb_pair': dp_lib/util_dp_drivers.c:1774:4: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'thread_pair': dp_lib/util_dp_drivers.c:1906:4: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'lsqman_pair': dp_lib/util_dp_drivers.c:1981:4: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'sap_pair': dp_lib/util_dp_drivers.c:2073:6: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2121:3: warning: ignoring return value of 'getcwd', declared with attribute warn_unused_result [-Wunused-result] getcwd (cdir, sizeof(char)*1000); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2122:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (get_cache_dir()); ^~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2142:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'rnapdb_pair': dp_lib/util_dp_drivers.c:2256:2: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_drivers.o] Error 1 (ignored) CC dp_lib/util_dp_est.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_est.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_est.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_est.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_est.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_est.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_est.o] Error 1 (ignored) CC dp_lib/util_dp_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_fasta_nw.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_fasta_nw.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_nw.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_fasta_nw.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_fasta_nw.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_fasta_nw.o] Error 1 (ignored) CC dp_lib/util_dp_fasta_sw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_fasta_sw.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_fasta_sw.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_sw.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_fasta_sw.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_fasta_sw.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_fasta_sw.o] Error 1 (ignored) CC dp_lib/util_dp_generic_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_generic_fasta_nw.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_generic_fasta_nw.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_generic_fasta_nw.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_generic_fasta_nw.o] Error 1 (ignored) CC dp_lib/util_dp_gotoh_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_gotoh_nw.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_gotoh_nw.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_nw.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_gotoh_nw.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_gotoh_nw.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_gotoh_nw.o] Error 1 (ignored) CC dp_lib/util_dp_gotoh_sw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_gotoh_sw.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_gotoh_sw.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_sw.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_gotoh_sw.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_gotoh_sw.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ dp_lib/util_dp_gotoh_sw.c: In function 'gotoh_pair_wise_sw': dp_lib/util_dp_gotoh_sw.c:391:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_gotoh_sw.o] Error 1 (ignored) CC dp_lib/util_dp_mm_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_mm_nw.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_mm_nw.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_mm_nw.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_mm_nw.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_mm_nw.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_mm_nw.o] Error 1 (ignored) CC dp_lib/util_dp_sim.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_sim.c:32: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_sim.c:32: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_sim.c:35: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_sim.c:35: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_sim.o] Error 1 (ignored) CC dp_lib/util_dp_ssec_pwaln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_ssec_pwaln.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_ssec_pwaln.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_ssec_pwaln.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_ssec_pwaln.o] Error 1 (ignored) CC dp_lib/util_dp_suboptimal_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_suboptimal_nw.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_dp_suboptimal_nw.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_suboptimal_nw.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_dp_suboptimal_nw.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_dp_suboptimal_nw.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_dp_suboptimal_nw.o] Error 1 (ignored) CC dp_lib/util_graph_maln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_graph_maln.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from dp_lib/util_graph_maln.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from dp_lib/util_graph_maln.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from dp_lib/util_graph_maln.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: dp_lib/util_graph_maln.o] Error 1 (ignored) CC fastal/diagonal.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/diagonal.c:31: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from fastal/diagonal.c:31: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/diagonal.c:31: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ fastal/diagonal.c: In function 'seq_pair2blast_diagonal2': fastal/diagonal.c:434:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^~~~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:439:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^~~~~~~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^~~~~~~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: fastal/diagonal.o] Error 1 (ignored) CC fastal/fastal.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/fastal.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from fastal/fastal.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/fastal.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from fastal/fastal.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from fastal/fastal.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ fastal/fastal.c: In function 'seq_pair2blast_diagonal': fastal/fastal.c:1924:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1929:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1976:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1980:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'seq_pair2blat_diagonal': fastal/fastal.c:2115:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'seq_pair2blastz_diagonal': fastal/fastal.c:2262:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'file_pos2profile': fastal/fastal.c:3201:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , seq_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'profile_file2profile': fastal/fastal.c:3323:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3326:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , profile_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'edit_seq2aligned_seq': fastal/fastal.c:3502:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , sequence_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'edit2alignment': fastal/fastal.c:3575:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(aligned_sequence, alignment_length+3, edit_seq_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: fastal/fastal.o] Error 1 (ignored) CC fastal/fastal_opt_parsing.c CC fastal/iteration.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/iteration.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from fastal/iteration.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/iteration.