Sun Mar 2 21:22:40 UTC 2025 I: starting to build paml/trixie/i386 on jenkins on '2025-03-02 21:22' Sun Mar 2 21:22:40 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_10/45551/console.log Sun Mar 2 21:22:40 UTC 2025 I: Downloading source for trixie/paml=4.9j+dfsg-6 --2025-03-02 21:22:41-- http://deb.debian.org/debian/pool/main/p/paml/paml_4.9j%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2244 (2.2K) [text/prs.lines.tag] Saving to: ‘paml_4.9j+dfsg-6.dsc’ 0K .. 100% 351M=0s 2025-03-02 21:22:41 (351 MB/s) - ‘paml_4.9j+dfsg-6.dsc’ saved [2244/2244] Sun Mar 2 21:22:41 UTC 2025 I: paml_4.9j+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: paml Binary: paml, paml-doc Architecture: any all Version: 4.9j+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Pjotr Prins , Steffen Moeller , Andreas Tille , Étienne Mollier Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html Standards-Version: 4.7.1 Vcs-Browser: https://salsa.debian.org/med-team/paml Vcs-Git: https://salsa.debian.org/med-team/paml.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: paml deb science optional arch=any paml-doc deb doc optional arch=all Checksums-Sha1: d40ca19fbd5a49c232a1bd1b863f0d5d69e21bc3 1375380 paml_4.9j+dfsg.orig.tar.xz ac943f52aa802f01708127c61315e578804544ec 8604 paml_4.9j+dfsg-6.debian.tar.xz Checksums-Sha256: af7ccf450cb26b6b235559f3e6e70241ac59ed87caacf57bd91d6cdfaf81b9b8 1375380 paml_4.9j+dfsg.orig.tar.xz ead9a11fa45e1b82590f3d9b61ec1649b8343aad8e99ec2eda8fe114bd66e9b1 8604 paml_4.9j+dfsg-6.debian.tar.xz Files: 1300f92065c7d3249a649caf2dad9417 1375380 paml_4.9j+dfsg.orig.tar.xz 28111169858649c8882ba71e1f6fd096 8604 paml_4.9j+dfsg-6.debian.tar.xz Dgit: 36613899524e0669e9efde127e45105c3fad2111 debian archive/debian/4.9j+dfsg-6 https://git.dgit.debian.org/paml -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAme/kKkUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqSaQ/+I0TWo48QioL8UpyPrmV6IZKuRt3j D32PtqKMit3F1TEENfT2u63b6mwimy7uM1aMrvnt6Tx7+mj+FOWzNIXw2blpahPm d78NW40swPwguMoVhISZyRKCHIL1N1aVDP2sjf8mjLd/ClXA73YSzNiDsSYltM6Q ZOwXPbygoK/u14KCXqIZVDc4UwVUW90sQp7PzAV9lYsDLjBRkNfeyLvYXcZqj0Hi VD3Mhz7zXJzkE4jNcypf42HwxPyQiAdqTGxigHMn6jab04RogDOfDO6j6Sjj1q2m qhx1gq6hTH2fi/hQkm3klWHT9dxvGE0O+gNZEHsbSMDLp5z+8xe/B/CtOPbQn10J 8QnWzLJF0ti6Bj5YwP5iaSxCoXmXBHSOPiDFXV8/X+hDE9icJ3EUoESabYHxKKTk FAccZUIKQRHXl9V0GkfrQJeSVhtfqXAdacCnYKcvj2CXov81TcPGbznrFL/ZHqKB ZM48fAXbMmmiIOThkEwTFVdhdwETDS2EQPEJYL+KWtVDwDjSs2XvYCSeSwxUXE8I iYIWWnu+t7TNmmlr2gAds1EIU6mRwF1E3PvshGpebWJmoKQJWvFNVe2wtBMEmbZf ExeiQboPlbrBsbqwI25SzbxW4eOKWk+A88B+TvU7P7Boz7Bp/obNAvjEsAiPFSw2 rXSfH6/CH4yW4Lw= =QfCJ -----END PGP SIGNATURE----- Sun Mar 2 21:22:41 UTC 2025 I: Checking whether the package is not for us Sun Mar 2 21:22:41 UTC 2025 I: Starting 1st build on remote node ionos16-i386.debian.net. Sun Mar 2 21:22:41 UTC 2025 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Sun Mar 2 21:23:51 UTC 2025 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 4 15:45:41 -12 2026 I: pbuilder-time-stamp: 1775360741 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [paml_4.9j+dfsg-6.dsc] I: copying [./paml_4.9j+dfsg.orig.tar.xz] I: copying [./paml_4.9j+dfsg-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./paml_4.9j+dfsg-6.dsc: unsupported subcommand dpkg-source: info: extracting paml in paml-4.9j+dfsg dpkg-source: info: unpacking paml_4.9j+dfsg.orig.tar.xz dpkg-source: info: unpacking paml_4.9j+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc10.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying add_clean_target.patch dpkg-source: info: applying gcc14.patch dpkg-source: info: applying c23.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/87748/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='5c9593cb78f44b77af1eff9fc8e91819' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='87748' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.5AHyCGzK/pbuilderrc_V7pu --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5AHyCGzK/b1 --logfile b1/build.log paml_4.9j+dfsg-6.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos16-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/87748/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19789 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.8 MB of archives. After unpacking 78.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB] Fetched 20.8 MB in 0s (57.1 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19789 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_i386.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_i386.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-5_i386.deb ... Unpacking bsdextrautils (2.40.4-5) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_i386.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../21-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:i386. Preparing to unpack .../23-libunistring5_1.3-1_i386.deb ... Unpacking libunistring5:i386 (1.3-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-6_i386.deb ... Unpacking libicu72:i386 (72.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_i386.