sbuild (Debian sbuild) 0.78.1 (09 February 2019) on 36857dea695f +==============================================================================+ | t-coffee 12.00.7fb08c2-4 (armhf) Thu, 07 Mar 2019 04:44:16 +0000 | +==============================================================================+ Package: t-coffee Version: 12.00.7fb08c2-4 Source Version: 12.00.7fb08c2-4 Distribution: unstable-amd64-sbuild Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-25fa5caf-736b-4914-8fc4-230156165922' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-zoP5i1/resolver-SdIgwg' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://cdn-fastly.deb.debian.org/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libmailtools-perl libnet-smtp-ssl-perl libyaml-0-2 libyaml-libyaml-perl uuid-runtime Use 'apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /home/build/sbuild-setup/repo/pool/main/t/t-coffee/t-coffee_12.00.7fb08c2-4.dsc exists in /home/build/sbuild-setup/repo/pool/main/t/t-coffee; copying to chroot I: NOTICE: Log filtering will replace 'build/t-coffee-zoP5i1/t-coffee-12.00.7fb08c2' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-zoP5i1' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 12~), build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper (>= 12~), build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [397 B] Get:5 copy:/<>/apt_archive ./ Packages [486 B] Fetched 1840 B in 0s (153 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libmailtools-perl libnet-smtp-ssl-perl libyaml-0-2 libyaml-libyaml-perl uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libbsd0 libc6:armhf libc6-dev:armhf libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libglib2.0-0 libgomp1:armhf libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf libstdc++6:armhf libtool libubsan1:armhf libuchardet0 linux-libc-dev:armhf 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:armhf libc-l10n:armhf locales:armhf manpages-dev:armhf libstdc++-8-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armhf 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:armhf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libbsd0 libc6:armhf libc6-dev:armhf libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libglib2.0-0 libgomp1:armhf libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf libstdc++6:armhf libtool libubsan1:armhf libuchardet0 linux-libc-dev:armhf m4 man-db po-debconf sbuild-build-depends-main-dummy:armhf 0 upgraded, 40 newly installed, 0 to remove and 0 not upgraded. Need to get 904 B/18.5 MB of archives. After this operation, 79.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [904 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 904 B in 0s (0 B/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 16441 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... 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Setting up libglib2.0-0:amd64 (2.58.3-1) ... No schema files found: doing nothing. Setting up linux-libc-dev:armhf (4.19.20-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up gcc-8-base:armhf (8.3.0-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1) ... Setting up libfile-stripnondeterminism-perl (1.1.1-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libtool (2.4.6-10) ... Setting up m4 (1.4.18-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... 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 autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libc6:armhf (2.28-8) ... Setting up libc6-dev:armhf (2.28-8) ... Setting up libgcc1:armhf (1:8.3.0-2) ... Setting up libgomp1:armhf (8.3.0-2) ... Setting up dh-autoreconf (19) ... Setting up libatomic1:armhf (8.3.0-2) ... Setting up dh-strip-nondeterminism (1.1.1-1) ... Setting up libstdc++6:armhf (8.3.0-2) ... Setting up debhelper (12.1.1) ... Setting up libasan5:armhf (8.3.0-2) ... 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Updating symlinks in /usr/lib/ccache ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Initial Foreign Architectures: armhf Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 3.16.0-4-amd64 #1 SMP Debian 3.16.51-3 (2017-12-13) amd64 (x86_64) Toolchain package versions: binutils_2.31.1-15 dpkg-dev_1.19.5 g++-8_8.3.0-2 gcc-8_8.3.0-2 libc6-dev_2.28-8 libstdc++-8-dev_8.3.0-2 libstdc++-8-dev-armhf-cross_8.3.0-2cross1 libstdc++6_8.3.0-2 libstdc++6-armhf-cross_8.3.0-2cross1 linux-libc-dev_4.19.20-1 Package versions: adduser_3.118 apt_1.8.0~rc4 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_3.5.46 bash_5.0-2 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libhttp-daemon-perl_6.01-3 libhttp-date-perl_6.02-1 libhttp-message-perl_6.18-1 libhttp-negotiate-perl_6.01-1 libicu63_63.1-6 libidn2-0_2.0.5-1 libio-html-perl_1.001-1 libio-socket-ssl-perl_2.060-3 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.3.0-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3 libldap-common_2.4.47+dfsg-3 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.3.0-2 liblwp-mediatypes-perl_6.02-1 liblwp-protocol-https-perl_6.07-2 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmailtools-perl_2.18-1 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-2 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnet-http-perl_6.18-1 libnet-smtp-ssl-perl_1.04-1 libnet-ssleay-perl_1.85-2+b1 libnettle6_3.4.1-1 libnpth0_1.6-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-11 libperl5.28_5.28.1-4 libpipeline1_1.5.1-2 libquadmath0_8.3.0-2 libreadline7_7.0-5 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 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 libsqlite3-0_3.27.2-1 libss2_1.44.6-1 libssl1.1_1.1.1b-1 libstdc++-8-dev_8.3.0-2 libstdc++-8-dev-armhf-cross_8.3.0-2cross1 libstdc++6_8.3.0-2 libstdc++6-armhf-cross_8.3.0-2cross1 libsystemd0_241-1 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtry-tiny-perl_0.30-1 libtsan0_8.3.0-2 libubsan1_8.3.0-2 libubsan1-armhf-cross_8.3.0-2cross1 libuchardet0_0.0.6-3 libudev1_241-1 libunistring2_0.9.10-1 liburi-perl_1.76-1 libuuid1_2.33.1-0.1 libwww-perl_6.36-1 libwww-robotrules-perl_6.02-1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-parser-perl_2.44-4 libxml-sax-base-perl_1.09-1 libxml-sax-expat-perl_0.51-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-0-2_0.2.1-1 libyaml-libyaml-perl_0.76+repack-1 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.20-1 linux-libc-dev-armhf-cross_4.19.20-1cross1 login_1:4.5-1.1 lsb-base_10.2018112800 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 openssl_1.1.1b-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 perl-openssl-defaults_3 pinentry-curses_1.1.0-1+b1 po-debconf_1.0.21 readline-common_7.0-5 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-5 tzdata_2018i-2 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 uuid-runtime_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: t-coffee Binary: t-coffee, t-coffee-examples Architecture: any all Version: 12.00.7fb08c2-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/t-coffee Vcs-Git: https://salsa.debian.org/med-team/t-coffee.git Testsuite: autopkgtest Build-Depends: debhelper (>= 12~) Package-List: t-coffee deb science optional arch=any t-coffee-examples deb science optional arch=all Checksums-Sha1: a6b5eb9a423b3497087105473ff4bfe106e7584b 3520829 t-coffee_12.00.7fb08c2.orig.tar.gz 949d3cc1e4694ec852f9a3920d746035d8bc691c 14812 t-coffee_12.00.7fb08c2-4.debian.tar.xz Checksums-Sha256: 6119514a0e36da4b4de88741b8c12f9c8ab653772b3952a011d4cb373beee44f 3520829 t-coffee_12.00.7fb08c2.orig.tar.gz 6774a081517f7bbe95e16e728b78545b5339b3966c9dde5af9a907dd7869fcb5 14812 t-coffee_12.00.7fb08c2-4.debian.tar.xz Files: c7eb2c67634a3a9b35d114fb6211f34d 3520829 t-coffee_12.00.7fb08c2.orig.tar.gz 0b1d876c508b0362e8aae3762be187fc 14812 t-coffee_12.00.7fb08c2-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxmYHsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHcPQ/9HyhnIuXpNsJsFt7lnrZb+SXXiWx6ws0+ KQ6arSbuUXCG6uuIOfTlsZ7rWU+wlg73MS5GLIda3csoL76sAmNKulYAmzcHK34l J1m3LUWSDotXxJq90x1nLo0lak10Ug+5lq6SVFafDVNQ+blf2g6v6i1wdQKxGlOl Vxvq0PIBd9PWrU+WXllJYHwRdhMIqRsKeIMJ2ckIFyh3flXttDy3kkI8VIcCkB8U N1ElsZysC+oYiY/J6qSkUYDTulFAz5N/8VMRPt2bhWZnc8dw2ady68PAWC2xsfD9 9DXFQp72HKT5HDI/ARy3ys1hDZz3Ot9BcFZnpxOVvN2rCJUP4PmALwNDsUb0jaK6 H9GqmhTR1BB8F1pTObllW7Fi3PuCzSsFpjeNl4iNLxb6cvyiWew46fwlwH+8rFfQ 7VJlb6P7PsZLTf6wb4SYbRT/MAkHwE6e4Rr+Rbx0XDsUb4Euiebsu6EPn3xvhO8y 9cN8JghCcWHeYJ0BPxGdDnO4gBywGDLH47n9fJTfHVYfGpINSXuMPrT3mfZ5Z5lQ 8oovBniuemv2/tM8SlJ0qQTpDDgTOKAxvWFg4A1ER5wSOhEOxffKyqVqK6VINN2T KYObCgmsOd4XukDyimffRlmfsB8QVkl25Q/bbf844/ip98Vo9aMya+13S7i0gtNY APTfIZ2vpQo= =pc4G -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Feb 15 06:47:23 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./t-coffee_12.00.7fb08c2-4.dsc dpkg-source: info: extracting t-coffee in /<> dpkg-source: info: unpacking t-coffee_12.00.7fb08c2.orig.tar.gz dpkg-source: info: unpacking t-coffee_12.00.7fb08c2-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying ncbi-blast++_has_dropped_pl_extension.patch dpkg-source: info: applying use_debian_packaged_TMalign.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying set_proper_dir_permissions.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying stable-linking-inputs.patch dpkg-source: info: applying clustalw2.patch dpkg-source: info: applying fix_tempfile_name_sharing.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CCACHE_COMPRESS=1 CCACHE_DIR=/var/cache/ccache-sbuild CCACHE_UMASK=002 CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=build PATH=/usr/lib/ccache:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=build SCHROOT_SESSION_ID=unstable-amd64-sbuild-25fa5caf-736b-4914-8fc4-230156165922 SCHROOT_UID=1000 SCHROOT_USER=build SHELL=/bin/sh USER=build dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot -j16 dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 12.00.7fb08c2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/t_coffee.log bin/t_coffee rm -rf t_coffee_source/TMalign find . -name "*.o" -delete find . -name "*.deps" -delete chmod 644 example/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules build-arch dh build-arch --sourcedirectory=t_coffee_source dh_update_autotools_config -a -O--sourcedirectory=t_coffee_source dh_autoreconf -a -O--sourcedirectory=t_coffee_source dh_auto_configure -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" 'CC=$(CXX)' all cd t_coffee_source && make -j16 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc USER_BIN=../bin/ "FCC=gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" CC=\$\(CXX\) all make[2]: Entering directory '/<>/t_coffee_source' CC dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate.c CC dp_lib/evaluate_dirichlet.c CC dp_lib/evaluate_for_struc.c CC dp_lib/evaluate_for_domain.c CC dp_lib/fsa_dp.c CC dp_lib/pavie_dp.c CC dp_lib/showpair.c CC dp_lib/util_domain_dp_drivers.c CC dp_lib/util_domain_dp.c CC dp_lib/util_dp_cdna_fasta_nw.c CC dp_lib/util_dp_clean_maln.c CC dp_lib/util_dp_drivers.c CC dp_lib/util_dp_est.c 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_est.