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ fastal/iteration.c: In function 'split_set': fastal/iteration.c:185:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'iterate': fastal/iteration.c:310:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system(command); ^~~~~~~~~~~~~~~ fastal/iteration.c: In function 'write_iterated_aln': fastal/iteration.c:501:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:535:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH, old_aln_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function 'edit2seq_pattern': fastal/iteration.c:563:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: fastal/iteration.o] Error 1 (ignored) CC fastal/parttree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/parttree.c:36: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from fastal/parttree.c:36: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/parttree.c:36: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from fastal/parttree.c:39: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from fastal/parttree.c:39: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ fastal/parttree.c: In function 'int_dist2upgma_tree_fastal': fastal/parttree.c:220:6: error: 'tnode' undeclared (first use in this function) NL=(tnode**)vcalloc (nseq, sizeof (NT_node)); ^~~~~ fastal/parttree.c:220:6: note: each undeclared identifier is reported only once for each function it appears in fastal/parttree.c:220:13: error: expected expression before ')' token NL=(tnode**)vcalloc (nseq, sizeof (NT_node)); ^ fastal/parttree.c: In function 'make_distance_matrix_sim': fastal/parttree.c:695:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ^~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:701:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ^~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'get_table': fastal/parttree.c:848:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:859:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'euclidean_dist': fastal/parttree.c:891:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'euclidean_dist_half': fastal/parttree.c:951:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: fastal/parttree.o] Error 1 (ignored) CC fastal/scoring.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/scoring.c:37: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from fastal/scoring.c:37: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/scoring.c:37: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ fastal/scoring.c: In function 'calculate_sum_of_pairs_score_affine': fastal/scoring.c:76:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'compute_ref_alignments': fastal/scoring.c:384:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system(aln_command); ^~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'make_ref_alignment': fastal/scoring.c:488:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_f); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system(command); ^~~~~~~~~~~~~~~ fastal/scoring.c: In function 'agreement_score': fastal/scoring.c:583:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: fastal/scoring.o] Error 1 (ignored) CC fastal/tree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from fastal/tree.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from fastal/tree.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/tree.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ make[2]: [makefile:11: fastal/tree.o] Error 1 (ignored) CC io_lib/io_func.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/io_func.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from io_lib/io_func.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from io_lib/io_func.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ io_lib/io_func.c: In function 'output_raw_score': io_lib/io_func.c:1235:17: warning: returning 'void *' from a function with return type 'int' makes integer from pointer without a cast [-Wint-conversion] if (!A)return NULL; ^~~~ io_lib/io_func.c: In function 'aln2compressed_ps': io_lib/io_func.c:2053:19: error: initializer element is not constant static Color *C=(Color*)vcalloc ( 1, sizeof (Color)); ^ io_lib/io_func.c: In function 'read_matrice': io_lib/io_func.c:511:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ^~~~~~~~~~~~~~~~~~ io_lib/io_func.c: In function 'get_rgb_values': io_lib/io_func.c:971:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: io_lib/io_func.o] Error 1 (ignored) CC io_lib/pb_util_read_seq_util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/pb_util_read_seq_util.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from io_lib/pb_util_read_seq_util.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_seq_util.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ io_lib/pb_util_read_seq_util.c: In function 'getstr': io_lib/pb_util_read_seq_util.c:269:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(outstr, 100, stdin); ^~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'getreal': io_lib/pb_util_read_seq_util.c:280:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'getint': io_lib/pb_util_read_seq_util.c:305:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: io_lib/pb_util_read_seq_util.o] Error 1 (ignored) CC io_lib/pb_util_read_sequence.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/pb_util_read_sequence.c:35: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from io_lib/pb_util_read_sequence.c:35: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_sequence.c:35: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ io_lib/pb_util_read_sequence.c: In function 'get_clustal_seq': io_lib/pb_util_read_sequence.c:144:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ ^~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_sequence.c:149:25: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for(i=1;iDM=cl2distance_matrix (CL,NOALN,const_cast( (mode==NULL)?"ktup":mode), NULL, 0); ^~~~~~~~~~ aln_cat io_lib/tree_util.c:75:39: note: each undeclared identifier is reported only once for each function it appears in io_lib/tree_util.c:75:50: error: expected expression before 'char' CL->DM=cl2distance_matrix (CL,NOALN,const_cast( (mode==NULL)?"ktup":mode), NULL, 0); ^~~~ io_lib/tree_util.c:75:10: error: too few arguments to function 'cl2distance_matrix' CL->DM=cl2distance_matrix (CL,NOALN,const_cast( (mode==NULL)?"ktup":mode), NULL, 0); ^~~~~~~~~~~~~~~~~~ In file included from ./util_lib_header.h:34, from io_lib/tree_util.c:34: ./util_lib/util_constraints_list.h:686:18: note: declared here Distance_matrix *cl2distance_matrix (Constraint_list *CL, Alignment *A, char *mode, char *sim_mode, int print); ^~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: In function 'tree_scan': io_lib/tree_util.c:836:19: warning: too many arguments for format [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ^~~~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: At top level: io_lib/tree_util.c:1196:13: error: conflicting types for 'phylotrim1' Alignment * phylotrim1 (Alignment *A, char *reftree,int narg,char **narglm, char *name); ^~~~~~~~~~ io_lib/tree_util.c:1193:13: note: previous declaration of 'phylotrim1' was here Alignment * phylotrim1 (Alignment *A, char *reftree,int narg,char **nargl); ^~~~~~~~~~ io_lib/tree_util.c: In function 'phylotrim': io_lib/tree_util.c:1258:26: error: initializer element is not constant static char * alnF=vtmpnam (NULL); ^~~~~~~ io_lib/tree_util.c: In function 'phylotrim2': io_lib/tree_util.c:1311:23: error: initializer element is not constant static char *tmpaln=vtmpnam (NULL); ^~~~~~~ io_lib/tree_util.c: At top level: io_lib/tree_util.c:1351:13: error: conflicting types for 'phylotrim1' Alignment * phylotrim1 (Alignment *A, char *reftree, int narg, char **argl, char *name) ^~~~~~~~~~ io_lib/tree_util.c:1193:13: note: previous declaration of 'phylotrim1' was here Alignment * phylotrim1 (Alignment *A, char *reftree,int narg,char **nargl); ^~~~~~~~~~ io_lib/tree_util.c: In function 'phylotrim1': io_lib/tree_util.c:1359:21: error: initializer element is not constant static char *alnF=vtmpnam (NULL); ^~~~~~~ io_lib/tree_util.c: In function 'main_aln2tree': io_lib/tree_util.c:1679:25: error: initializer element is not constant static char *tmpA=vtmpnam(NULL); ^~~~~~~ io_lib/tree_util.c: In function 'aln2trmsd_tree': io_lib/tree_util.c:1871:22: error: initializer element is not constant static char *fname=vtmpnam (NULL); ^~~~~~~ io_lib/tree_util.c:1872:21: error: initializer element is not constant static char *tree=vtmpnam (NULL); ^~~~~~~ io_lib/tree_util.c: In function 'output_fasta_tree': io_lib/tree_util.c:4644:49: warning: passing argument 2 of 'output_fasta_tree' from incompatible pointer type [-Wincompatible-pointer-types] if (A->Tree)return output_fasta_tree (fname, A->Tree); ~^~~~~~ io_lib/tree_util.c:4638:48: note: expected 'Alignment *' {aka 'struct Alignment *'} but argument is of type 'int *' void output_fasta_tree (char *fname, Alignment*A) ~~~~~~~~~~^ io_lib/tree_util.c: In function 'output_treelist': io_lib/tree_util.c:4660:47: warning: passing argument 2 of 'output_treelist' from incompatible pointer type [-Wincompatible-pointer-types] if (A->Tree)return output_treelist (fname, A->Tree); ~^~~~~~ io_lib/tree_util.c:4654:46: note: expected 'Alignment *' {aka 'struct Alignment *'} but argument is of type 'int *' void output_treelist (char *fname, Alignment*A) ~~~~~~~~~~^ io_lib/tree_util.c: In function 'newick_string2tree': io_lib/tree_util.c:6313:20: error: initializer element is not constant static char *tmp=vtmpnam (NULL); ^~~~~~~ io_lib/tree_util.c: In function 'treelist2cons': io_lib/tree_util.c:7482:43: warning: passing argument 1 of 'treelist2cons' from incompatible pointer type [-Wincompatible-pointer-types] else if (T->Tree)return treelist2cons (T->Tree); ~^~~~~~ io_lib/tree_util.c:7474:38: note: expected 'Alignment *' {aka 'struct Alignment *'} but argument is of type 'int *' Alignment *treelist2cons (Alignment *T) ~~~~~~~~~~~^ io_lib/tree_util.c: In function 'treelist2node_support_best': io_lib/tree_util.c:7570:51: warning: passing argument 1 of 'treelist2node_support_best' from incompatible pointer type [-Wincompatible-pointer-types] if (T->Tree)return treelist2node_support_best (T->Tree); ~^~~~~~ io_lib/tree_util.c:7562:51: note: expected 'Alignment *' {aka 'struct Alignment *'} but argument is of type 'int *' Alignment *treelist2node_support_best (Alignment *T) ~~~~~~~~~~~^ io_lib/tree_util.c: In function 'treelist2node_support': io_lib/tree_util.c:7668:51: warning: passing argument 1 of 'treelist2node_support' from incompatible pointer type [-Wincompatible-pointer-types] else if (T->Tree)return treelist2node_support (T->Tree); ~^~~~~~ io_lib/tree_util.c:7665:46: note: expected 'Alignment *' {aka 'struct Alignment *'} but argument is of type 'int *' Alignment *treelist2node_support (Alignment *T) ~~~~~~~~~~~^ io_lib/tree_util.c: At top level: io_lib/tree_util.c:8125:9: error: conflicting types for 'kmsa2msa' char *kmsa2msa (KT_node K,Sequence *S, ALNcol***S2,ALNcol*PG); ^~~~~~~~ In file included from ./io_lib_header.h:33, from io_lib/tree_util.c:33: ./io_lib/tree_util.h:389:7: note: previous declaration of 'kmsa2msa' was here char *kmsa2msa (Sequence *S,KT_node *KL, int n); ^~~~~~~~ io_lib/tree_util.c:8317:7: error: conflicting types for 'kmsa2msa' char *kmsa2msa (KT_node K,Sequence *S, ALNcol***S2,ALNcol*start) ^~~~~~~~ In file included from ./io_lib_header.h:33, from io_lib/tree_util.c:33: ./io_lib/tree_util.h:389:7: note: previous declaration of 'kmsa2msa' was here char *kmsa2msa (Sequence *S,KT_node *KL, int n); ^~~~~~~~ io_lib/tree_util.c: In function 'kseq2kmsa_nextflow': io_lib/tree_util.c:8673:21: error: initializer element is not constant static char *list=vtmpnam (NULL); ^~~~~~~ io_lib/tree_util.c: At top level: io_lib/tree_util.c:8781:7: error: conflicting types for 'kmsa2msa_serial' char* kmsa2msa_serial (KT_node K, int max, int *cn) ^~~~~~~~~~~~~~~ io_lib/tree_util.c:8135:8: note: previous declaration of 'kmsa2msa_serial' was here char * kmsa2msa_serial (Sequence *S,KT_node K, int max, int *cn); ^~~~~~~~~~~~~~~ io_lib/tree_util.c:8875:13: error: conflicting types for 'msa2graph' ALN_node ** msa2graph (Sequence *S, Alignment *A, ALN_node**lu); ^~~~~~~~~ io_lib/tree_util.c:8390:10: note: previous definition of 'msa2graph' was here ALNcol * msa2graph (Alignment *A, Sequence *S, ALNcol***S2,ALNcol*msa,int seq) ^~~~~~~~~ io_lib/tree_util.c:8881:7: error: conflicting types for 'graph2aln' char* graph2aln (Sequence *S, ALN_node *aln, int nseq,char *out); ^~~~~~~~~ In file included from ./dp_lib_header.h:30, from io_lib/tree_util.c:35: ./dp_lib/util_graph_maln.h:43:12: note: previous declaration of 'graph2aln' was here Alignment* graph2aln (Alignment *A, CL_node *G, Sequence *S); ^~~~~~~~~ io_lib/tree_util.c:8914:7: error: conflicting types for 'graph2aln' char* graph2aln (Sequence *S, ALN_node *aln, int nseq,char *out) ^~~~~~~~~ In file included from ./dp_lib_header.h:30, from io_lib/tree_util.c:35: ./dp_lib/util_graph_maln.h:43:12: note: previous declaration of 'graph2aln' was here Alignment* graph2aln (Alignment *A, CL_node *G, Sequence *S); ^~~~~~~~~ io_lib/tree_util.c:9142:13: error: conflicting types for 'msa2graph' ALN_node ** msa2graph (Sequence *S, Alignment *A, ALN_node**lu) ^~~~~~~~~ io_lib/tree_util.c:8390:10: note: previous definition of 'msa2graph' was here ALNcol * msa2graph (Alignment *A, Sequence *S, ALNcol***S2,ALNcol*msa,int seq) ^~~~~~~~~ io_lib/tree_util.c: In function 'graph2master_seq': io_lib/tree_util.c:9344:20: error: initializer element is not constant static int *aa=(int*)vcalloc(256, sizeof (int)); ^ io_lib/tree_util.c: In function 'graph2cons': io_lib/tree_util.c:9386:18: error: initializer element is not constant static int *aa=(int*)vcalloc(256, sizeof (int)); ^ io_lib/tree_util.c: In function 'declare_aln_node': io_lib/tree_util.c:9587:38: error: 'alnnode' undeclared (first use in this function) buf=(ALN_node)vmalloc (sizeof (alnnode)*chunk); ^~~~~~~ io_lib/tree_util.c: In function 'graph2cons_d': io_lib/tree_util.c:10014:18: error: initializer element is not constant static int *aa=(int*)vcalloc(256, sizeof (int)); ^ io_lib/tree_util.c:10027:25: warning: comparison between pointer and integer while ((c=rn_c(s))!=NULL) ^~ io_lib/tree_util.c: In function 'insert_gap_in_graph_d': io_lib/tree_util.c:10045:20: warning: initialization of 'long unsigned int' from 'void *' makes integer from pointer without a cast [-Wint-conversion] unsigned long pn=NULL; ^~~~ io_lib/tree_util.c:10047:22: warning: returning 'void *' from a function with return type 'long unsigned int' makes integer from pointer without a cast [-Wint-conversion] if (!start) return NULL; ^~~~ io_lib/tree_util.c:10060:14: warning: passing argument 2 of 'wn_c' makes integer from pointer without a cast [-Wint-conversion] wn_c(n,NULL); ^~~~ io_lib/tree_util.c:9811:46: note: expected 'long unsigned int' but argument is of type 'void *' void wn_c (unsigned long n, unsigned long t); ~~~~~~~~~~~~~~^ io_lib/tree_util.c: In function 'create_tree': io_lib/tree_util.c:3872:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%f",&dist); ^~~~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c:3880:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%f",&bootstrap); ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: io_lib/tree_util.o] Error 1 (ignored) CC km_coffee/Stack.c CC km_coffee/Vector.c km_coffee/Vector.c:28:9: fatal error: iostream: No such file or directory #include ^~~~~~~~~~ compilation terminated. make[2]: [makefile:11: km_coffee/Vector.o] Error 1 (ignored) CC km_coffee/classes.c CC km_coffee/km_coffee.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from km_coffee/km_coffee.c:43: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from km_coffee/km_coffee.c:43: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from km_coffee/km_coffee.c:43: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ km_coffee/km_coffee.c: In function 'km_coffee_align3': km_coffee/km_coffee.c:491:2: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir(km_tmp_dir); ^~~~~~~~~~~~~~~~~ make[2]: [makefile:11: km_coffee/km_coffee.o] Error 1 (ignored) CC km_coffee/km_util.c km_coffee/km_util.c: In function 'my_make_temp_dir': km_coffee/km_util.c:96:55: warning: format '%s' expects a matching 'char *' argument [-Wformat=] fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); ~^ CC km_coffee/kmeans.c km_coffee/kmeans.c:28:10: fatal error: iostream: No such file or directory #include ^~~~~~~~~~ compilation terminated. make[2]: [makefile:11: km_coffee/kmeans.o] Error 1 (ignored) CC t_coffee_lib/t_coffee.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from t_coffee_lib/t_coffee.c:35: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from t_coffee_lib/t_coffee.c:35: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from t_coffee_lib/t_coffee.c:35: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from t_coffee_lib/t_coffee.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from t_coffee_lib/t_coffee.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ t_coffee_lib/t_coffee.c: In function 'batch_main': t_coffee_lib/t_coffee.c:4996:42: error: 'const_cast' undeclared (first use in this function); did you mean 'aln_cat'? CL->gop=get_avg_matrix_mm ( CL->M, const_cast( (strm3((CL->S)->type,"PROTEIN", "Protein", "protein")?AA_ALPHABET:"gcuta")) )*10; ^~~~~~~~~~ aln_cat t_coffee_lib/t_coffee.c:4996:42: note: each undeclared identifier is reported only once for each function it appears in t_coffee_lib/t_coffee.c:4996:53: error: expected expression before 'char' CL->gop=get_avg_matrix_mm ( CL->M, const_cast( (strm3((CL->S)->type,"PROTEIN", "Protein", "protein")?AA_ALPHABET:"gcuta")) )*10; ^~~~ t_coffee_lib/t_coffee.c: At top level: t_coffee_lib/t_coffee.c:6401:12: error: conflicting types for 'km_coffee_align3' Alignment* km_coffee_align3 (Sequence *S, char *km_tree, int k, char *outfile, int argc, char **argv); ^~~~~~~~~~~~~~~~ In file included from ./km_coffee_header.h:30, from t_coffee_lib/t_coffee.c:40: ./km_coffee/km_coffee.h:82:1: note: previous declaration of 'km_coffee_align3' was here km_coffee_align3(char *seq_f, int k, int k_leaf, char *method, char *aln_f, int n_cores, int gapopen, int gapext, char *init); ^~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 'km_coffee': t_coffee_lib/t_coffee.c:6515:23: warning: passing argument 1 of 'km_coffee_align3' from incompatible pointer type [-Wincompatible-pointer-types] km_coffee_align3(seq_f, k, k_leaf, method, out_f, n_core, gapopen, gapext, km_init ); ^~~~~ t_coffee_lib/t_coffee.c:6401:12: note: expected 'Sequence *' {aka 'struct Sequence *'} but argument is of type 'char *' Alignment* km_coffee_align3 (Sequence *S, char *km_tree, int k, char *outfile, int argc, char **argv); ^~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c:6515:30: warning: passing argument 2 of 'km_coffee_align3' makes pointer from integer without a cast [-Wint-conversion] km_coffee_align3(seq_f, k, k_leaf, method, out_f, n_core, gapopen, gapext, km_init ); ^ t_coffee_lib/t_coffee.c:6401:12: note: expected 'char *' but argument is of type 'int' Alignment* km_coffee_align3 (Sequence *S, char *km_tree, int k, char *outfile, int argc, char **argv); ^~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c:6515:49: warning: passing argument 5 of 'km_coffee_align3' makes integer from pointer without a cast [-Wint-conversion] km_coffee_align3(seq_f, k, k_leaf, method, out_f, n_core, gapopen, gapext, km_init ); ^~~~~ t_coffee_lib/t_coffee.c:6401:12: note: expected 'int' but argument is of type 'char *' Alignment* km_coffee_align3 (Sequence *S, char *km_tree, int k, char *outfile, int argc, char **argv); ^~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c:6515:56: warning: passing argument 6 of 'km_coffee_align3' makes pointer from integer without a cast [-Wint-conversion] km_coffee_align3(seq_f, k, k_leaf, method, out_f, n_core, gapopen, gapext, km_init ); ^~~~~~ t_coffee_lib/t_coffee.c:6401:12: note: expected 'char **' but argument is of type 'int' Alignment* km_coffee_align3 (Sequence *S, char *km_tree, int k, char *outfile, int argc, char **argv); ^~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c:6515:6: error: too many arguments to function 'km_coffee_align3' km_coffee_align3(seq_f, k, k_leaf, method, out_f, n_core, gapopen, gapext, km_init ); ^~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c:6401:12: note: declared here Alignment* km_coffee_align3 (Sequence *S, char *km_tree, int k, char *outfile, int argc, char **argv); ^~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 'kmir': t_coffee_lib/t_coffee.c:6554:17: warning: passing argument 2 of 'aln2prf' makes integer from pointer without a cast [-Wint-conversion] prf=aln2prf(A, "blosum62mt"); ^~~~~~~~~~~~ In file included from ./dp_lib_header.h:49, from t_coffee_lib/t_coffee.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: note: expected 'int' but argument is of type 'char *' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ t_coffee_lib/t_coffee.c:6554:6: error: too few arguments to function 'aln2prf' prf=aln2prf(A, "blosum62mt"); ^~~~~~~ In file included from ./dp_lib_header.h:49, from t_coffee_lib/t_coffee.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: note: declared here double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ t_coffee_lib/t_coffee.c: At top level: t_coffee_lib/t_coffee.c:6937:13: error: conflicting types for 'km_coffee_align3' Alignment * km_coffee_align3 (Sequence *S, char *km_tree, int k, char *out_f, int argc, char **argv) ^~~~~~~~~~~~~~~~ In file included from ./km_coffee_header.h:30, from t_coffee_lib/t_coffee.c:40: ./km_coffee/km_coffee.h:82:1: note: previous declaration of 'km_coffee_align3' was here km_coffee_align3(char *seq_f, int k, int k_leaf, char *method, char *aln_f, int n_cores, int gapopen, int gapext, char *init); ^~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 't_coffee_dpa': t_coffee_lib/t_coffee.c:7129:61: warning: too many arguments for format [-Wformat-extra-args] else { w=seq2dpa_weight (S, "longuest");fprintf ( stderr, "default longuest\n", dpa_weight);} ^~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: t_coffee_lib/t_coffee.o] Error 1 (ignored) CC util_lib/aln_compare.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/aln_compare.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/aln_compare.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/aln_compare.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/aln_compare.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: util_lib/aln_compare.o] Error 1 (ignored) CC util_lib/aln_convertion_util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/aln_convertion_util.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/aln_convertion_util.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/aln_convertion_util.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/aln_convertion_util.c:35: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/aln_convertion_util.c:35: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ util_lib/aln_convertion_util.c: In function 'seq2swv': util_lib/aln_convertion_util.c:1491:23: error: initializer element is not constant static int **matrix=read_matrice ("blosum62mt"); ^~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'seq2swr': util_lib/aln_convertion_util.c:1505:23: error: initializer element is not constant static int **matrix=read_matrice ("blosum62mt"); ^~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'set_blast_default_values': util_lib/aln_convertion_util.c:1710:40: error: 'const_cast' undeclared (first use in this function); did you mean 'aln_cat'? set_string_variable ("blast_server", const_cast( (getenv ("blast_server_4_TCOFFEE"))?getenv ("blast_server_4_TCOFFEE"):"EBI") ); ^~~~~~~~~~ aln_cat util_lib/aln_convertion_util.c:1710:40: note: each undeclared identifier is reported only once for each function it appears in util_lib/aln_convertion_util.c:1710:51: error: expected expression before 'char' set_string_variable ("blast_server", const_cast( (getenv ("blast_server_4_TCOFFEE"))?getenv ("blast_server_4_TCOFFEE"):"EBI") ); ^~~~ util_lib/aln_convertion_util.c:1711:45: error: expected expression before 'char' set_string_variable ("pdb_db", const_cast( (getenv ("pdb_db_4_TCOFFEE"))?getenv ("pdb_db_4_TCOFFEE"):"pdb") ); ^~~~ util_lib/aln_convertion_util.c:1712:46: error: expected expression before 'char' set_string_variable ("prot_db", const_cast( (getenv ("prot_db_4_TCOFFEE"))?getenv ("prot_db_4_TCOFFEE"):"uniprot") ); ^~~~ util_lib/aln_convertion_util.c: In function 'fix_seq_seq': util_lib/aln_convertion_util.c:5144:63: error: 'const_cast' undeclared (first use in this function); did you mean 'aln_cat'? Alignment *B=align_two_sequences (S0->seq[s0], Sx->seq[i], const_cast( (strm(S0->type, "PROTEIN"))?"blosum62mt":"idmat"), -4,-1, "myers_miller_pair_wise"); ^~~~~~~~~~ aln_cat util_lib/aln_convertion_util.c:5144:74: error: expected expression before 'char' Alignment *B=align_two_sequences (S0->seq[s0], Sx->seq[i], const_cast( (strm(S0->type, "PROTEIN"))?"blosum62mt":"idmat"), -4,-1, "myers_miller_pair_wise"); ^~~~ util_lib/aln_convertion_util.c:5144:17: error: too few arguments to function 'align_two_sequences' Alignment *B=align_two_sequences (S0->seq[s0], Sx->seq[i], const_cast( (strm(S0->type, "PROTEIN"))?"blosum62mt":"idmat"), -4,-1, "myers_miller_pair_wise"); ^~~~~~~~~~~~~~~~~~~ In file included from ./dp_lib_header.h:44, from util_lib/aln_convertion_util.c:35: ./dp_lib/util_dp_drivers.h:107:13: note: declared here Alignment * align_two_sequences ( char *seq1, char *seq2, char *matrix, int gop, int gep, char *align_mode); ^~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'msa2master_seq': util_lib/aln_convertion_util.c:13902:18: error: initializer element is not constant static int *aa=(int*)vcalloc(256, sizeof (int)); ^ util_lib/aln_convertion_util.c: In function 'thread_msa2msa': util_lib/aln_convertion_util.c:13973:23: error: initializer element is not constant static char *smallT=vtmpnam (NULL); ^~~~~~~ util_lib/aln_convertion_util.c:13974:21: error: initializer element is not constant static char *bigT=vtmpnam (NULL); ^~~~~~~ util_lib/aln_convertion_util.c:13976:23: error: initializer element is not constant static Alignment *S=declare_aln2 (1,1); ^~~~~~~~~~~~ util_lib/aln_convertion_util.c:13977:23: error: initializer element is not constant static Alignment *B=declare_aln2 (1,1); ^~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function 'extract_aln3': util_lib/aln_convertion_util.c:7459:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7478:25: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7482:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: util_lib/aln_convertion_util.o] Error 1 (ignored) CC util_lib/hsearch.c util_lib/hsearch.c:33:10: fatal error: climits: No such file or directory #include ^~~~~~~~~ compilation terminated. make[2]: [makefile:11: util_lib/hsearch.o] Error 1 (ignored) CC util_lib/random.c CC util_lib/reformat.