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up libicu72:i386 (72.1-6) ... Setting up bsdextrautils (2.40.4-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:i386 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/paml-4.9j+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../paml_4.9j+dfsg-6_source.changes dpkg-buildpackage: info: source package paml dpkg-buildpackage: info: source version 4.9j+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg' dh_auto_clean cd src && make -j22 clean make[2]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg/src' rm -f baseml codeml basemlg mcmctree pamp evolver yn00 chi2 infinitesites make[2]: Leaving directory '/build/reproducible-path/paml-4.9j+dfsg/src' rm -f src/baseml src/basemlg src/chi2 src/codeml src/evolver src/infinitesites src/mcmctree src/pamp src/yn00 make[1]: Leaving directory '/build/reproducible-path/paml-4.9j+dfsg' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src cd src && make -j22 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg/src' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o baseml baseml.c tools.c -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o codeml codeml.c tools.c -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o basemlg basemlg.c tools.c -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o mcmctree mcmctree.c tools.c -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o pamp pamp.c tools.c -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o evolver evolver.c tools.c -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o yn00 yn00.c tools.c -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o chi2 chi2.c -Wl,-z,relro -Wl,-z,now -lm chi2.c: In function 'main': chi2.c:54:10: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | scanf ("%d%lf", &df, &chi2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from yn00.c:70: treesub.c: In function 'ReadSeq': treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from basemlg.c:82: treesub.c: In function 'ReadSeq': treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from pamp.c:66: treesub.c: In function 'ReadSeq': treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeB': treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeN': treesub.c:3091:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'readx': treesub.c:3956:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3956 | fscanf(finitials, "%lf", &xin[i = 0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeB': treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeN': treesub.c:3091:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pamp.c: In function 'main': pamp.c:115:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mcmctree.c:192: treesub.c: In function 'ReadMorphology': treesub.c:447:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 447 | fscanf(fin, "%s", com.spname[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:450:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 450 | fscanf(fin, "%lf", &data.zmorph[locus][i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadSeq': treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeB': treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeN': treesub.c:3091:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeSeqs': treesub.c:8742:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function 'ReadBlengthGH': mcmctree.c:840:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 840 | fscanf(fBGH, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:861:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 861 | fscanf(fBGH, "%lf", &data.blMLE[locus][i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:868:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 868 | fscanf(fBGH, "%lf", &data.Gradient[locus][i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:870:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 870 | fscanf(fBGH, "%s", line); | ^~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function 'GenerateBlengthGH': mcmctree.c:1028:7: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1028 | system(line); | ^~~~~~~~~~~~ mcmctree.c: In function 'Infinitesites': mcmctree.c:1385:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1385 | fscanf(fin, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~ mcmctree.c:1396:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1396 | fscanf(fin, "%lf", &FixedDs[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from evolver.c:67: treesub.c: In function 'ReadTreeB': treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeN': treesub.c:3091:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'GetNSfromTreeFile': treesub.c:4159:16: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4159 | fscanf(ftree, "%lf", &y); | ^~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function 'DescriptiveStatisticsSimpleMCMCTREE': mcmctree.c:3824:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3824 | fscanf(fin, "%lf", &dat[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'CladeSupport': treesub.c:4369:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4369 | fscanf(fM, "%d%d", &i, &ntreeM); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:4397:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4397 | fgets(line, lline, ft); | ^~~~~~~~~~~~~~~~~~~~~~ treesub.c:4419:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4419 | fscanf(fM, "%d%d", &s, &ntreeM); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from codeml.c:238: treesub.c: In function 'ReadSeq': treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function 'main': evolver.c:156:10: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 156 | scanf("%d", &option); | ^~~~~~~~~~~~~~~~~~~~ evolver.c:162:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 162 | scanf("%d", &com.ns); | ^~~~~~~~~~~~~~~~~~~~ evolver.c:169:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 169 | scanf("%d%d", &ntree, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:172:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 172 | scanf("%d", &BD); | ^~~~~~~~~~~~~~~~ evolver.c:192:16: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 