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_est.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_fasta_sw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_generic_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dev_lib/dev1.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ dev_lib/dev1.c: In function ‘void aln2hitMat(Alignment*, char*)’: dev_lib/dev1.c:89:19: warning: too many arguments for format [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ^~~~~~~~~~~~~~~~~~~~~ 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/evaluate_for_domain.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/evaluate_for_domain.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_gotoh_sw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_clean_maln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_clean_maln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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_domain_dp.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_domain_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_sim.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_fasta_sw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_fasta_sw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/showpair.c:32: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_ssec_pwaln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_domain_dp_drivers.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC dp_lib/util_dp_suboptimal_nw.c 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/evaluate_dirichlet.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/evaluate_dirichlet.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ dp_lib/evaluate_dirichlet.c: In function ‘Mixture* read_dirichlet(char*)’: dp_lib/evaluate_dirichlet.c:317:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f\n", &f); ~~~~~~^~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ~~~~~~^~~~~~~~~~ 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 dp_lib/util_dp_generic_fasta_nw.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 dp_lib/util_dp_cdna_fasta_nw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC fastal/fastal_opt_parsing.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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_mm_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 dp_lib/util_dp_gotoh_sw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_gotoh_sw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ dp_lib/util_dp_gotoh_sw.c: In function ‘int gotoh_pair_wise_sw(Alignment*, int*, int**, Constraint_list*)’: dp_lib/util_dp_gotoh_sw.c:391:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/diagonal.c:31: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from fastal/diagonal.c:31: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ fastal/diagonal.c: In function ‘int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)’: fastal/diagonal.c:434:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/diagonal.c:439:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ CC fastal/scoring.c 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 dp_lib/util_graph_maln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC io_lib/io_func.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/util_dp_ssec_pwaln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 dp_lib/util_dp_fasta_nw.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 dp_lib/pavie_dp.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/pavie_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ dp_lib/pavie_dp.c: In function ‘double** pavie_seq2pavie_aln(Sequence*, char*, char*)’: dp_lib/pavie_dp.c:127:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",mat_list[nch++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’: dp_lib/pavie_dp.c:1079:15: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c:1081:14: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c: In function ‘Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)’: dp_lib/pavie_dp.c:1365:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", mat); ~~~~~~~^~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’: dp_lib/pavie_dp.c:1078:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] sprintf ( command, "cp %s %s", mat_name[a], latest); ^~~~~~~~~~ ~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from dp_lib/pavie_dp.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 1004) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c:1080:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] sprintf ( command, "cp %s %s", latest, current); ^~~~~~~~~~ ~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from dp_lib/pavie_dp.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 2003 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC io_lib/tree_util.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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from fastal/iteration.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ fastal/iteration.c: In function ‘void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)’: fastal/iteration.c:185:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function ‘void iterate(Fastal_param*, void*, char*, char*, int)’: fastal/iteration.c:310:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(command); ~~~~~~^~~~~~~~~ fastal/iteration.c: In function ‘void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)’: fastal/iteration.c:501:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:535:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH, old_aln_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function ‘void edit2seq_pattern(FILE*, char*, char*)’: fastal/iteration.c:563:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC km_coffee/Stack.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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from fastal/tree.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC km_coffee/Vector.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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from fastal/scoring.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ fastal/scoring.c: In function ‘double calculate_sum_of_pairs_score_affine(char*, int**, double, double)’: fastal/scoring.c:76:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function ‘void compute_ref_alignments(char*, char*, int, int)’: fastal/scoring.c:384:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(aln_command); ~~~~~~^~~~~~~~~~~~~ fastal/scoring.c: In function ‘void make_ref_alignment(char*, char*, char*, int)’: fastal/scoring.c:488:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(command); ~~~~~~^~~~~~~~~ fastal/scoring.c: In function ‘double agreement_score(char*, char*)’: fastal/scoring.c:583:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function ‘int complete_agreement_score(char*, const char*)’: fastal/scoring.c:624:27: warning: ‘%s’ directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] sprintf(ref_file_name, "%s/%s",directory, dp->d_name); ^~~~~~~ ~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from fastal/scoring.c:28: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 756 bytes into a destination of size 200 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC km_coffee/classes.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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from io_lib/pb_util_read_seq_util.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘void getstr(char*, char*)’: io_lib/pb_util_read_seq_util.c:269:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(outstr, 100, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘double getreal(char*, double, double, double)’: io_lib/pb_util_read_seq_util.c:280:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘int getint(char*, int, int, int)’: io_lib/pb_util_read_seq_util.c:305:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ 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 io_lib/pb_util_read_sequence.c:35: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from io_lib/pb_util_read_sequence.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ io_lib/pb_util_read_sequence.c: In function ‘void get_clustal_seq(char*, char*, int*, char*, int)’: io_lib/pb_util_read_sequence.c:144:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_sequence.c:149:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] for(i=1;iid); ^~~~~ ~~~~~~~~~~~ km_coffee/km_coffee.c:157:22: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ km_coffee/km_coffee.c:157:22: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] km_coffee/km_coffee.c:159:22: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %s -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, gapopen, gapext, method); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ km_coffee/km_coffee.c:169:22: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] sprintf(command, "%li",current->id); ^~~~~ ~~~~~~~~~~~ km_coffee/km_coffee.c:172:22: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ km_coffee/km_coffee.c:172:22: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] km_coffee/km_coffee.c:174:22: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %s -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, gapopen, gapext, method); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ km_coffee/km_coffee.c:185:22: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] sprintf(command, "%li.fa",current->id); ^~~~~~~~ ~~~~~~~~~~~ km_coffee/km_coffee.c:195:23: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] sprintf(command, "t_coffee -output fasta_aln -method %s -quiet -outfile %li.fa -n_core %i -gapopen %i -profile FILE::prf.fa ", method, current->id,n_cores, gapopen); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ km_coffee/km_coffee.c:201:21: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] fprintf(prf_F, "%li.fa\n", current->children[j]->id); ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ km_coffee/km_coffee.c: In function ‘int km_coffee_align3(char*, int, int, char*, char*, int, int, int, char*)’: km_coffee/km_coffee.c:491:7: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir(km_tmp_dir); ~~~~~^~~~~~~~~~~~ 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 dp_lib/fsa_dp.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC util_lib/hsearch.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from dp_lib/evaluate_for_struc.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC util_lib/random.c CC util_lib/reformat.c CC util_lib/reformat_struc.c 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/hsearch.c:35: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/hsearch.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 dp_lib/util_dp_gotoh_nw.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_gotoh_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC util_lib/util_analyse_constraints_list.c 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_analyse_constraints_list.