Diff of the two buildlogs: -- --- b1/build.log 2019-06-22 03:37:23.009924153 +0000 +++ b2/build.log 2019-06-22 03:48:45.118364721 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 23 21:59:49 -12 2020 -I: pbuilder-time-stamp: 1595584789 +I: Current time: Sat Jun 22 17:37:31 +14 2019 +I: pbuilder-time-stamp: 1561174651 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 14 18:47:23 2019 -12 +gpgv: Signature made Fri Feb 15 20:47:23 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -38,6 +38,18 @@ dpkg-source: info: applying fix_tempfile_name_sharing.patch I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/16082/tmp/hooks/D01_modify_environment starting +disorder-fs debug: Running on profitbricks-build12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/16082/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -106,7 +118,7 @@ Get: 31 http://cdn-fastly.deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://cdn-fastly.deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://cdn-fastly.deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] -Fetched 19.3 MB in 1s (28.6 MB/s) +Fetched 19.3 MB in 10s (1876 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19231 files and directories currently installed.) @@ -259,9 +271,41 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 182 kB of additional disk space will be used. +Get:1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libnumber-compare-perl all 0.03-1 [7642 B] +Get:2 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtext-glob-perl all 0.10-1 [8362 B] +Get:3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://cdn-fastly.deb.debian.org/debian buster/main i386 usrmerge all 21 [12.8 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 1s (95.9 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21275 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.10-1_all.deb ... +Unpacking libtext-glob-perl (0.10-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_21_all.deb ... +Unpacking usrmerge (21) ... +Setting up libtext-glob-perl (0.10-1) ... +Setting up libnumber-compare-perl (0.03-1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (21) ... +The system has been successfully converted. +Processing triggers for man-db (2.8.5-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/t-coffee-12.00.7fb08c2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/t-coffee-12.00.7fb08c2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 12.00.7fb08c2-4 dpkg-buildpackage: info: source distribution unstable @@ -288,7 +332,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/t-coffee-12.00.7fb08c2' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-12.00.7fb08c2=. -fstack-protector-strong" 'CC=$(CXX)' all - cd t_coffee_source && make -j18 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-12.00.7fb08c2=. -fstack-protector-strong" CC=\$\(CXX\) all + cd t_coffee_source && make -j10 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-12.00.7fb08c2=. -fstack-protector-strong" CC=\$\(CXX\) all make[2]: Entering directory '/build/t-coffee-12.00.7fb08c2/t_coffee_source' CC dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c @@ -300,18 +344,10 @@ CC dp_lib/pavie_dp.c CC dp_lib/showpair.c CC dp_lib/util_domain_dp.c - CC dp_lib/util_domain_dp_drivers.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 - CC dp_lib/util_dp_fasta_sw.c - CC dp_lib/util_dp_generic_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/CUSTOM_evaluate_for_struc.c:33: + 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" ^ @@ -348,31 +384,31 @@ ./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 ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/showpair.c:32: + 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: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:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ +./programmes_define.h:384: warning: "x3dna" redefined + #define x3dna-ssr_update_action "never" + ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" +./programmes_define.h:383: note: this is the location of the previous definition + #define x3dna-ssr_mode "saracoffee" + ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" @@ -415,7 +451,7 @@ 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: + 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" ^ @@ -467,7 +503,7 @@ 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: + 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" ^ @@ -501,197 +537,80 @@ ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ -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: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:380:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ^ ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ -./programmes_define.h:380: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ./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" -./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" - ^ -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" - ^ 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: + 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: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:380:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ^ ./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:384:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_update_action "never" - ^ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" -./programmes_define.h:384: warning: "x3dna" redefined - #define x3dna-ssr_update_action "never" - -./programmes_define.h:380: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:383: note: this is the location of the previous definition - #define x3dna-ssr_mode "saracoffee" - ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" -./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:381:14: 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: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: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:382:14: 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: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: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:383:14: 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: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: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:384:14: 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: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" - ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" 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" - ^ -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: + 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: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ @@ -704,72 +623,33 @@ ./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:379: note: this is the location of the previous definition - #define x3dna-ssr_4_TCOFFEE "x3dna" - ./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: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: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:380: note: this is the location of the previous definition - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ./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: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:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" -./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:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ -./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: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" -./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name - #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:383: warning: "x3dna" redefined - #define x3dna-ssr_mode "saracoffee" - -./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_update_action "never" - ^ ./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: warning: "x3dna" redefined - #define x3dna-ssr_update_action "never" - ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ -./programmes_define.h:383: note: this is the location of the previous definition - #define x3dna-ssr_mode "saracoffee" - ./programmes_define.h:384: warning: "x3dna" redefined #define x3dna-ssr_update_action "never" @@ -779,111 +659,59 @@ 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" - ^ -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: + 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:380:14: 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: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: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:381:14: 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: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: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:382:14: 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: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: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:383:14: 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: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: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:384:14: 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: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" - ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" 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: + 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" ^ @@ -935,7 +763,7 @@ 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: + 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" ^ @@ -987,7 +815,7 @@ 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: + 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" ^ @@ -1036,10 +864,100 @@ ./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 ./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 + ^~~~~~~ +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 + ^~~~~~~ +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 + ^~~~~~~ +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 + ^~~~~~~ +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 + ^~~~~~~ +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 + ^~~~~~~ +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 + ^~~~~~~ +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 + ^~~~~~~ +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 + ^~~~~~~ +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"); + ~~~~~~^~~~~~~~~~ +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); + ^~~~~~~~~~~~~~~~~~~~~ +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/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=] + CC dp_lib/util_domain_dp_drivers.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_generic_fasta_nw.c:34: + 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" ^ @@ -1049,9 +967,19 @@ ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" +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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" +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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ @@ -1088,6 +1016,38 @@ ./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 + ^~~~~~~ +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 ); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/include/stdio.h:873, + from dp_lib/pavie_dp.c:27: +/usr/include/i386-linux-gnu/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/include/stdio.h:873, + from dp_lib/pavie_dp.c:27: +/usr/include/i386-linux-gnu/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 dp_lib/util_dp_cdna_fasta_nw.c + CC dp_lib/util_dp_clean_maln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -1143,7 +1103,7 @@ 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: + 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" ^ @@ -1192,10 +1152,21 @@ ./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 + ^~~~~~~ +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 dp_lib/util_dp_drivers.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/pavie_dp.c:33: + 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" ^ @@ -1244,141 +1215,12 @@ ./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 - ^~~~~~~ -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 - ^~~~~~~ -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 - ^~~~~~~ -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 - ^~~~~~~ -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 - ^~~~~~~ -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 ./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 - ^~~~~~~ -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 - ^~~~~~~ -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 - ^~~~~~~ -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 - ^~~~~~~ -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 ./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 - ^~~~~~~ -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 - ^~~~~~~ -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 - ^~~~~~~ -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 - ^~~~~~~ -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 - ^~~~~~~ -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 - ^~~~~~~ -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); - ^~~~~~~~~~~~~~~~~~~~~ -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 - ^~~~~~~ -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 dp_lib/util_dp_gotoh_nw.c -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/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=] - CC dp_lib/util_dp_gotoh_sw.c -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); - ~~~~~~~^~~~~~~~~~~~~~~ + 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_gotoh_nw.c:34: + 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" ^ @@ -1427,11 +1269,15 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC dp_lib/util_dp_mm_nw.c +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_drivers.