192 | scanf("%lf%lf%lf%lf", &birth, &death, &sample, &mut); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:214:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 214 | scanf("%s%s", treefile, mastertreefile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function 'between_f_and_x': evolver.c:244:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 244 | scanf("%d", &fromf); | ^~~~~~~~~~~~~~~~~~~ evolver.c:246:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 246 | scanf("%d", &n); if (n > 100) error2("too many classes"); | ^~~~~~~~~~~~~~~ evolver.c:248:21: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 248 | FOR(i, n - 1) scanf("%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~ evolver.c: In function 'LabelClades': evolver.c:270:4: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 270 | scanf("%s", treef); | ^~~~~~~~~~~~~~~~~~ evolver.c:272:4: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 272 | scanf("%d", &unrooted); | ^~~~~~~~~~~~~~~~~~~~~~ evolver.c:275:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 275 | fscanf(ftree, "%d%d", &com.ns, &j); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:292:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | scanf("%s", key); | ^~~~~~~~~~~~~~~~ In file included from baseml.c:131: treesub.c: In function 'ReadSeq': evolver.c: In function 'TreeDistanceDistribution': evolver.c:391:4: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 391 | scanf("%s", treef); | ^~~~~~~~~~~~~~~~~~ evolver.c:394:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 394 | fscanf(ftree, "%d%d", &com.ns, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function 'TreeDistances': evolver.c:447:4: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 447 | scanf("%s", treef); | ^~~~~~~~~~~~~~~~~~ evolver.c:450:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 450 | fscanf(ftree, "%d%d", &com.ns, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:459:4: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 459 | scanf("%d", &k); | ^~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeB': treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeN': treesub.c:3091:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function 'GetDaa': evolver.c:639:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 639 | fscanf(fdaa, "%lf", &daa[i*n + j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function 'Simulate': evolver.c:810:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | fscanf(fin, "%d", &format); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:811:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 811 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:815:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 815 | fscanf(fin, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~ evolver.c:816:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 816 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:818:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 818 | fscanf(fin, "%d%d%d", &com.ns, &com.ls, &nr); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:819:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 819 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:831:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 831 | fscanf(fin, "%lf", &tlength); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:831:39: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 831 | fscanf(fin, "%lf", &tlength); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:855:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 855 | fscanf(fin, "%lf%lf%lf%lf", &birth, &death, &sample, &mut); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:856:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 856 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:861:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 861 | fscanf(fin, "%d", &com.model); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:862:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 862 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:869:21: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 869 | FOR(i, nrate) fscanf(fin, "%lf", &Qrates[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:870:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 870 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:883:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 883 | fscanf(fin, "%d", &com.ncatG); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:883:43: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 883 | fscanf(fin, "%d", &com.ncatG); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:885:28: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 885 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.freqK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:885:64: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 885 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.freqK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:886:28: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 886 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.rK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:886:64: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 886 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.rK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:892:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 892 | fscanf(fin, "%d", &com.ncatG); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:892:43: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 892 | fscanf(fin, "%d", &com.ncatG); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:894:28: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 894 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.freqK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:894:64: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 894 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.freqK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:925:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 925 | fscanf(fin, "%lf", &com.omega); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:926:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 926 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:932:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 932 | fscanf(fin, "%lf", &com.kappa); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:932:41: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 932 | fscanf(fin, "%lf", &com.kappa); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:937:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 937 | fscanf(fin, "%lf%d", &com.alpha, &com.ncatG); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:938:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 938 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:954:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 954 | fscanf(fin, "%d", &com.model); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:956:29: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 956 | if (com.model >= 2) { fscanf(fin, "%s", com.daafile); GetDaa(NULL, com.daa); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:957:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 957 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:964:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 964 | for (k = 0; k < com.ncode; k++) fscanf(fin, "%lf", &com.pi[k]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:971:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 971 | fscanf(fin, "%d", &com.icode); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:971:40: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 971 | fscanf(fin, "%d", &com.icode); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'readx': treesub.c:3956:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3956 | fscanf(finitials, "%lf", &xin[i = 0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'Perturbation': treesub.c:4565:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4565 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'StarDecomposition': treesub.c:4867:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4867 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function 'CladeMrBayesProbabilities': evolver.c:1269:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1269 | fscanf(ftree, "%d%d", &i, &k); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeB': treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'rell': treesub.c:5728:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5728 | fscanf(flnf, "%d%d%d", &ntree0, &ls0, &npatt0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:5752:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5752 | fscanf(flnf, "%d", &j); | ^~~~~~~~~~~~~~~~~~~~~~ treesub.c:5758:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5758 | fscanf(flnf, "%d%d%lf", &j, &k, &y); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:5763:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5763 | fgets(line, lline, flnf); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeN': treesub.c:3091:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'readx': treesub.c:3956:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3956 | fscanf(finitials, "%lf", &xin[i = 0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'Perturbation': treesub.c:4565:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4565 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'StarDecomposition': treesub.c:4867:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4867 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeSeqs': treesub.c:8742:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'rell': treesub.c:5728:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5728 | fscanf(flnf, "%d%d%d", &ntree0, &ls0, &npatt0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:5752:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5752 | fscanf(flnf, "%d", &j); | ^~~~~~~~~~~~~~~~~~~~~~ treesub.c:5758:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5758 | fscanf(flnf, "%d%d%lf", &j, &k, &y); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:5763:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5763 | fgets(line, lline, flnf); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'AdHocRateSmoothing': treesub.c:9574:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9574 | fscanf(finStep1, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9672:36: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9672 | for (i = 0; i < com.np; i++) fscanf(finStep2, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9765:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9765 | scanf("%lf", &Rj[j]); | ^~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'DatingHeteroData': treesub.c:9884:10: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9884 | scanf("%lf%d? ", &nu_AHRS, &nbrate); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeSeqs': treesub.c:8742:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codeml.c: In function 'GetDaa': codeml.c:3911:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3911 | fscanf(fdaa, "%lf", &daa[i*naa + j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codeml.c: In function 'GetOmegaAA': codeml.c:4036:16: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4036 | if (fin) fscanf(fin, "%d", &com.nOmegaType); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codeml.c:4052:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4052 | fscanf(fin, "%d", &j); | ^~~~~~~~~~~~~~~~~~~~~ codeml.c:4056:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4056 | fgets(line, nline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ codeml.c: In function 'PairwiseCodon': codeml.c:4318:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4318 | scanf("%d%d", &is, &js); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'AdHocRateSmoothing': treesub.c:9574:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9574 | fscanf(finStep1, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9672:36: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9672 | for (i = 0; i < com.np; i++) fscanf(finStep2, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9765:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9765 | scanf("%lf", &Rj[j]); | ^~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'DatingHeteroData': treesub.c:9884:10: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9884 | scanf("%lf%d? ", &nu_AHRS, &nbrate); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codeml.c: In function 'lfunNSsites_rate': codeml.c:5238:10: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5238 | scanf("%d", &continuous); | ^~~~~~~~~~~~~~~~~~~~~~~~ codeml.c:5251:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5251 | fscanf(fsites, "%d%s", &it, sitelabel); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'scanfile': tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'DescriptiveStatistics': tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'scanfile': tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'DescriptiveStatistics': tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'scanfile': tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'DescriptiveStatistics': tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'scanfile': tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'DescriptiveStatistics': tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:3861:54: warning: '%.6g' directive writing between 1 and 13 bytes into a region of size between 7 and 19 [-Wformat-overflow=] 3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]); | ^~~~ mcmctree.c:3861:36: note: assuming directive output of 12 bytes 3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from paml.h:7, from mcmctree.c:22: In function 'sprintf', inlined from 'DescriptiveStatisticsSimpleMCMCTREE' at mcmctree.c:3861:7: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 17 and 41 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'scanfile': tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'DescriptiveStatistics': tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'scanfile': tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'DescriptiveStatistics': tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o infinitesites -D INFINITESITES mcmctree.c tools.c -Wl,-z,relro -Wl,-z,now -lm In file included from mcmctree.c:192: treesub.c: In function 'ReadMorphology': treesub.c:447:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 447 | fscanf(fin, "%s", com.spname[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:450:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 450 | fscanf(fin, "%lf", &data.zmorph[locus][i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadSeq': treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeB': treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeN': treesub.c:3091:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeSeqs': treesub.c:8742:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function 'ReadBlengthGH': mcmctree.c:840:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 840 | fscanf(fBGH, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:861:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 861 | fscanf(fBGH, "%lf", &data.blMLE[locus][i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:868:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 868 | fscanf(fBGH, "%lf", &data.Gradient[locus][i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:870:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 870 | fscanf(fBGH, "%s", line); | ^~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function 'GenerateBlengthGH': mcmctree.c:1028:7: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1028 | system(line); | ^~~~~~~~~~~~ mcmctree.c: In function 'Infinitesites': mcmctree.c:1385:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1385 | fscanf(fin, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~ mcmctree.c:1396:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1396 | fscanf(fin, "%lf", &FixedDs[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function 'DescriptiveStatisticsSimpleMCMCTREE': mcmctree.c:3824:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3824 | fscanf(fin, "%lf", &dat[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'scanfile': tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'DescriptiveStatistics': tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:3861:54: warning: '%.6g' directive writing between 1 and 13 bytes into a region of size between 7 and 19 [-Wformat-overflow=] 3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]); | ^~~~ mcmctree.c:3861:36: note: assuming directive output of 12 bytes 3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from paml.h:7, from mcmctree.c:22: In function 'sprintf', inlined from 'DescriptiveStatisticsSimpleMCMCTREE' at mcmctree.c:3861:7: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 17 and 41 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'scanfile': tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'DescriptiveStatistics': tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/paml-4.9j+dfsg/src' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg' dh_install -a for datfile in debian/paml//usr/lib/paml/data/*.ctl ; do \ for item in seqfile treefile ; do \ sed -i -e "s?