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/util_analyse_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 dp_lib/util_dp_suboptimal_nw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_suboptimal_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ fastal/parttree.c: In function ‘int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)’: fastal/parttree.c:695:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c:701:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘void get_table(short int*, FILE*, long int)’: fastal/parttree.c:848:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:859:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘int euclidean_dist(FILE*, long int, long int, short int*, short int*, int)’: fastal/parttree.c:891:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘int euclidean_dist_half(FILE*, long int, short int*, short int*, int)’: fastal/parttree.c:951:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_domain_constraints_list.c 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/aln_compare.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ CC util_lib/util_job_handling.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/io_func.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from io_lib/io_func.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ io_lib/io_func.c: In function ‘int output_raw_score(Alignment*, Alignment*, char*)’: io_lib/io_func.c:1235:17: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] if (!A)return NULL; ^~~~ io_lib/io_func.c: In function ‘int aln2compressed_ps(Alignment*, char*)’: io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/io_func.c: In function ‘int** read_matrice(char*)’: io_lib/io_func.c:511:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ~~~~~~~^~~~~~~~~~~ io_lib/io_func.c: In function ‘void get_rgb_values(int, Color*)’: io_lib/io_func.c:971:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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_dps.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/util_dps.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/util_domain_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:1924:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1929:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1976:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1980:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:2115:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:2262:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)’: fastal/fastal.c:3201:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , seq_file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)’: fastal/fastal.c:3323:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3326:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)’: fastal/fastal.c:3502:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , sequence_file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)’: fastal/fastal.c:3575:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(aligned_sequence, alignment_length+3, edit_seq_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/util_job_handling.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/reformat_struc.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/reformat_struc.c: In function ‘void bfactor2x_in_pdb(char*, char*, float*)’: util_lib/reformat_struc.c:125:18: warning: too many arguments for format [-Wformat-extra-args] fprintf (out, "ATOM ", lw[1]);//ATOM ^~~~~~~~ util_lib/reformat_struc.c: In function ‘Ca_trace* simple_read_ca_trace(char*)’: util_lib/reformat_struc.c:370:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:372:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:378:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:405:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:407:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:416:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ dp_lib/util_dp_drivers.c: In function ‘char* seq_file2msa_file(char*, char*, char*)’: dp_lib/util_dp_drivers.c:1014:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ dp_lib/util_dp_drivers.c:1028:16: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* align_pdb_pair_2(char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1080:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* align_pdb_pair(char*, char*, char*, char*, Constraint_list*, Job_TC*)’: dp_lib/util_dp_drivers.c:1108:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* hh_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1149:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1160:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln1); ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1161:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln2); ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1164:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] tmpnam(hhfile); ~~~~~~^~~~~~~~ dp_lib/util_dp_drivers.c:1211:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (buf2, 10000, fp); ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1280:6: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1363:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", bufname); ~~~~~~~^~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_pair_decomposed(TC_method*, char*, Constraint_list*, char*)’: dp_lib/util_dp_drivers.c:1445:7: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_subset_pair_old(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1581:7: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* pdbid_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1717:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* pdb_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1774:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* thread_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1906:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* lsqman_pair(char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1981:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* sap_pair(char*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:2073:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2121:10: warning: ignoring return value of ‘char* getcwd(char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] getcwd (cdir, sizeof(char)*1000); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2122:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (get_cache_dir()); ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2142:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* rnapdb_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:2256:6: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* method2pw_cl(TC_method*, Constraint_list*)’: dp_lib/util_dp_drivers.c:382:23: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:373:22: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:386:40: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Alignment* realign_block(Alignment*, int, int, char*)’: dp_lib/util_dp_drivers.c:920:22: warning: ‘ -infile=’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 38 or more bytes (assuming 1037) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1854:22: warning: ‘%s’ directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 71 or more bytes (assuming 6067) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)’: dp_lib/util_dp_drivers.c:3717:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( dp_mode, "%s", CL->dp_mode); ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)’: dp_lib/util_dp_drivers.c:3717:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( dp_mode, "%s", CL->dp_mode); ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from dp_lib/util_dp_drivers.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util_make_tree.c: In function ‘tnode* redundate(Sequence*, NT_node, char*, char*)’: util_lib/util_make_tree.c:66:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util_make_tree.c: In function ‘char* seq2co_aln_file(char*, char*)’: util_lib/util_make_tree.c:124:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:127:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* seq2mafft_aln_file(char*, char*)’: util_lib/util_make_tree.c:157:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:159:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* seq2cw_aln_file(char*, char*)’: util_lib/util_make_tree.c:189:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:191:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* prf_pair2cw_aln_file(char*, char*, char*)’: util_lib/util_make_tree.c:222:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:225:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns1_dnd(Sequence*)’: util_lib/util_make_tree.c:1854:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1867:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns2_dnd(Sequence*)’: util_lib/util_make_tree.c:1883:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1896:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2mafft_dnd(Sequence*)’: util_lib/util_make_tree.c:1912:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1925:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2parttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1942:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1955:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2dpparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1972:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:1987:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fastparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:2005:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2018:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cwquick_dnd(Sequence*)’: util_lib/util_make_tree.c:2034:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2042:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_dnd(Sequence*)’: util_lib/util_make_tree.c:2059:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2067:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* aln2cw_tree(Alignment*)’: util_lib/util_make_tree.c:2087:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2094:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_tree(Sequence*)’: util_lib/util_make_tree.c:2109:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (dir); ~~~~~~^~~~~ util_lib/util_make_tree.c:2118:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/util_declare.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ dp_lib/evaluate.c: In function ‘Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)’: dp_lib/evaluate.c:2956:22: 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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ dp_lib/evaluate.c:2956:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘double’ [-Wformat=] dp_lib/evaluate.c:2956:22: warning: format ‘%f’ expects argument of type ‘double’, but argument 6 has type ‘int’ [-Wformat=] dp_lib/evaluate.c:2956:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘double’ [-Wformat=] dp_lib/evaluate.c: In function ‘Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)’: dp_lib/evaluate.c:809:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &res); ~~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:814:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:819:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c: In function ‘float** initialise_aa_physico_chemical_property_table(int*)’: dp_lib/evaluate.c:7511:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %c %*s",&v1, &c1 ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from t_coffee_lib/t_coffee.