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 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_gotoh_sw.c:33: + 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" ^ @@ -1480,6 +1326,16 @@ ./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 + ^~~~~~~ +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 + ^~~~~~~ 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); @@ -1555,30 +1411,68 @@ 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); ~~~~~~^~~~~~ - CC dp_lib/util_dp_sim.c 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/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); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 dp_lib/util_dp_fasta_sw.c + CC dp_lib/util_dp_generic_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_mm_nw.c:33: + 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 ./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" ^ @@ -1627,21 +1521,21 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" + CC dp_lib/util_dp_gotoh_nw.c In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_sw.c: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 ./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 dp_lib/util_dp_ssec_pwaln.c - CC dp_lib/util_dp_suboptimal_nw.c -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 dp_lib/util_dp_ssec_pwaln.c:33: + 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" ^ @@ -1691,14 +1585,16 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_mm_nw.c: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 dp_lib/util_dp_gotoh_sw.c + CC dp_lib/util_dp_mm_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_sim.c:32: + 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" ^ @@ -1750,7 +1646,7 @@ 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: + 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" ^ @@ -1799,46 +1695,67 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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 ./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 + ^~~~~~~ +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 + ^~~~~~~ +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); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/include/stdio.h:873, - from dp_lib/pavie_dp.c:27: -/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 1004) into a destination of size 1000 + from dp_lib/util_dp_drivers.c:27: +/usr/include/i386-linux-gnu/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/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); - ^~~~~~~~~~ ~~~~~~ +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/include/stdio.h:873, - from dp_lib/pavie_dp.c:27: -/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 2003 bytes into a destination of size 1000 + from dp_lib/util_dp_drivers.c:27: +/usr/include/i386-linux-gnu/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_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 dp_lib/util_graph_maln.c -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_ssec_pwaln.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ -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 - ^~~~~~~ +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/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/i386-linux-gnu/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/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/i386-linux-gnu/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 ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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_graph_maln.c:33: + 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" ^ @@ -1892,17 +1809,70 @@ ./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_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_graph_maln.c: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 fastal/diagonal.c - CC fastal/fastal.c + 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 fastal/diagonal.c:31: + 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" ^ @@ -1951,11 +1921,84 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - 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 fastal/fastal.c:34: + 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_graph_maln.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 '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/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/i386-linux-gnu/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 ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + ^~~~~~~ + CC fastal/diagonal.c +In file included from ./define_header.h:31, + from ./io_lib/io_structures.h:33, + from ./io_lib_header.h:30, + from fastal/diagonal.c:31: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -2009,7 +2052,6 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC fastal/iteration.c 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); @@ -2023,15 +2065,11 @@ 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); ~~~~~^~~~~~~~~~~~~~~~~~~ -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 - ^~~~~~~ + CC fastal/fastal.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from fastal/iteration.c:34: + 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" ^ @@ -2080,12 +2118,12 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC fastal/parttree.c In file included from ./io_lib_header.h:33, - from fastal/iteration.c:34: + from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ + CC fastal/fastal_opt_parsing.c 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); @@ -2162,46 +2200,11 @@ 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); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 fastal/scoring.c - CC fastal/tree.c + CC fastal/iteration.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from fastal/parttree.c:36: + 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" ^ @@ -2250,10 +2253,50 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" + CC fastal/parttree.c +In file included from ./io_lib_header.h:33, + from fastal/iteration.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 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); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: + 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" ^ @@ -2302,13 +2345,47 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC io_lib/io_func.c In file included from ./io_lib_header.h:33, from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC io_lib/pb_util_read_seq_util.c +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 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, @@ -2361,15 +2438,10 @@ ./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 - ^~~~~~~ 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: + 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" ^ @@ -2418,75 +2490,16 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/i386-linux-gnu/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/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/i386-linux-gnu/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/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/i386-linux-gnu/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 ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + ^~~~~~~ + CC io_lib/io_func.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from io_lib/pb_util_read_seq_util.c:34: + 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" ^ @@ -2535,21 +2548,55 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +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); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from fastal/scoring.c:37: + from fastal/tree.