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/reformat.c:35: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/reformat.c:35: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/reformat.c:35: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/reformat.c:37: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/reformat.c:37: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ util_lib/reformat.c: In function 'quick_read_seq': util_lib/reformat.c:1281:25: error: initializer element is not constant static char *tmp_name=vtmpnam (NULL); ^~~~~~~ util_lib/reformat.c: In function 'quick_read_aln_static': util_lib/reformat.c:1328:25: error: initializer element is not constant static char *tmp_name=vtmpnam (NULL); ^~~~~~~ util_lib/reformat.c: In function 'quick_read_aln': util_lib/reformat.c:1366:25: error: initializer element is not constant static char *tmp_name=vtmpnam (NULL); ^~~~~~~ util_lib/reformat.c: In function 'main_read_aln': util_lib/reformat.c:1527:27: error: initializer element is not constant static char*tmp_name1=vtmpnam (NULL); ^~~~~~~ util_lib/reformat.c:1528:27: error: initializer element is not constant static char*tmp_name2=vtmpnam (NULL); ^~~~~~~ util_lib/reformat.c: In function 'main_output': util_lib/reformat.c:3706:57: error: request for member 'dmF_list' in something not a structure or union if (D1 && D1->A && (D1->A)->Tree && ((D1->A)->Tree)->dmF_list) ^~ util_lib/reformat.c:3708:16: warning: initialization of 'Alignment *' {aka 'struct Alignment *'} from incompatible pointer type 'int *' [-Wincompatible-pointer-types] Alignment *T=(D1->A)->Tree; ^ util_lib/reformat.c:3727:57: error: request for member 'dmF_list' in something not a structure or union if (D1 && D1->A && (D1->A)->Tree && ((D1->A)->Tree)->dmF_list) ^~ util_lib/reformat.c:3729:16: warning: initialization of 'Alignment *' {aka 'struct Alignment *'} from incompatible pointer type 'int *' [-Wincompatible-pointer-types] Alignment *T=(D1->A)->Tree; ^ util_lib/reformat.c:3762:7: warning: assignment to 'Alignment *' {aka 'struct Alignment *'} from incompatible pointer type 'int *' [-Wincompatible-pointer-types] T=(D1->A)->Tree; ^ util_lib/reformat.c: In function 'read_aln': util_lib/reformat.c:5686:25: error: initializer element is not constant static char *tmp_name=vtmpnam (NULL); ^~~~~~~ util_lib/reformat.c: In function 'modify_data': util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:11288:35: note: in expansion of macro 'ATOI_ACTION' (D1->A)=aln2bootstrap (D1->A, ATOI_ACTION (1)); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:11294:32: note: in expansion of macro 'ATOI_ACTION' (D1->A)=aln2sample (D1->A, ATOI_ACTION (1)); ^~~~~~~~~~~ util_lib/reformat.c:11527:26: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION (3))D=atof (ACTION(3)); ^~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:11561:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:11594:59: error: 'const_cast' undeclared (first use in this function); did you mean 'aln_cat'? D1->T= tree2dpa_tree(D1->T,(D2 && D2->A)?D2->A:D1->A, const_cast( (n_actions==1)?"idmat":action_list[1]) ); ^~~~~~~~~~ aln_cat util_lib/reformat.c:11594:59: note: each undeclared identifier is reported only once for each function it appears in util_lib/reformat.c:11594:70: error: expected expression before 'char' D1->T= tree2dpa_tree(D1->T,(D2 && D2->A)?D2->A:D1->A, const_cast( (n_actions==1)?"idmat":action_list[1]) ); ^~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:11660:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:11661:34: note: in expansion of macro 'ATOI_ACTION' treelist2lti (D1->S,TS, (int)ATOI_ACTION(1), stdout ); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:11668:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:11675:35: note: in expansion of macro 'ATOI_ACTION' D1->S=treelist2sub_seq (D1->S,ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:11698:74: error: request for member 'seq_al' in something not a structure or union if (!D1->T && (D1->A)->Tree)D1->T=newick_string2tree (((D1->A)->Tree)->seq_al[0]); ^~ util_lib/reformat.c:11703:12: warning: null argument where non-null required (argument 1) [-Wnonnull] ng=atoi(ACTION (2))+1; ^~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:11731:31: note: in expansion of macro 'ATOI_ACTION' tree2bucket (D2->T, D1->S,ATOI_ACTION(1), ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:11741:14: warning: null argument where non-null required (argument 1) [-Wnonnull] int shuf=atoi (ACTION(1)); ^~~~ util_lib/reformat.c:11752:14: warning: null argument where non-null required (argument 1) [-Wnonnull] int shuf=atoi (ACTION(1)); ^~~~ util_lib/reformat.c:11832:71: error: request for member 'seq_al' in something not a structure or union else if (D1->A && (D1->A)->Tree)bs=newick2avg_bs (((D1->A)->Tree)->seq_al[0]); ^~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:11878:44: note: in expansion of macro 'ATOI_ACTION' D1->T= aln2km_tree(D1->A, (ACTION(1)), ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:11961:15: warning: null argument where non-null required (argument 1) [-Wnonnull] else max=atof(ACTION(na+1)); ^~~~ util_lib/reformat.c:11964:15: warning: null argument where non-null required (argument 1) [-Wnonnull] else enb=atoi(ACTION(na+2)); ^~~~ util_lib/reformat.c:11976:60: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1)&& !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); ^~~~ util_lib/reformat.c:11977:60: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2)&& !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); ^~~~ util_lib/reformat.c:11985:61: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1) && !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); ^~~~ util_lib/reformat.c:11986:61: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2) && !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); ^~~~ util_lib/reformat.c:12020:16: warning: null argument where non-null required (argument 1) [-Wnonnull] radius=atof(ACTION(1)); ^~~~ util_lib/reformat.c:12028:19: warning: null argument where non-null required (argument 1) [-Wnonnull] threshold=atof(ACTION(2)); ^~~~ util_lib/reformat.c:12035:13: warning: null argument where non-null required (argument 1) [-Wnonnull] min=atoi(ACTION(3)); ^~~~ util_lib/reformat.c:12071:15: warning: null argument where non-null required (argument 1) [-Wnonnull] else max=atof(ACTION(na+1)); ^~~~ util_lib/reformat.c:12074:15: warning: null argument where non-null required (argument 1) [-Wnonnull] else enb=atoi(ACTION(na+2)); ^~~~ util_lib/reformat.c:12086:60: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1)&& !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); ^~~~ util_lib/reformat.c:12087:60: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2)&& !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); ^~~~ util_lib/reformat.c:12095:61: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1) && !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); ^~~~ util_lib/reformat.c:12096:61: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2) && !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); ^~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12144:44: note: in expansion of macro 'ATOI_ACTION' float results=shuff (D1->S, ACTION (1),ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12264:37: note: in expansion of macro 'ATOI_ACTION' D1->A=aln2conservation ( D1->A, ATOI_ACTION (1), ACTION (2)); ^~~~~~~~~~~ util_lib/reformat.c:12273:50: error: expected expression before 'char' cons_seq=aln2cons_seq_mat (D1->A, const_cast( (n_actions==1)?"blosum62mt":action_list[1]) ); ^~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12388:31: note: in expansion of macro 'ATOI_ACTION' D1->A=shuffle_aln (D1->A, ATOI_ACTION(1), ACTION(2), ACTION (3)); ^~~~~~~~~~~ util_lib/reformat.c:12899:14: warning: null argument where non-null required (argument 1) [-Wnonnull] else if (strstr (ACTION(1), "h")) ^~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12906:10: note: in expansion of macro 'ATOI_ACTION' F->t=ATOI_ACTION(2); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12907:10: note: in expansion of macro 'ATOI_ACTION' F->f=ATOI_ACTION(3); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12908:11: note: in expansion of macro 'ATOI_ACTION' F->p1=ATOI_ACTION(4); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12909:11: note: in expansion of macro 'ATOI_ACTION' F->p2=ATOI_ACTION(5); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12910:11: note: in expansion of macro 'ATOI_ACTION' F->p3=ATOI_ACTION(6); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12911:11: note: in expansion of macro 'ATOI_ACTION' F->p3=ATOI_ACTION(7); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:12934:34: note: in expansion of macro 'ATOI_ACTION' D1->A=unalign_aln (D1->A,SA, ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:13020:41: error: expected expression before 'char' D1->A=mutate_aln( D1->A, const_cast( (n_actions==1)?"0":action_list[1]) ); ^~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:13074:10: note: in expansion of macro 'ATOI_ACTION' if (!ATOI_ACTION(1))myexit(fprintf_error (stderr,"-kmeans ")); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:13075:19: note: in expansion of macro 'ATOI_ACTION' km_seq (D1->A,ATOI_ACTION (1),ACTION(2),ACTION(3)); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:13079:27: note: in expansion of macro 'ATOI_ACTION' D1->A=gap_trim (D1->A,ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:13086:34: note: in expansion of macro 'ATOI_ACTION' D1->A=trim_RNA(D1->A, D2->S, ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:13126:116: error: expected expression before 'char' group_file=tree2Ngroup( (D1)?D1->A:NULL, (D2)?D2->T:NULL, atoi (action_list[0]), vtmpnam(NULL), const_cast( (n_actions==1)?"idmat":action_list[1]) ); ^~~~ util_lib/reformat.c:13130:119: error: expected expression before 'char' group_file=tree2Ngroup( (D1)?D1->A:NULL, (D2)?D2->T:NULL, -1*atoi (action_list[0]), vtmpnam(NULL), const_cast( (n_actions==1)?"idmat":action_list[1]) ); ^~~~ util_lib/reformat.c:13548:62: error: expected expression before 'char' pavie_seq2pavie_aln ( D1->S, action_list[1], const_cast( (n_actions==3)?action_list[2]:"_MATDIST_") ); ^~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:13614:7: note: in expansion of macro 'ATOI_ACTION' t=ATOI_ACTION(1); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:13615:7: note: in expansion of macro 'ATOI_ACTION' f=ATOI_ACTION(2); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:13616:8: note: in expansion of macro 'ATOI_ACTION' p1=ATOI_ACTION(3); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:13617:8: note: in expansion of macro 'ATOI_ACTION' p2=ATOI_ACTION(4); ^~~~~~~~~~~ util_lib/reformat.c:43:44: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^~~~ util_lib/reformat.c:13618:8: note: in expansion of macro 'ATOI_ACTION' p3=ATOI_ACTION(5); ^~~~~~~~~~~ util_lib/reformat.c: In function 'read_nameseq': util_lib/reformat.c:1416:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "#NAMESEQ_01\n"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1417:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "# %d\n", &nseq); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1427:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d %d ", &l1, &l2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1430:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1435:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &l1); ^~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1437:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets (com[0][nseq],l1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'read_nameseq_old': util_lib/reformat.c:1461:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "#NAMESEQ_01\n"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1462:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "# %d\n", &nseq); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1472:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d %d ", &l1, &l2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1475:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1480:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &l1); ^~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1482:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets (com[0][nseq],l1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'is_pdb_name': util_lib/reformat.c:1777:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d", &result); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'get_pdb_id': util_lib/reformat.c:1815:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n%s\n", buf); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'get_amps_sd_scores': util_lib/reformat.c:3924:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3931:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3940:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3946:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",W->seq_name[a]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3948:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3959:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'read_rna_struc_number': util_lib/reformat.c:4232:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4235:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] 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 'get_struc_gor': util_lib/reformat.c:4462:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d", name, &len); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4483:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4488:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'get_sequence_dali': util_lib/reformat.c:4525:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s",name); ^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'get_dialign_sequence': util_lib/reformat.c:4600:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%s",name); ^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'fscanf_seq_name': util_lib/reformat.c:5634:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", name); ^~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'get_amps_seq_name': util_lib/reformat.c:5987:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%*d >%s", name[nseq++]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'read_gotoh_aln': util_lib/reformat.c:6036:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6058:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'output_maln_pval': util_lib/reformat.c:6256:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",string); ^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'similarities_file2aln': util_lib/reformat.c:6421:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %d", name,&i); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'read_blast_matrix': util_lib/reformat.c:14163:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14176:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14201:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'read_blast_matrix_old': util_lib/reformat.c:14226:6: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14243:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14256:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14283:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'read_pavie_matrix': util_lib/reformat.c:14394:6: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: util_lib/reformat.o] Error 1 (ignored) CC util_lib/reformat_struc.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/reformat_struc.c:34: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/reformat_struc.c:34: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/reformat_struc.c:34: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/reformat_struc.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/reformat_struc.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ util_lib/reformat_struc.c: In function 'bfactor2x_in_pdb': util_lib/reformat_struc.c:125:18: warning: too many arguments for format [-Wformat-extra-args] fprintf (out, "ATOM ", lw[1]);//ATOM ^~~~~~~~ util_lib/reformat_struc.c: In function 'simple_read_ca_trace': util_lib/reformat_struc.c:370:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:372:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:378:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:405:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:407:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:416:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: util_lib/reformat_struc.o] Error 1 (ignored) CC util_lib/util.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util.c:52: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/util.c:52: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util.c:52: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/util.c:56: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/util.c:56: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ util_lib/util.c: In function 'pg_is_installed': util_lib/util.c:2399:21: error: initializer element is not constant static char *fname=vtmpnam(NULL); ^~~~~~~ util_lib/util.c: In function 'perl_strstr': util_lib/util.c:2446:20: error: initializer element is not constant static char *tmp=vtmpnam (NULL); ^~~~~~~ util_lib/util.c: In function 'lock': util_lib/util.c:4683:5: error: 'const_cast' undeclared (first use in this function); did you mean 'aln_cat'? r=const_cast( (file_exists (NULL,fname))?"x":NULL ); ^~~~~~~~~~ aln_cat util_lib/util.c:4683:5: note: each undeclared identifier is reported only once for each function it appears in util_lib/util.c:4683:16: error: expected expression before 'char' r=const_cast( (file_exists (NULL,fname))?"x":NULL ); ^~~~ util_lib/util.c:4712:41: error: expected expression before 'char' string2file_direct (fname, const_cast( (action==LSET)?"a":"w"), value); ^~~~ util_lib/util.c:4712:3: error: too few arguments to function 'string2file_direct' string2file_direct (fname, const_cast( (action==LSET)?"a":"w"), value); ^~~~~~~~~~~~~~~~~~ In file included from ./util_lib_header.h:30, from util_lib/util.c:53: ./util_lib/util.h:628:5: note: declared here int string2file_direct (char *file, char *mode, char *string,...); ^~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'find_token_in_file_nlines_old': util_lib/util.c:7944:26: error: initializer element is not constant static char *tmp_name=vtmpnam (NULL); ^~~~~~~ util_lib/util.c: In function 'simple_check_internet_connection': util_lib/util.c:8423:17: error: 'const_cast' undeclared (first use in this function); did you mean 'aln_cat'? if (url2file( const_cast( (ref_site)?ref_site:TEST_WWWSITE_4_TCOFFEE),test )!=EXIT_SUCCESS)internet=0; ^~~~~~~~~~ aln_cat util_lib/util.c:8423:28: error: expected expression before 'char' if (url2file( const_cast( (ref_site)?ref_site:TEST_WWWSITE_4_TCOFFEE),test )!=EXIT_SUCCESS)internet=0; ^~~~ util_lib/util.c:8423:7: error: too few arguments to function 'url2file' if (url2file( const_cast( (ref_site)?ref_site:TEST_WWWSITE_4_TCOFFEE),test )!