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ t_coffee_lib/t_coffee.c: In function ‘char** km_coffee(int, char**)’: t_coffee_lib/t_coffee.c:6544:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ t_coffee_lib/t_coffee.c: In function ‘Alignment* t_coffee_dpa(int, char**)’: 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);} ^~~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function ‘Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)’: t_coffee_lib/t_coffee.c:6783:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ t_coffee_lib/t_coffee.c: In function ‘int batch_main(int, char**)’: t_coffee_lib/t_coffee.c:5621:32: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); ^~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from t_coffee_lib/t_coffee.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 10 or more bytes (assuming 1018) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, from io_lib/tree_util.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from io_lib/tree_util.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ io_lib/tree_util.c: In function ‘tnode* tree_scan(Alignment*, NT_node, char*, char*)’: 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: In function ‘Alignment* phylotrim(Alignment*, NT_node, char*, char*, char*)’: io_lib/tree_util.c:1299:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/tree_util.c: In function ‘tnode* no_rec_free_tree(NT_node)’: io_lib/tree_util.c:2317:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/tree_util.c: In function ‘int node_sort(char*, NT_node)’: io_lib/tree_util.c:6172:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/tree_util.c: In function ‘int treelist2leafgroup(Sequence*, Sequence*, char*)’: io_lib/tree_util.c:6465:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/tree_util.c: In function ‘int count_tree_groups(Sequence*, char*)’: io_lib/tree_util.c:6568:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/tree_util.c: In function ‘int treelist2splits(Sequence*, Sequence*)’: io_lib/tree_util.c:6946:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/tree_util.c: In function ‘int treelist2splits_old(Sequence*, Sequence*)’: io_lib/tree_util.c:7030:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/tree_util.c: In function ‘int treelist2frame(Sequence*, Sequence*)’: io_lib/tree_util.c:7103:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ io_lib/tree_util.c: In function ‘char* graph2cons_d(long unsigned int, int)’: io_lib/tree_util.c:10027:27: warning: NULL used in arithmetic [-Wpointer-arith] while ((c=rn_c(s))!=NULL) ^~~~ io_lib/tree_util.c: In function ‘long unsigned int insert_gap_in_graph_d(long unsigned int)’: io_lib/tree_util.c:10045:20: warning: converting to non-pointer type ‘long unsigned int’ from NULL [-Wconversion-null] unsigned long pn=NULL; ^~~~ io_lib/tree_util.c:10047:22: warning: converting to non-pointer type ‘long unsigned int’ from NULL [-Wconversion-null] if (!start) return NULL; ^~~~ io_lib/tree_util.c:10060:18: warning: passing NULL to non-pointer argument 2 of ‘void wn_c(long unsigned int, long unsigned int)’ [-Wconversion-null] wn_c(n,NULL); ^ io_lib/tree_util.c: In function ‘FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)’: io_lib/tree_util.c:3872:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%f",&dist); ~~~~~~^~~~~~~~~~~~~~~ io_lib/tree_util.c:3880:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%f",&bootstrap); ~~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: In function ‘int check_node(ALN_node, char*)’: io_lib/tree_util.c:9636:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/util_constraints_list.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* unfreeze_constraint_list(Constraint_list*)’: util_lib/util_constraints_list.c:1312:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util_constraints_list.c: In function ‘Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)’: util_lib/util_constraints_list.c:2225:28: warning: too many arguments for format [-Wformat-extra-args] fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* read_constraint_list_file(Constraint_list*, char*)’: util_lib/util_constraints_list.c:2852:19: warning: too many arguments for format [-Wformat-extra-args] x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); ^~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Job_TC* submit_lib_job(Job_TC*)’: util_lib/util_constraints_list.c:582:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (tdir); ~~~~~~^~~~~~ util_lib/util_constraints_list.c:585:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function ‘char* method_file_tag2value(char*, char*)’: util_lib/util_constraints_list.c:1151:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘TC_method* method_file2TC_method(char*)’: util_lib/util_constraints_list.c:1194:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘int read_cpu_in_list(char*)’: util_lib/util_constraints_list.c:2600:20: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] if ( c=='C')fscanf( fp, "PU %d\n", &cpu); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)’: util_lib/util_constraints_list.c:2918:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &max_nseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2923:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %d %*s\n", &l); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2955:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2980:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (line , 200 , fp); ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)’: util_lib/util_constraints_list.c:4054:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘char* make_aln_command(TC_method*, char*, char*)’: util_lib/util_constraints_list.c:1287:17: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] sprintf ( buf, "%s %s %s%s %s %s%s %s", m->executable, m->param1, m->in_flag, seq,m->param2, m->out_flag,aln, m->param); ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util_constraints_list.c:29: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)’: util_lib/util_constraints_list.c:695:23: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( aln_mode, "%s", method->aln_mode); ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util_constraints_list.c:29: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:696:23: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] sprintf ( out_mode, "%s", method->out_mode); ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util_constraints_list.c:29: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/util_aln_analyze.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util_aln_analyze.c: In function ‘Alignment* sar_analyze(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util_aln_analyze.c: In function ‘Alignment* or_scan(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/util.c:52: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/util.c: In function ‘int cherry(int, char**)’: util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util.c: In function ‘int dump_nfc(char*, char*)’: util_lib/util.c:4455:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util.c: In function ‘int set_nproc(int)’: util_lib/util.c:5488:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util.c: In function ‘char* vremove3(char*, char*)’: util_lib/util.c:6920:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/util.c: In function ‘FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))’: util_lib/util.c:281:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[--l]*/ ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:286:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[ir]*/ ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:289:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread( rrb, size, len,fp); /*rrb=ra[0]*/ ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:306:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ra_j, size, len, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:311:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ra_j_1, size, len, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))’: util_lib/util.c:420:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread ( key2, el_size, entry_len,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* get_number_list_in_file(FILE*, int*, int*, int*)’: util_lib/util.c:847:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d",&list[n[0]++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int quantile(int, char**)’: util_lib/util.c:1321:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %s\n", s1, s2); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** input_array_int(char*)’: util_lib/util.c:1805:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &len); ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1809:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &len2); ~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1812:8: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &array[a][b]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1813:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "\n"); ~~~~~~~^~~~~~~~~~ util_lib/util.c: In function ‘int perl_strstr(char*, char*)’: util_lib/util.c:2468:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d", &r); ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int printf_system_direct_check(char*, ...)’: util_lib/util.c:4439:19: warning: control reaches end of non-void function [-Wreturn-type] printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* count_strings_in_file(char*, char*)’: util_lib/util.c:5760:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",list[n]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stderr(char*)’: util_lib/util.c:6300:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] freopen(stderr_file, "w", stderr); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stdout(char*)’: util_lib/util.c:6343:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] freopen(stdout_file, "w", stdout); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)’: util_lib/util.c:7554:2: warning: second parameter of ‘va_start’ not last named argument [-Wvarargs] va_start (ap, usage); ^~~~~~~~ util_lib/util.c: In function ‘char** get_parameter(char*, int*, char*)’: util_lib/util.c:7821:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* set_fp_id(FILE*, char*)’: util_lib/util.c:7841:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", string); ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** get_file_block_pattern(char*, int*, int)’: util_lib/util.c:8228:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:8258:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_for_update(char*)’: util_lib/util.c:8345:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "Version_%f", &new_version); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_internet_connection(int)’: util_lib/util.c:8437:10: warning: control reaches end of non-void function [-Wreturn-type] myexit (EXIT_FAILURE); ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int km_main(int, char**)’: util_lib/util.c:10370:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/util.c: In function ‘char* get_cache_4_tcoffee()’: util_lib/util.c:5392:39: warning: ‘/cache/’ directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); ^~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util.c:32: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 8 and 1007 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_mcoffee_4_tcoffee()’: util_lib/util.c:5407:41: warning: ‘/mcoffee/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util.c:32: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_methods_4_tcoffee()’: util_lib/util.c:5420:41: warning: ‘/methods/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util.c:32: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_plugins_4_tcoffee()’: util_lib/util.c:5434:40: warning: ‘/plugins/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); ^~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util.c:32: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 11 and 1109 bytes into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* long_tmpnam_2(char*)’: util_lib/util.c:6808:16: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf (buf, "%s/%s%d%s",tmpdir,root2, file++,set_file2remove_extension (NULL, GET)); ^~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util.c:32: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 3 or more bytes (assuming 10101) into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* ultrashort_tmpnam_2(char*)’: util_lib/util.c:6840:16: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf (buf, "%s/%s%d%s",tmpdir,root2, file++,set_file2remove_extension (NULL, GET)); ^~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util.c:32: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 3 or more bytes (assuming 10101) into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* short_tmpnam_2(char*)’: util_lib/util.c:6871:17: warning: ‘%s’ directive writing up to 99 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf (buf, "%s%d%s",root2, file++,set_file2remove_extension (NULL, GET)); ^~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/util.c:32: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10110 bytes into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/aln_convertion_util.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2conservation(Alignment*, int, char*)’: util_lib/aln_convertion_util.c:4446:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2N_replicate(Alignment*, char*, char*)’: util_lib/aln_convertion_util.c:7697:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/aln_convertion_util.c: In function ‘Alignment* extract_aln3(Alignment*, char*)’: util_lib/aln_convertion_util.c:7459:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7478:31: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7482:13: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function ‘float** get_weight(Alignment*, Sequence*, char*)’: util_lib/aln_convertion_util.c:12082:26: warning: ‘ -w ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/aln_convertion_util.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 1005) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:12076:26: warning: ‘ -i ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/aln_convertion_util.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 10 or more bytes (assuming 1009) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 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 C++11 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 C++11 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 C++11 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 C++11 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:33, from util_lib/reformat.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration typedef struct ALNcol ^~~~~~~ util_lib/reformat.c: In function ‘int output_suchard_aln(char*, Alignment*)’: util_lib/reformat.c:7441:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/reformat.c: In function ‘void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’: util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11290:35: note: in expansion of macro ‘ATOI_ACTION’ (D1->A)=aln2bootstrap (D1->A, ATOI_ACTION (1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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:11296:32: note: in expansion of macro ‘ATOI_ACTION’ (D1->A)=aln2sample (D1->A, ATOI_ACTION (1)); ^~~~~~~~~~~ util_lib/reformat.c:11529:41: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION (3))D=atof (ACTION(3)); ^ util_lib/reformat.c:43:58: 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:11563:38: note: in expansion of macro ‘ATOI_ACTION’ else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11662:38: note: in expansion of macro ‘ATOI_ACTION’ else TS=treelist2sub_seq((D1->S),ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11663:34: note: in expansion of macro ‘ATOI_ACTION’ treelist2lti (D1->S,TS, (int)ATOI_ACTION(1), stdout ); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11670:38: note: in expansion of macro ‘ATOI_ACTION’ else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11677:35: note: in expansion of macro ‘ATOI_ACTION’ D1->S=treelist2sub_seq (D1->S,ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:11705:27: warning: null argument where non-null required (argument 1) [-Wnonnull] ng=atoi(ACTION (2))+1; ^ util_lib/reformat.c:43:58: 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:11733:31: note: in expansion of macro ‘ATOI_ACTION’ tree2bucket (D2->T, D1->S,ATOI_ACTION(1), ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:11743:29: warning: null argument where non-null required (argument 1) [-Wnonnull] int shuf=atoi (ACTION(1)); ^ util_lib/reformat.c:11754:29: warning: null argument where non-null required (argument 1) [-Wnonnull] int shuf=atoi (ACTION(1)); ^ util_lib/reformat.c:43:58: 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:11880:44: note: in expansion of macro ‘ATOI_ACTION’ D1->T= aln2km_tree(D1->A, (ACTION(1)), ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:11963:32: warning: null argument where non-null required (argument 1) [-Wnonnull] else max=atof(ACTION(na+1)); ^ util_lib/reformat.c:11966:32: warning: null argument where non-null required (argument 1) [-Wnonnull] else enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:11978:77: 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:11979:77: 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:11987:78: 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:11988:78: 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:12022:30: warning: null argument where non-null required (argument 1) [-Wnonnull] radius=atof(ACTION(1)); ^ util_lib/reformat.c:12030:33: warning: null argument where non-null required (argument 1) [-Wnonnull] threshold=atof(ACTION(2)); ^ util_lib/reformat.c:12037:27: warning: null argument where non-null required (argument 1) [-Wnonnull] min=atoi(ACTION(3)); ^ util_lib/reformat.c:12073:32: warning: null argument where non-null required (argument 1) [-Wnonnull] else max=atof(ACTION(na+1)); ^ util_lib/reformat.c:12076:32: warning: null argument where non-null required (argument 1) [-Wnonnull] else enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:12088:77: 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:12089:77: 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:12097:78: 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:12098:78: 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:43:58: 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:12146:44: note: in expansion of macro ‘ATOI_ACTION’ float results=shuff (D1->S, ACTION (1),ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12266:37: note: in expansion of macro ‘ATOI_ACTION’ D1->A=aln2conservation ( D1->A, ATOI_ACTION (1), ACTION (2)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12390:31: note: in expansion of macro ‘ATOI_ACTION’ D1->A=shuffle_aln (D1->A, ATOI_ACTION(1), ACTION(2), ACTION (3)); ^~~~~~~~~~~ util_lib/reformat.c:12901:36: warning: null argument where non-null required (argument 1) [-Wnonnull] else if (strstr (ACTION(1), "h")) ^ util_lib/reformat.c:43:58: 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:12908:10: note: in expansion of macro ‘ATOI_ACTION’ F->t=ATOI_ACTION(2); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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:12909:10: note: in expansion of macro ‘ATOI_ACTION’ F->f=ATOI_ACTION(3); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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->p1=ATOI_ACTION(4); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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->p2=ATOI_ACTION(5); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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:12912:11: note: in expansion of macro ‘ATOI_ACTION’ F->p3=ATOI_ACTION(6); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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:12913:11: note: in expansion of macro ‘ATOI_ACTION’ F->p3=ATOI_ACTION(7); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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:12936:34: note: in expansion of macro ‘ATOI_ACTION’ D1->A=unalign_aln (D1->A,SA, ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13076:10: note: in expansion of macro ‘ATOI_ACTION’ if (!ATOI_ACTION(1))myexit(fprintf_error (stderr,"-kmeans ")); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13077:19: note: in expansion of macro ‘ATOI_ACTION’ km_seq (D1->A,ATOI_ACTION (1),ACTION(2),ACTION(3)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13081:27: note: in expansion of macro ‘ATOI_ACTION’ D1->A=gap_trim (D1->A,ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13088:34: note: in expansion of macro ‘ATOI_ACTION’ D1->A=trim_RNA(D1->A, D2->S, ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13616:7: note: in expansion of macro ‘ATOI_ACTION’ t=ATOI_ACTION(1); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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:13617:7: note: in expansion of macro ‘ATOI_ACTION’ f=ATOI_ACTION(2); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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’ p1=ATOI_ACTION(3); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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:13619:8: note: in expansion of macro ‘ATOI_ACTION’ p2=ATOI_ACTION(4); ^~~~~~~~~~~ util_lib/reformat.c:43:58: 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:13620:8: note: in expansion of macro ‘ATOI_ACTION’ p3=ATOI_ACTION(5); ^~~~~~~~~~~ util_lib/reformat.c: In function ‘int output_header_mat(int**, char*)’: util_lib/reformat.c:14324:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ util_lib/reformat.c: In function ‘Sequence* quick_read_seq(char*)’: util_lib/reformat.c:1321:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln_static(char*)’: util_lib/reformat.c:1360:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln(char*)’: util_lib/reformat.c:1402:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c: In function ‘int read_nameseq(char*, char***, char***, char***)’: util_lib/reformat.c:1416:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "#NAMESEQ_01\n"); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1417:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "# %d\n", &nseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1427:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d %d ", &l1, &l2); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1430:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1435:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &l1); ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1437:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (com[0][nseq],l1, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int read_nameseq_old(char*, char***, char***, char***)’: util_lib/reformat.c:1461:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "#NAMESEQ_01\n"); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1462:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "# %d\n", &nseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1472:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d %d ", &l1, &l2); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1475:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1480:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &l1); ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1482:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (com[0][nseq],l1, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int is_pdb_name(char*)’: util_lib/reformat.c:1779:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d", &result); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘char* get_pdb_id(char*)’: util_lib/reformat.c:1817:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n%s\n", buf); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fast_format_determination(char*)’: util_lib/reformat.c:2486:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c: In function ‘Weights* get_amps_sd_scores(char*)’: util_lib/reformat.c:3926:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3933:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3942:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3948:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",W->seq_name[a]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3950:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3961:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ~~~~~~~^~~~~~~~~~~ util_lib/reformat.c: In function ‘Structure* read_rna_struc_number(Alignment*, char*)’: util_lib/reformat.c:4234:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4237:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d %d %d %c %c %f\n", &(ST)->list[a][0],&(ST)->list[a][1],&(ST)->list[a][2], &x, &y, &f); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_struc_gor(char*)’: util_lib/reformat.c:4464:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d", name, &len); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4485:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4490:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_sequence_dali(char*)’: util_lib/reformat.c:4527:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s",name); ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_dialign_sequence(char*)’: util_lib/reformat.c:4602:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%s",name); ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fscanf_seq_name(FILE*, char*)’: util_lib/reformat.c:5636:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", name); ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int get_amps_seq_name(char**, char*)’: util_lib/reformat.c:5989:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%*d >%s", name[nseq++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* read_gotoh_aln(char*, Alignment*)’: util_lib/reformat.c:6038:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6060:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘float output_maln_pval(char*, Alignment*)’: util_lib/reformat.c:6258:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",string); ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* similarities_file2aln(char*)’: util_lib/reformat.c:6423:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %d", name,&i); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix(char*)’: util_lib/reformat.c:14165:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14178:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14203:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix_old(char*)’: util_lib/reformat.c:14228:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14245:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14258:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14285:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_pavie_matrix(char*)’: util_lib/reformat.c:14396:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’: util_lib/reformat.c:13510:24: warning: ‘ -method ’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] sprintf ( command, "%s -method %s -aln %s -tree %s -dmatrix %s -weightfile %s %s",method_4_msa_weights, action_list[1],aln_name, tree_name, dist_matrix_name,weight_name, TO_NULL_DEVICE); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from util_lib/reformat.c:27: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 64 or more bytes (assuming 3059) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:11528:24: warning: ‘%s’ directive argument is null [-Wformat-overflow=] sprintf (type, "%s", ACTION (2)); ^~~~ Linking... /usr/lib/gcc-cross/arm-linux-gnueabihf/8/../../../../arm-linux-gnueabihf/bin/ld: dp_lib/util_dp_drivers.o: in function `hh_pair(TC_method*, char*, Constraint_list*)': ./t_coffee_source/dp_lib/util_dp_drivers.c:1160: warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/<>/t_coffee_source' make[1]: Leaving directory '/<>' dh_auto_test -a -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --sourcedirectory=t_coffee_source dh_testroot -a -O--sourcedirectory=t_coffee_source dh_prep -a -O--sourcedirectory=t_coffee_source dh_auto_install -a -O--sourcedirectory=t_coffee_source dh_install -a -O--sourcedirectory=t_coffee_source dh_installdocs -a -O--sourcedirectory=t_coffee_source dh_installchangelogs -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples mkdir -p /<>/debian/t-coffee/usr/share/doc/t-coffee/examples; cp -aR example/* /<>/debian/t-coffee/usr/share/doc/t-coffee/examples/; make[1]: Leaving directory '/<>' dh_installman -a -O--sourcedirectory=t_coffee_source dh_installinit -a -O--sourcedirectory=t_coffee_source dh_installsystemduser -a -O--sourcedirectory=t_coffee_source dh_perl -a -O--sourcedirectory=t_coffee_source dh_link -a -O--sourcedirectory=t_coffee_source dh_strip_nondeterminism -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_compress make[1]: Entering directory '/<>' #Compressing most of the files in examples/ makes them unusable dh_compress -Xt-coffee-examples ( cd debian/t-coffee-examples/ && \ chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \ gzip -9 -n usr/share/doc/t-coffee-examples/changelog.Debian ) || true /bin/sh: 1: cd: can't cd to debian/t-coffee-examples/ make[1]: Leaving directory '/<>' dh_fixperms -a -O--sourcedirectory=t_coffee_source dh_missing -a -O--sourcedirectory=t_coffee_source dh_dwz -a -O--sourcedirectory=t_coffee_source dh_strip -a -O--sourcedirectory=t_coffee_source dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -O--sourcedirectory=t_coffee_source dpkg-shlibdeps: warning: debian/t-coffee/usr/bin/t_coffee contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a -O--sourcedirectory=t_coffee_source dh_gencontrol -a -O--sourcedirectory=t_coffee_source dh_md5sums -a -O--sourcedirectory=t_coffee_source dh_builddeb -a -O--sourcedirectory=t_coffee_source dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_12.00.7fb08c2-4_armhf.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_12.00.7fb08c2-4_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../t-coffee_12.00.7fb08c2-4_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-03-07T04:44:55Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ t-coffee_12.00.7fb08c2-4_armhf.changes: --------------------------------------- Format: 1.8 Date: Fri, 15 Feb 2019 07:43:22 +0100 Source: t-coffee Binary: t-coffee t-coffee-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 12.00.7fb08c2-4 Distribution: unstable-amd64-sbuild Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: t-coffee - Multiple Sequence Alignment Closes: 922196 Changes: t-coffee (12.00.7fb08c2-4) unstable; urgency=medium . [ Helmut Grohne ] * Fix FTCBFS: Pass C++ compiler as CC. Closes: #922196 Checksums-Sha1: bcbfe2c7ac81ba42b6dabb49d841b573b5859674 2753448 t-coffee-dbgsym_12.00.7fb08c2-4_armhf.deb 942e5b3d0fa424f3d16f2e4fb49f5b0088716286 4571 t-coffee_12.00.7fb08c2-4_armhf.buildinfo 651499302378b890c235c0c4f37af0f1c2be750b 1387696 t-coffee_12.00.7fb08c2-4_armhf.deb Checksums-Sha256: dca23b3e756dd6bd09b628acb8636efc54c1cd0aa99b9d8acc6a5ea597642487 2753448 t-coffee-dbgsym_12.00.7fb08c2-4_armhf.deb f49bdf61135f1ae741e6182b0dca2a2bb703b5ec3d8cf26899cd51c7feb100b1 4571 t-coffee_12.00.7fb08c2-4_armhf.buildinfo 26b90317c5a3aad168d5e9cf29ceea512940b0ae8d034cd96f647ede7f443ea7 1387696 t-coffee_12.00.7fb08c2-4_armhf.deb Files: 022cbf4921881150b776c5818d58abcc 2753448 debug optional t-coffee-dbgsym_12.00.7fb08c2-4_armhf.deb 6f038b970c7a7b7c3dfb4bb095d12c64 4571 science optional t-coffee_12.00.7fb08c2-4_armhf.buildinfo 0f19d33faf2c693fed6c4f8c1883a9cb 1387696 science optional t-coffee_12.00.7fb08c2-4_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: armhf Version: 12.00.7fb08c2-4 Checksums-Md5: 022cbf4921881150b776c5818d58abcc 2753448 t-coffee-dbgsym_12.00.7fb08c2-4_armhf.deb 0f19d33faf2c693fed6c4f8c1883a9cb 1387696 t-coffee_12.00.7fb08c2-4_armhf.deb Checksums-Sha1: bcbfe2c7ac81ba42b6dabb49d841b573b5859674 2753448 t-coffee-dbgsym_12.00.7fb08c2-4_armhf.deb 651499302378b890c235c0c4f37af0f1c2be750b 1387696 t-coffee_12.00.7fb08c2-4_armhf.deb Checksums-Sha256: dca23b3e756dd6bd09b628acb8636efc54c1cd0aa99b9d8acc6a5ea597642487 2753448 t-coffee-dbgsym_12.00.7fb08c2-4_armhf.deb 26b90317c5a3aad168d5e9cf29ceea512940b0ae8d034cd96f647ede7f443ea7 1387696 t-coffee_12.00.7fb08c2-4_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 07 Mar 2019 04:44:55 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 10.1), base-passwd (= 3.5.46), bash (= 5.0-2), binutils (= 2.31.1-15), binutils-common (= 2.31.1-15), binutils-x86-64-linux-gnu (= 2.31.1-15), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.33.1-0.1), build-essential (= 12.6), bzip2 (= 1.0.6-9), coreutils (= 8.30-3), cpp (= 4:8.3.0-1), cpp-8 (= 8.3.0-2), dash (= 0.5.10.2-5), debconf (= 1.5.71), debhelper (= 12.1.1), debianutils (= 4.8.6.