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 ./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 ^~~~~~~ - CC io_lib/pb_util_read_sequence.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from io_lib/pb_util_read_sequence.c:35: + 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" ^ @@ -2603,41 +2650,22 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC io_lib/tree_util.c -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); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -2650,23 +2678,22 @@ 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); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -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/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] - } - ^ +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/include/stdio.h:873, + from fastal/scoring.c:28: +/usr/include/i386-linux-gnu/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 io_lib/pb_util_read_sequence.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from io_lib/tree_util.c:33: + 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" ^ @@ -2715,14 +2742,11 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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]); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 */ @@ -2753,24 +2777,65 @@ io_lib/pb_util_read_sequence.c:280:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE+1,fin); ~~~~~^~~~~~~~~~~~~~~~~~~~ -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/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/i386-linux-gnu/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 ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC io_lib/tree_util.c + 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 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 ^~~~~~~ - CC km_coffee/Stack.c - CC km_coffee/Vector.c 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); @@ -2783,7 +2848,6 @@ io_lib/tree_util.c:2317:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ - CC km_coffee/classes.c 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] } @@ -2808,18 +2872,6 @@ io_lib/tree_util.c:7103:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ -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/include/stdio.h:873, - from fastal/scoring.c:28: -/usr/include/i386-linux-gnu/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/km_coffee.c 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) @@ -2834,6 +2886,20 @@ 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); + ~~~~~~^~~~~~~~~~~~~~~~~~~~ + CC km_coffee/Vector.c +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] + } + ^ + CC km_coffee/classes.c + CC km_coffee/km_coffee.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2886,24 +2952,11 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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); - ~~~~~~^~~~~~~~~~~~~~~~~~~~ - CC km_coffee/km_util.c -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 ./io_lib_header.h:33, from km_coffee/km_coffee.c:43: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ - CC km_coffee/kmeans.c km_coffee/km_coffee.c: In function 'void traverse_km_tree(KM_node*, int*, const SeqSet*, char*, int, int, int, char*)': km_coffee/km_coffee.c:148:22: 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); @@ -2938,6 +2991,7 @@ 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 km_coffee/km_util.c km_coffee/km_util.c: In function 'void* my_malloc(size_t)': km_coffee/km_util.c:49:19: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); @@ -2954,8 +3008,19 @@ km_coffee/km_util.c:96:19: warning: format '%s' expects a matching 'char*' argument [-Wformat=] fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/i386-linux-gnu/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 ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC km_coffee/kmeans.c CC t_coffee_lib/t_coffee.c - CC util_lib/aln_compare.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -3008,7 +3073,20 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC util_lib/aln_convertion_util.c + CC util_lib/aln_compare.c +In file included from ./io_lib_header.h:33, + from t_coffee_lib/t_coffee.c:35: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 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);} + ^~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -3061,19 +3139,13 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/i386-linux-gnu/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 ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC util_lib/aln_convertion_util.c +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] + } + ^ In file included from ./io_lib_header.h:33, - from t_coffee_lib/t_coffee.c:35: + from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ @@ -3130,12 +3202,29 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, - from util_lib/aln_compare.c:34: + 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); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/hsearch.c - CC util_lib/random.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -3189,28 +3278,24 @@ #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 - ^~~~~~~ -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);} - ^~~~~~~~~~~~~~~~~~~~ - CC util_lib/reformat.c -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] - } - ^ -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/random.c +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/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/i386-linux-gnu/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 ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC util_lib/reformat.c + CC util_lib/reformat_struc.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -3263,34 +3348,106 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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] - } - ^ +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.c:35: ./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* 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); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] } ^ - CC util_lib/reformat_struc.c +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/include/stdio.h:873, + from t_coffee_lib/t_coffee.c:27: +/usr/include/i386-linux-gnu/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 ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) @@ -3313,14 +3470,12 @@ util_lib/reformat.c:11563:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^~~~~~~~~~~ - CC util_lib/util.c 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)); ^~~~~~~~~~~ - CC util_lib/util_aln_analyze.c 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) ^ @@ -3423,58 +3578,6 @@ 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)); ^~~~~~~~~~~ -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" - util_lib/reformat.c:12901:36: warning: null argument where non-null required (argument 1) [-Wnonnull] else if (strstr (ACTION(1), "h")) ^ @@ -3544,58 +3647,6 @@ util_lib/reformat.c:13088:34: note: in expansion of macro 'ATOI_ACTION' D1->A=trim_RNA(D1->A, D2->S, ATOI_ACTION(1)); ^~~~~~~~~~~ -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" - 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) ^ @@ -3626,58 +3677,6 @@ util_lib/reformat.c:13620:8: note: in expansion of macro 'ATOI_ACTION' p3=ATOI_ACTION(5); ^~~~~~~~~~~ -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" - 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] } @@ -3694,11 +3693,6 @@ util_lib/reformat.c:1402:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ -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.