=EXIT_SUCCESS)internet=0; ^~~~~~~~ util_lib/util.c:8390:5: note: declared here int url2file (char *address, char *out) ^~~~~~~~ util_lib/util.c: In function 'my_mkdir': util_lib/util.c:8727:23: error: initializer element is not constant static char *home = getenv ("HOME"); ^~~~~~ util_lib/util.c:8728:27: error: initializer element is not constant static mode_t oldmask = umask(0); ^~~~~ util_lib/util.c: In function 'signal_exit': util_lib/util.c:9993:19: error: parameter name omitted void signal_exit (int) ^~~ util_lib/util.c: In function 'hsort_file': util_lib/util.c:281:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[--l]*/ ^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:286:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[ir]*/ ^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:289:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( rrb, size, len,fp); /*rrb=ra[0]*/ ^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:306:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread (ra_j, size, len, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:311:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread (ra_j_1, size, len, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'bsearch_file': util_lib/util.c:420:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread ( key2, el_size, entry_len,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'get_number_list_in_file': util_lib/util.c:847:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d",&list[n[0]++]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'quantile': util_lib/util.c:1321:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %s\n", s1, s2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'input_array_int': util_lib/util.c:1805:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &len); ^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1809:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &len2); ^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1812:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &array[a][b]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1813:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "\n"); ^~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'perl_strstr': util_lib/util.c:2468:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d", &r); ^~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'count_strings_in_file': util_lib/util.c:5760:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",list[n]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'redirect_stderr': util_lib/util.c:6300:5: warning: ignoring return value of 'freopen', declared with attribute warn_unused_result [-Wunused-result] freopen(stderr_file, "w", stderr); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'redirect_stdout': util_lib/util.c:6343:5: warning: ignoring return value of 'freopen', declared with attribute warn_unused_result [-Wunused-result] freopen(stdout_file, "w", stdout); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'get_cl_param': util_lib/util.c:7554:2: warning: second parameter of 'va_start' not last named argument [-Wvarargs] va_start (ap, usage); ^~~~~~~~ util_lib/util.c: In function 'get_parameter': util_lib/util.c:7821:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'set_fp_id': util_lib/util.c:7841:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", string); ^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'get_file_block_pattern': util_lib/util.c:8228:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:8258:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'check_for_update': util_lib/util.c:8345:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "Version_%f", &new_version); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: util_lib/util.o] Error 1 (ignored) CC util_lib/util_aln_analyze.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_aln_analyze.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/util_aln_analyze.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_aln_analyze.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/util_aln_analyze.c:35: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/util_aln_analyze.c:35: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: util_lib/util_aln_analyze.o] Error 1 (ignored) CC util_lib/util_analyse_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_analyse_constraints_list.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/util_analyse_constraints_list.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_analyse_constraints_list.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ make[2]: [makefile:11: util_lib/util_analyse_constraints_list.o] Error 1 (ignored) CC util_lib/util_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_constraints_list.c:37: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/util_constraints_list.c:37: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_constraints_list.c:37: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/util_constraints_list.c:40: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/util_constraints_list.c:40: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ util_lib/util_constraints_list.c: In function 'fork_read_n_constraint_list': util_lib/util_constraints_list.c:2225:28: warning: too many arguments for format [-Wformat-extra-args] fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'read_constraint_list_file': util_lib/util_constraints_list.c:2852:19: warning: too many arguments for format [-Wformat-extra-args] x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); ^~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'submit_lib_job': util_lib/util_constraints_list.c:582:6: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (tdir); ^~~~~~~~~~~~ util_lib/util_constraints_list.c:585:6: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'method_file_tag2value': util_lib/util_constraints_list.c:1151:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'method_file2TC_method': util_lib/util_constraints_list.c:1194:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'read_cpu_in_list': util_lib/util_constraints_list.c:2600:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] if ( c=='C')fscanf( fp, "PU %d\n", &cpu); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'read_seq_in_list': util_lib/util_constraints_list.c:2918:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &max_nseq); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2923:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %d %*s\n", &l); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2955:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2980:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets (line , 200 , fp); ^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'nfork_relax_constraint_list_4gp': util_lib/util_constraints_list.c:4054:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: [makefile:11: util_lib/util_constraints_list.o] Error 1 (ignored) CC util_lib/util_declare.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_declare.c:37: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/util_declare.c:37: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_declare.c:37: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/util_declare.c:40: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/util_declare.c:40: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ util_lib/util_declare.c: In function 'free_data_in_aln': util_lib/util_declare.c:1271:32: warning: passing argument 1 of 'free_Alignment' from incompatible pointer type [-Wincompatible-pointer-types] if (A->Tree)free_Alignment (A->Tree); ~^~~~~~ In file included from ./util_lib_header.h:40, from util_lib/util_declare.c:38: ./util_lib/util_declare.h:210:12: note: expected 'Alignment *' {aka 'struct Alignment *'} but argument is of type 'int *' Sequence *free_Alignment ( Alignment *A); ^~~~~~~~~~~~~~ util_lib/util_declare.c: In function 'free_Alignment': util_lib/util_declare.c:1307:37: warning: passing argument 1 of 'free_Alignment' from incompatible pointer type [-Wincompatible-pointer-types] if ( LA->Tree){free_Alignment (LA->Tree);LA->Tree=NULL;} ~~^~~~~~ util_lib/util_declare.c:1278:39: note: expected 'Alignment *' {aka 'struct Alignment *'} but argument is of type 'int *' Sequence* free_Alignment ( Alignment *LA) ~~~~~~~~~~~^~ make[2]: [makefile:11: util_lib/util_declare.o] Error 1 (ignored) CC util_lib/util_domain_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_domain_constraints_list.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/util_domain_constraints_list.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_domain_constraints_list.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ make[2]: [makefile:11: util_lib/util_domain_constraints_list.o] Error 1 (ignored) CC util_lib/util_dps.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_dps.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/util_dps.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_dps.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/util_dps.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/util_dps.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: util_lib/util_dps.o] Error 1 (ignored) CC util_lib/util_job_handling.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_job_handling.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/util_job_handling.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_job_handling.