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.1.1-1), diffutils (= 1:3.7-2), dpkg (= 1.19.5), dpkg-dev (= 1.19.5), dwz (= 0.12-3), fdisk (= 2.33.1-0.1), file (= 1:5.35-4), findutils (= 4.6.0+git+20190209-2), g++ (= 4:8.3.0-1), g++-8 (= 8.3.0-2), gcc (= 4:8.3.0-1), gcc-8 (= 8.3.0-2), gcc-8-base (= 8.3.0-2), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3), hostname (= 3.21), init-system-helpers (= 1.56+nmu1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-4), libarchive-zip-perl (= 1.64-1), libasan5 (= 8.3.0-2), libatomic1 (= 8.3.0-2), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.4-2), libaudit1 (= 1:2.8.4-2), libbinutils (= 2.31.1-15), libblkid1 (= 2.33.1-0.1), libbsd0 (= 0.9.1-2), libbz2-1.0 (= 1.0.6-9), libc-bin (= 2.28-8), libc-dev-bin (= 2.28-8), libc6 (= 2.28-8), libc6-dev (= 2.28-8), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 8.3.0-2), libcroco3 (= 0.6.12-3), libdb5.3 (= 5.3.28+dfsg1-0.5), libdebconfclient0 (= 0.248), libdpkg-perl (= 1.19.5), libelf1 (= 0.176-1), libfdisk1 (= 2.33.1-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.1.1-1), libgcc-8-dev (= 8.3.0-2), libgcc1 (= 1:8.3.0-2), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-3), libgdbm6 (= 1.18.1-3), libglib2.0-0 (= 2.58.3-1), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 8.3.0-2), libgpg-error0 (= 1.35-1), libicu63 (= 63.1-6), libisl19 (= 0.20-2), libitm1 (= 8.3.0-2), liblsan0 (= 8.3.0-2), liblz4-1 (= 1.8.3-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.35-4), libmagic1 (= 1:5.35-4), libmount1 (= 2.33.1-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-2), libncurses6 (= 6.1+20181013-2), libncursesw6 (= 6.1+20181013-2), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre3 (= 2:8.39-11), libperl5.28 (= 5.28.1-4), libpipeline1 (= 1.5.1-2), libquadmath0 (= 8.3.0-2), libseccomp2 (= 2.3.3-4), libselinux1 (= 2.8-1+b1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.33.1-0.1), libstdc++-8-dev (= 8.3.0-2), libstdc++6 (= 8.3.0-2), libsystemd0 (= 241-1), libtinfo6 (= 6.1+20181013-2), libtool (= 2.4.6-10), libtsan0 (= 8.3.0-2), libubsan1 (= 8.3.0-2), libuchardet0 (= 0.0.6-3), libudev1 (= 241-1), libunistring2 (= 0.9.10-1), libuuid1 (= 2.33.1-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 4.19.20-1), login (= 1:4.5-1.1), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.5-2), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20181013-2), ncurses-bin (= 6.1+20181013-2), 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), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.93-8), tar (= 1.30+dfsg-5), util-linux (= 2.33.1-0.1), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=16" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" MAKEFLAGS=" -j16" SOURCE_DATE_EPOCH="1550213002" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ t-coffee-dbgsym_12.00.7fb08c2-4_armhf.deb ----------------------------------------- new Debian package, version 2.0. size 2753448 bytes: control archive=544 bytes. 391 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: t-coffee-dbgsym Source: t-coffee Version: 12.00.7fb08c2-4 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 2936 Depends: t-coffee (= 12.00.7fb08c2-4) Section: debug Priority: optional Description: debug symbols for t-coffee Build-Ids: 15f7d15cd3768b77e27a46a1738af0f94ee58ffe drwxr-xr-x root/root 0 2019-02-15 06:43 ./ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/lib/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/lib/debug/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/lib/debug/.build-id/15/ -rw-r--r-- root/root 2995772 2019-02-15 06:43 ./usr/lib/debug/.build-id/15/f7d15cd3768b77e27a46a1738af0f94ee58ffe.debug drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-02-15 06:43 ./usr/share/doc/t-coffee-dbgsym -> t-coffee t-coffee_12.00.7fb08c2-4_armhf.deb ---------------------------------- new Debian package, version 2.0. size 1387696 bytes: control archive=5728 bytes. 1602 bytes, 29 lines control 16306 bytes, 197 lines md5sums Package: t-coffee Version: 12.00.7fb08c2-4 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 6608 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.5), libstdc++6 (>= 4.3.0) Recommends: amap-align, clustalo, clustalw, dialign-tx, fsa, kalign, libsoap-lite-perl, libxml-simple-perl, mafft, muscle, mustang, ncbi-blast+, poa, prank, probcons, proda, tm-align Suggests: boxshade, seaview, t-coffee-examples Section: science Priority: optional Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Description: Multiple Sequence Alignment T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. . T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information . T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer. drwxr-xr-x root/root 0 2019-02-15 06:43 ./ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/bin/ -rwxr-xr-x root/root 1932684 2019-02-15 06:43 ./usr/bin/t_coffee drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/doc/t-coffee/ -rw-r--r-- root/root 1744 2019-02-15 06:43 ./usr/share/doc/t-coffee/README.Debian -rw-r--r-- root/root 261 2019-02-15 06:43 ./usr/share/doc/t-coffee/README.test -rw-r--r-- root/root 3765 2019-02-15 06:43 ./usr/share/doc/t-coffee/changelog.Debian.gz -rw-r--r-- root/root 1433 2019-02-15 06:43 ./usr/share/doc/t-coffee/copyright drwxr-xr-x root/root 0 2019-02-15 06:43 ./usr/share/doc/t-coffee/examples/ -rw-r--r-- root/root 16443 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1D4V-1.pdb -rw-r--r-- root/root 27540 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1D4V-2.pdb -rw-r--r-- root/root 26325 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1D4V-3.pdb -rw-r--r-- root/root 24300 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1EXT-1.pdb -rw-r--r-- root/root 26649 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1EXT-2.pdb -rw-r--r-- root/root 27783 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1EXT-3.pdb -rw-r--r-- root/root 18548 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1EXT-4.pdb -rw-r--r-- root/root 20816 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1JMA-1.pdb -rw-r--r-- root/root 25758 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1JMA-2.pdb -rw-r--r-- root/root 18955 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1OQE-1.pdb -rw-r--r-- root/root 19439 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1SG1-1.pdb -rw-r--r-- root/root 24866 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1SG1-2.pdb -rw-r--r-- root/root 24542 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1SG1-3.pdb -rw-r--r-- root/root 26513 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1SG1-4.pdb -rw-r--r-- root/root 21950 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1XU1-2.pdb -rw-r--r-- root/root 22551 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/1XU2-1.pdb -rw-r--r-- root/root 22194 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/2HEY-1.pdb -rw-r--r-- root/root 26406 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/2HEY-2.pdb -rw-r--r-- root/root 23328 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/2HEY-4.pdb -rw-r--r-- root/root 35800 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/2RPJ-1.pdb -rw-r--r-- root/root 22842 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/2UWI-1.pdb -rw-r--r-- root/root 27863 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/2UWI-2.pdb -rw-r--r-- root/root 26215 2018-12-11 09:27 ./usr/share/doc/t-coffee/examples/2UWI-3.pdb -rw-r--r-- root/root 496 2018-12-11 09:27 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Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [527 B] Get:5 copy:/<>/apt_archive ./ Packages [612 B] Fetched 2102 B in 0s (154 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: diffstat libapt-pkg-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libio-async-perl libio-pty-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libparse-debianchangelog-perl libpath-tiny-perl libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl lintian patchutils t1utils Suggested packages: libhtml-template-perl binutils-multiarch libtext-template-perl Recommended packages: libcgi-fast-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libunicode-utf8-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat libapt-pkg-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libio-async-perl libio-pty-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libparse-debianchangelog-perl libpath-tiny-perl libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl lintian patchutils sbuild-build-depends-lintian-dummy:armhf t1utils 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. Need to get 2847 kB/2971 kB of archives. After this operation, 9356 kB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [844 B] Get:2 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libapt-pkg-perl amd64 0.1.34+b1 [71.2 kB] Get:3 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:4 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libcgi-pm-perl all 4.40-1 [222 kB] Get:5 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:6 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:7 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:8 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:9 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:10 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libnet-dns-perl all 1.19-1 [372 kB] Get:11 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:12 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:13 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:14 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:15 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:16 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libfuture-perl all 0.39-1 [74.5 kB] Get:17 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:18 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libio-async-perl all 0.72-1 [262 kB] Get:19 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:20 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:21 http://cdn-fastly.deb.debian.org/debian sid/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:22 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libparse-debianchangelog-perl all 1.2.0-13 [59.5 kB] Get:23 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:24 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:25 http://cdn-fastly.deb.debian.org/debian sid/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:26 http://cdn-fastly.deb.debian.org/debian sid/main amd64 lintian all 2.9.1 [1193 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2847 kB in 7s (426 kB/s) Selecting previously unselected package diffstat. (Reading database ... 