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"); @@ -3749,11 +3743,6 @@ util_lib/reformat.c:2486:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ -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/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); @@ -3798,15 +3787,6 @@ 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); ~~~~~~~^~~~~~~~~~~~~~~ -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/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.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); @@ -3830,38 +3810,39 @@ 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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/util_analyse_constraints_list.c -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/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); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/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); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC util_lib/util.c + CC util_lib/util_aln_analyze.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from util_lib/util_analyse_constraints_list.c:33: + 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" ^ @@ -3910,46 +3891,80 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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_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.c:52: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +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.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_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/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/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/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); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - ^~~~~~~ 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] } @@ -3958,8 +3973,10 @@ util_lib/util.c:6920:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ - CC util_lib/util_constraints_list.c - CC util_lib/util_declare.c +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] + } + ^ 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]*/ @@ -4001,10 +4018,62 @@ 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"); ~~~~~~~^~~~~~~~~~ + CC util_lib/util_analyse_constraints_list.c +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] + } + ^ 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: + 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" ^ @@ -4053,58 +4122,65 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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); - ~~~~~~~^~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/util_constraints_list.c:37: + 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_constraints_list.c + CC util_lib/util_declare.c +In file included from ./define_header.h:31, + from ./io_lib/io_structures.h:33, + from ./io_lib_header.h:30, + from util_lib/util_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 ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -4157,10 +4233,16 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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] - } - ^ +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 + ^~~~~~~ +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 + ^~~~~~~ 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] } @@ -4173,12 +4255,6 @@ 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); ^~~~~~~~~~~~~~~~~~~ -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 - ^~~~~~~ - CC util_lib/util_domain_constraints_list.c 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); @@ -4198,17 +4274,6 @@ 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); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -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/include/stdio.h:873, - from t_coffee_lib/t_coffee.c:27: -/usr/include/i386-linux-gnu/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 ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -4226,6 +4291,7 @@ 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]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC util_lib/util_domain_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -4283,9 +4349,18 @@ ./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 '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/include/stdio.h:873, + from util_lib/util_constraints_list.c:29: +/usr/include/i386-linux-gnu/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 ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_dps.c - CC util_lib/util_job_handling.c - 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, @@ -4338,6 +4413,12 @@ ./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 + ^~~~~~~ + 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, @@ -4390,6 +4471,12 @@ ./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 + ^~~~~~~ + 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, @@ -4443,16 +4530,6 @@ #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 ./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 ./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 @@ -4559,39 +4636,6 @@ 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); ~~~~~~~~~^~~~~~ -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/include/stdio.h:873, - from util_lib/util_constraints_list.c:29: -/usr/include/i386-linux-gnu/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 ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/i386-linux-gnu/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/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/i386-linux-gnu/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.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()); @@ -4770,8 +4814,8 @@ dh_gencontrol -O--sourcedirectory=t_coffee_source dh_md5sums -O--sourcedirectory=t_coffee_source dh_builddeb -O--sourcedirectory=t_coffee_source -dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_12.00.7fb08c2-4_i386.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_12.00.7fb08c2-4_i386.deb'. +dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_12.00.7fb08c2-4_i386.deb'. dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_12.00.7fb08c2-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../t-coffee_12.00.7fb08c2-4_i386.changes @@ -4779,12 +4823,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/16082/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/16082/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/55354 and its subdirectories -I: Current time: Thu Jul 23 22:00:23 -12 2020 -I: pbuilder-time-stamp: 1595584823 +I: removing directory /srv/workspace/pbuilder/16082 and its subdirectories +I: Current time: Sat Jun 22 17:48:44 +14 2019 +I: pbuilder-time-stamp: 1561175324