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/util_job_handling.c:36: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/util_job_handling.c:36: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ make[2]: [makefile:11: util_lib/util_job_handling.o] Error 1 (ignored) CC util_lib/util_make_tree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from util_lib/util_make_tree.c:33: ./programmes_define.h:379:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" ./programmes_define.h:381:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ ./programmes_define.h:381: warning: "x3dna" redefined #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:382:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ ./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" ./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ./programmes_define.h:384:14: warning: ISO C99 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:30, from util_lib/util_make_tree.c:33: ./io_lib/io_structures.h:297:7: error: unknown type name 'Alignment' Alignment *Tree; ^~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:35:1: warning: useless storage class specifier in empty declaration }; ^ In file included from ./dp_lib_header.h:49, from util_lib/util_make_tree.c:35: ./dp_lib/evaluate_dirichlet.h:59:10: error: conflicting types for 'aln2prf' double **aln2prf (Alignment *A, int ns, int *ls, int len, double **prf); ^~~~~~~ In file included from ./dp_lib_header.h:35, from util_lib/util_make_tree.c:35: ./dp_lib/util_dp_gotoh_nw.h:55:7: note: previous declaration of 'aln2prf' was here int **aln2prf (Alignment *A, char *matrix); ^~~~~~~ util_lib/util_make_tree.c: In function 'seq2dnd': util_lib/util_make_tree.c:1710:24: error: initializer element is not constant static char *tmptree=vtmpnam (NULL); ^~~~~~~ util_lib/util_make_tree.c: In function 'seq2co_aln_file': util_lib/util_make_tree.c:124:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:127:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2mafft_aln_file': util_lib/util_make_tree.c:157:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:159:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2cw_aln_file': util_lib/util_make_tree.c:189:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:191:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'prf_pair2cw_aln_file': util_lib/util_make_tree.c:222:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:225:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2fftns1_dnd': util_lib/util_make_tree.c:1854:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:1867:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2fftns2_dnd': util_lib/util_make_tree.c:1883:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:1896:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2mafft_dnd': util_lib/util_make_tree.c:1912:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:1925:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2parttree_dnd': util_lib/util_make_tree.c:1942:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:1955:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2dpparttree_dnd': util_lib/util_make_tree.c:1972:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:1987:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2fastparttree_dnd': util_lib/util_make_tree.c:2005:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:2018:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2cwquick_dnd': util_lib/util_make_tree.c:2034:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:2042:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2cw_dnd': util_lib/util_make_tree.c:2059:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:2067:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'aln2cw_tree': util_lib/util_make_tree.c:2087:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:2094:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ util_lib/util_make_tree.c: In function 'seq2cw_tree': util_lib/util_make_tree.c:2109:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ^~~~~~~~~~~ util_lib/util_make_tree.c:2118:3: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^~~~~~~~~~~~~~~ make[2]: [makefile:11: util_lib/util_make_tree.o] Error 1 (ignored) Linking... s390x-linux-gnu-gcc: error: dev_lib/dev1.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/CUSTOM_evaluate_for_struc.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/evaluate.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/evaluate_dirichlet.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/evaluate_for_domain.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/evaluate_for_struc.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/fsa_dp.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/pavie_dp.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/showpair.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_domain_dp.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_domain_dp_drivers.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_cdna_fasta_nw.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_clean_maln.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_drivers.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_est.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_fasta_nw.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_fasta_sw.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_generic_fasta_nw.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_gotoh_nw.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_gotoh_sw.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_mm_nw.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_sim.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_ssec_pwaln.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_dp_suboptimal_nw.o: No such file or directory s390x-linux-gnu-gcc: error: dp_lib/util_graph_maln.o: No such file or directory s390x-linux-gnu-gcc: error: fastal/diagonal.o: No such file or directory s390x-linux-gnu-gcc: error: fastal/fastal.o: No such file or directory s390x-linux-gnu-gcc: error: fastal/iteration.o: No such file or directory s390x-linux-gnu-gcc: error: fastal/parttree.o: No such file or directory s390x-linux-gnu-gcc: error: fastal/scoring.o: No such file or directory s390x-linux-gnu-gcc: error: fastal/tree.o: No such file or directory s390x-linux-gnu-gcc: error: io_lib/io_func.o: No such file or directory s390x-linux-gnu-gcc: error: io_lib/pb_util_read_seq_util.o: No such file or directory s390x-linux-gnu-gcc: error: io_lib/pb_util_read_sequence.o: No such file or directory s390x-linux-gnu-gcc: error: io_lib/tree_util.o: No such file or directory s390x-linux-gnu-gcc: error: km_coffee/Vector.o: No such file or directory s390x-linux-gnu-gcc: error: km_coffee/km_coffee.o: No such file or directory s390x-linux-gnu-gcc: error: km_coffee/kmeans.o: No such file or directory s390x-linux-gnu-gcc: error: t_coffee_lib/t_coffee.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/aln_compare.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/aln_convertion_util.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/hsearch.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/reformat.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/reformat_struc.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/util.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/util_aln_analyze.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/util_analyse_constraints_list.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/util_constraints_list.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/util_declare.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/util_domain_constraints_list.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/util_dps.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/util_job_handling.o: No such file or directory s390x-linux-gnu-gcc: error: util_lib/util_make_tree.o: No such file or directory make[2]: [makefile:8: t_coffee] Error 1 (ignored) make[2]: Leaving directory '/<>/t_coffee_source' make[1]: Leaving directory '/<>' dh_auto_test -a -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --sourcedirectory=t_coffee_source dh_testroot -a -O--sourcedirectory=t_coffee_source dh_prep -a -O--sourcedirectory=t_coffee_source dh_auto_install -a -O--sourcedirectory=t_coffee_source dh_install -a -O--sourcedirectory=t_coffee_source dh_install: Cannot find (any matches for) "t_coffee_source/t_coffee" (tried in ., debian/tmp) dh_install: t-coffee missing files: t_coffee_source/t_coffee dh_install: missing files, aborting make: *** [debian/rules:11: binary-arch] Error 25 dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2019-02-03T16:44:49Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 17764 Build-Time: 12 Distribution: unstable Fail-Stage: build Foreign Architectures: s390x Host Architecture: s390x Install-Time: 22 Job: t-coffee_12.00.7fb08c2-1 Machine Architecture: amd64 Package: t-coffee Package-Time: 43 Source-Version: 12.00.7fb08c2-1 Space: 17764 Status: attempted Version: 12.00.7fb08c2-1 -------------------------------------------------------------------------------- Finished at 2019-02-03T16:44:49Z Build needed 00:00:43, 17764k disk space