19151 files and directories currently installed.) Preparing to unpack .../00-diffstat_1.62-1_amd64.deb ... Unpacking diffstat (1.62-1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../01-libapt-pkg-perl_0.1.34+b1_amd64.deb ... Unpacking libapt-pkg-perl (0.1.34+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../02-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../03-libcgi-pm-perl_4.40-1_all.deb ... Unpacking libcgi-pm-perl (4.40-1) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../04-libsub-name-perl_0.21-1+b3_amd64.deb ... Unpacking libsub-name-perl (0.21-1+b3) ... Selecting previously unselected package libclass-accessor-perl. Preparing to unpack .../05-libclass-accessor-perl_0.51-1_all.deb ... Unpacking libclass-accessor-perl (0.51-1) ... Selecting previously unselected package libclone-perl. Preparing to unpack .../06-libclone-perl_0.41-1+b1_amd64.deb ... Unpacking libclone-perl (0.41-1+b1) ... Selecting previously unselected package libdigest-hmac-perl. Preparing to unpack .../07-libdigest-hmac-perl_1.03+dfsg-2_all.deb ... Unpacking libdigest-hmac-perl (1.03+dfsg-2) ... Selecting previously unselected package libnet-ip-perl. Preparing to unpack .../08-libnet-ip-perl_1.26-2_all.deb ... Unpacking libnet-ip-perl (1.26-2) ... Selecting previously unselected package libnet-dns-perl. Preparing to unpack .../09-libnet-dns-perl_1.19-1_all.deb ... Unpacking libnet-dns-perl (1.19-1) ... Selecting previously unselected package libnet-domain-tld-perl. Preparing to unpack .../10-libnet-domain-tld-perl_1.75-1_all.deb ... Unpacking libnet-domain-tld-perl (1.75-1) ... Selecting previously unselected package libemail-valid-perl. Preparing to unpack .../11-libemail-valid-perl_1.202-1_all.deb ... Unpacking libemail-valid-perl (1.202-1) ... Selecting previously unselected package libexporter-tiny-perl. Preparing to unpack .../12-libexporter-tiny-perl_1.002001-1_all.deb ... Unpacking libexporter-tiny-perl (1.002001-1) ... Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../13-libipc-system-simple-perl_1.25-4_all.deb ... Unpacking libipc-system-simple-perl (1.25-4) ... Selecting previously unselected package libfile-basedir-perl. Preparing to unpack .../14-libfile-basedir-perl_0.08-1_all.deb ... Unpacking libfile-basedir-perl (0.08-1) ... Selecting previously unselected package libfuture-perl. Preparing to unpack .../15-libfuture-perl_0.39-1_all.deb ... Unpacking libfuture-perl (0.39-1) ... Selecting previously unselected package libstruct-dumb-perl. Preparing to unpack .../16-libstruct-dumb-perl_0.09-1_all.deb ... Unpacking libstruct-dumb-perl (0.09-1) ... Selecting previously unselected package libio-async-perl. Preparing to unpack .../17-libio-async-perl_0.72-1_all.deb ... Unpacking libio-async-perl (0.72-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../18-libio-pty-perl_1%3a1.08-1.1+b5_amd64.deb ... Unpacking libio-pty-perl (1:1.08-1.1+b5) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../19-libipc-run-perl_20180523.0-1_all.deb ... Unpacking libipc-run-perl (20180523.0-1) ... Selecting previously unselected package liblist-moreutils-perl. Preparing to unpack .../20-liblist-moreutils-perl_0.416-1+b4_amd64.deb ... Unpacking liblist-moreutils-perl (0.416-1+b4) ... Selecting previously unselected package libparse-debianchangelog-perl. Preparing to unpack .../21-libparse-debianchangelog-perl_1.2.0-13_all.deb ... Unpacking libparse-debianchangelog-perl (1.2.0-13) ... Selecting previously unselected package libpath-tiny-perl. Preparing to unpack .../22-libpath-tiny-perl_0.108-1_all.deb ... Unpacking libpath-tiny-perl (0.108-1) ... Selecting previously unselected package libtext-levenshtein-perl. Preparing to unpack .../23-libtext-levenshtein-perl_0.13-1_all.deb ... Unpacking libtext-levenshtein-perl (0.13-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../24-patchutils_0.3.4-2_amd64.deb ... Unpacking patchutils (0.3.4-2) ... Selecting previously unselected package t1utils. Preparing to unpack .../25-t1utils_1.41-3_amd64.deb ... Unpacking t1utils (1.41-3) ... Selecting previously unselected package lintian. Preparing to unpack .../26-lintian_2.9.1_all.deb ... Unpacking lintian (2.9.1) ... Selecting previously unselected package sbuild-build-depends-lintian-dummy:armhf. Preparing to unpack .../27-sbuild-build-depends-lintian-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.34+b1) ... Setting up libstruct-dumb-perl (0.09-1) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libclone-perl (0.41-1+b1) ... Setting up libfuture-perl (0.39-1) ... Setting up libcgi-pm-perl (4.40-1) ... Setting up libtext-levenshtein-perl (0.13-1) ... Setting up libio-async-perl (0.72-1) ... Setting up patchutils (0.3.4-2) ... Setting up libdigest-hmac-perl (1.03+dfsg-2) ... Setting up libipc-system-simple-perl (1.25-4) ... Setting up libnet-domain-tld-perl (1.75-1) ... Setting up t1utils (1.41-3) ... Setting up diffstat (1.62-1) ... Setting up libipc-run-perl (20180523.0-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libsub-name-perl (0.21-1+b3) ... Setting up libpath-tiny-perl (0.108-1) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b4) ... Setting up libnet-dns-perl (1.19-1) ... Setting up libparse-debianchangelog-perl (1.2.0-13) ... Setting up libemail-valid-perl (1.202-1) ... Setting up lintian (2.9.1) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl uuid-runtime Use 'apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libmailtools-perl libnet-smtp-ssl-perl libyaml-0-2 libyaml-libyaml-perl uuid-runtime Use 'apt autoremove' to remove them. The following packages will be REMOVED: autoconf* automake* autopoint* autotools-dev* bsdmainutils* debhelper* dh-autoreconf* dh-strip-nondeterminism* diffstat* dwz* gcc-8-base:armhf* gettext* gettext-base* groff-base* intltool-debian* libapt-pkg-perl* libarchive-zip-perl* libasan5:armhf* libatomic1:armhf* libbsd0* libc6:armhf* libc6-dev:armhf* libcapture-tiny-perl* libcgi-pm-perl* libclass-accessor-perl* libclone-perl* libcroco3* libdigest-hmac-perl* libelf1* libemail-valid-perl* libexporter-tiny-perl* libfile-basedir-perl* libfile-stripnondeterminism-perl* libfuture-perl* libgcc-8-dev:armhf* libgcc1:armhf* libglib2.0-0* libgomp1:armhf* libio-async-perl* libio-pty-perl* libipc-run-perl* libipc-system-simple-perl* liblist-moreutils-perl* libncurses6* libnet-dns-perl* libnet-domain-tld-perl* libnet-ip-perl* libparse-debianchangelog-perl* libpath-tiny-perl* libpipeline1* libsigsegv2* libstdc++-8-dev:armhf* libstdc++6:armhf* libstruct-dumb-perl* libsub-name-perl* libtext-levenshtein-perl* libtool* libubsan1:armhf* libuchardet0* lintian* linux-libc-dev:armhf* m4* man-db* patchutils* po-debconf* sbuild-build-depends-lintian-dummy:armhf* sbuild-build-depends-main-dummy:armhf* t1utils* 0 upgraded, 0 newly installed, 68 to remove and 0 not upgraded. After this operation, 88.5 MB disk space will be freed. (Reading database ... 20429 files and directories currently installed.) Removing sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Removing sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Removing lintian (2.9.1) ... Removing diffstat (1.62-1) ... Removing libstdc++-8-dev:armhf (8.3.0-2) ... Removing libgcc-8-dev:armhf (8.3.0-2) ... Removing libubsan1:armhf (8.3.0-2) ... Removing libasan5:armhf (8.3.0-2) ... Removing libstdc++6:armhf (8.3.0-2) ... Removing libapt-pkg-perl (0.1.34+b1) ... Removing libatomic1:armhf (8.3.0-2) ... Removing libc6-dev:armhf (2.28-8) ... Removing libgomp1:armhf (8.3.0-2) ... Removing libcapture-tiny-perl (0.48-1) ... Removing libparse-debianchangelog-perl (1.2.0-13) ... Removing libcgi-pm-perl (4.40-1) ... Removing libclass-accessor-perl (0.51-1) ... Removing libclone-perl (0.41-1+b1) ... Removing libemail-valid-perl (1.202-1) ... Removing libnet-dns-perl (1.19-1) ... Removing libdigest-hmac-perl (1.03+dfsg-2) ... Removing liblist-moreutils-perl (0.416-1+b4) ... Removing libexporter-tiny-perl (1.002001-1) ... Removing libfile-basedir-perl (0.08-1) ... Removing libio-async-perl (0.72-1) ... Removing libfuture-perl (0.39-1) ... Removing libipc-run-perl (20180523.0-1) ... Removing libio-pty-perl (1:1.08-1.1+b5) ... Removing libipc-system-simple-perl (1.25-4) ... Removing libnet-domain-tld-perl (1.75-1) ... Removing libnet-ip-perl (1.26-2) ... Removing libpath-tiny-perl (0.108-1) ... Removing libstruct-dumb-perl (0.09-1) ... Removing libsub-name-perl (0.21-1+b3) ... Removing libtext-levenshtein-perl (0.13-1) ... Removing linux-libc-dev:armhf (4.19.20-1) ... Removing patchutils (0.3.4-2) ... Removing t1utils (1.41-3) ... Removing libgcc1:armhf (1:8.3.0-2) ... Removing debhelper (12.1.1) ... Removing dh-strip-nondeterminism (1.1.1-1) ... Removing man-db (2.8.5-2) ... Removing bsdmainutils (11.1.2+b1) ... Removing dwz (0.12-3) ... Removing gcc-8-base:armhf (8.3.0-2) ... Removing po-debconf (1.0.21) ... Removing intltool-debian (0.35.0+20060710.5) ... Removing gettext (0.19.8.1-9) ... Removing gettext-base (0.19.8.1-9) ... Removing groff-base (1.22.4-3) ... Removing libfile-stripnondeterminism-perl (1.1.1-1) ... Removing libarchive-zip-perl (1.64-1) ... Removing libbsd0:amd64 (0.9.1-2) ... Removing libc6:armhf (2.28-8) ... Removing libcroco3:amd64 (0.6.12-3) ... Removing libelf1:amd64 (0.176-1) ... Removing libglib2.0-0:amd64 (2.58.3-1) ... Removing libncurses6:amd64 (6.1+20181013-2) ... Removing libpipeline1:amd64 (1.5.1-2) ... Removing libuchardet0:amd64 (0.0.6-3) ... Removing dh-autoreconf (19) ... Removing automake (1:1.16.1-4) ... Removing autoconf (2.69-11) ... Removing autopoint (0.19.8.1-9) ... Removing libtool (2.4.6-10) ... Removing autotools-dev (20180224.1) ... Removing m4 (1.4.18-2) ... Removing libsigsegv2:amd64 (2.12-2) ... Processing triggers for ccache (3.6-1) ... Updating symlinks in /usr/lib/ccache ... Processing triggers for libc-bin (2.28-8) ... (Reading database ... 16459 files and directories currently installed.) Purging configuration files for libglib2.0-0:amd64 (2.58.3-1) ... Purging configuration files for lintian (2.9.1) ... Purging configuration files for man-db (2.8.5-2) ... Purging configuration files for bsdmainutils (11.1.2+b1) ... Purging configuration files for autoconf (2.69-11) ... Purging configuration files for libc6:armhf (2.28-8) ... Purging configuration files for groff-base (1.22.4-3) ... +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 28 Distribution: unstable-amd64-sbuild Foreign Architectures: armhf Host Architecture: armhf Install-Time: 7 Job: /home/build/sbuild-setup/repo/pool/main/t/t-coffee/t-coffee_12.00.7fb08c2-4.dsc Lintian: pass Machine Architecture: amd64 Package: t-coffee Package-Time: 39 Source-Version: 12.00.7fb08c2-4 Space: n/a Status: successful Version: 12.00.7fb08c2-4 -------------------------------------------------------------------------------- Finished at 2019-03-07T04:44:55Z Build needed 00:00:39, no disk space