\(${item} =\).*[^a-z^A-Z^0-9^.^ ]\+\([a-zA-Z0-9]\+\.[a-z]\+\)?\1 /usr/lib/paml/data/\2?" \ -e "s?\(${item} =\) \([a-zA-Z0-9]\+\.[a-z]\+\)?\1 /usr/lib/paml/data/\2?" \ ${datfile} ; \ done ; \ done sed -i 's?\(aaRatefile = \)\(dat/jones.dat\)?\1/usr/lib/paml/data/\2?' debian/paml//usr/lib/paml/data/codeml.ctl make[1]: Leaving directory '/build/reproducible-path/paml-4.9j+dfsg' dh_install -O--sourcedirectory=src -Npaml dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg' dh_installexamples for d in `find debian -name examples -a -type d`; do \ find $d \! -type d | xargs -r chmod -x ; \ done make[1]: Leaving directory '/build/reproducible-path/paml-4.9j+dfsg' dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src debian/rules override_dh_link-arch make[1]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg' dh_link -a mkdir -p debian/paml/etc/paml/ for datfile in debian/paml//usr/lib/paml/data/*.ctl ; do \ ln -s /usr/lib/paml/data/`basename ${datfile}` debian/paml/etc/paml ; \ done make[1]: Leaving directory '/build/reproducible-path/paml-4.9j+dfsg' dh_link -O--sourcedirectory=src -Npaml dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg' dh_fixperms -a find debian/*/usr/lib/paml/data -type f -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/paml-4.9j+dfsg' dh_fixperms -O--sourcedirectory=src -Npaml dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'paml' in '../paml_4.9j+dfsg-6_i386.deb'. dpkg-deb: building package 'paml-dbgsym' in '../paml-dbgsym_4.9j+dfsg-6_i386.deb'. dpkg-deb: building package 'paml-doc' in '../paml-doc_4.9j+dfsg-6_all.deb'. dpkg-genbuildinfo --build=binary -O../paml_4.9j+dfsg-6_i386.buildinfo dpkg-genchanges --build=binary -O../paml_4.9j+dfsg-6_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/87748 and its subdirectories I: Current time: Sat Apr 4 15:46:49 -12 2026 I: pbuilder-time-stamp: 1775360809 Sun Mar 2 21:23:52 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Sun Mar 2 21:23:52 UTC 2025 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Sun Mar 2 21:25:32 UTC 2025 I: Deleting $TMPDIR on ionos2-i386.debian.net. Sun Mar 2 21:25:32 UTC 2025 I: paml_4.9j+dfsg-6_i386.changes: Format: 1.8 Date: Wed, 26 Feb 2025 22:45:25 +0100 Source: paml Binary: paml paml-dbgsym paml-doc Architecture: i386 all Version: 4.9j+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: paml - Phylogenetic Analysis by Maximum Likelihood (PAML) paml-doc - Documentation for PAML Closes: 1097542 Changes: paml (4.9j+dfsg-6) unstable; urgency=medium . * c23.patch: new: fix ftbfs with gcc-15. (Closes: #1097542) * d/control: declare compliance to standards version 4.7.1. Checksums-Sha1: 71eb7cbdebbeb7529ba0fb883e79ef7563b1945a 1943368 paml-dbgsym_4.9j+dfsg-6_i386.deb f8dad268e2c9b1721e99a4325329ea0edab10107 956176 paml-doc_4.9j+dfsg-6_all.deb 719674576751b80ca1ded37019c17a8e8359c848 5074 paml_4.9j+dfsg-6_i386.buildinfo 95c383fa1bfc7f33b57871f8bed7e1c951fa6497 647048 paml_4.9j+dfsg-6_i386.deb Checksums-Sha256: 7adb3ae76813e516096b33f8b98c8454f33d8397cc49e395d18c399154c75041 1943368 paml-dbgsym_4.9j+dfsg-6_i386.deb 42a152fdd7d737064061144c4346102401bcc6115d0f8ad0c0e08da96f470f94 956176 paml-doc_4.9j+dfsg-6_all.deb eceb83610df61132e0a806b677724e175ae902d14d9fc178773075e5c786b5e0 5074 paml_4.9j+dfsg-6_i386.buildinfo d6e83efe94ef190dc8f2767b592fbf6e48dae4fddb25b97b52a88050c1e1c36a 647048 paml_4.9j+dfsg-6_i386.deb Files: de68eae7f8b1a9abed3cf6c8ba4bf21a 1943368 debug optional paml-dbgsym_4.9j+dfsg-6_i386.deb 56ca581342eac70dc14a449fde3f9ada 956176 doc optional paml-doc_4.9j+dfsg-6_all.deb 83149eede0ee9e4e287c24d54e911696 5074 science optional paml_4.9j+dfsg-6_i386.buildinfo d45ed2f7ae3ab9d2c74bf9972cdbae8c 647048 science optional paml_4.9j+dfsg-6_i386.deb Sun Mar 2 21:25:33 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_10-45551.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.5AHyCGzK/paml_4.9j+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.5AHyCGzK/paml_4.9j+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.5AHyCGzK/paml_4.9j+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.5AHyCGzK/b1/paml_4.9j+dfsg-6_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.5AHyCGzK/b2/paml_4.9j+dfsg-6_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 224ms CPU time consumed: 225ms Sun Mar 2 21:25:34 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Sun Mar 2 21:25:34 UTC 2025 I: paml from trixie built successfully and reproducibly on i386. Sun Mar 2 21:25:35 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Mar 2 21:25:35 UTC 2025 I: Submitting 8.0K b1/paml_4.9j+dfsg-6_i386.buildinfo.asc Sun Mar 2 21:25:36 UTC 2025 I: Submitting 8.0K b2/paml_4.9j+dfsg-6_i386.buildinfo.asc Sun Mar 2 21:25:37 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Mar 2 21:25:37 UTC 2025 I: Done submitting .buildinfo files. Sun Mar 2 21:25:37 UTC 2025 I: Removing signed paml_4.9j+dfsg-6_i386.buildinfo.asc files: removed './b1/paml_4.9j+dfsg-6_i386.buildinfo.asc' removed './b2/paml_4.9j+dfsg-6_i386.buildinfo.asc'