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 <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Pjotr Prins <pjotr.debian@thebird.nl>, Steffen Moeller <moeller@debian.org>, Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
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
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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 <pbuilder-maint@lists.alioth.debian.org>
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 ...
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(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) ...
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Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
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Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
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Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ...
Unpacking file (1:5.45-3+b1) ...
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Preparing to unpack .../04-gettext-base_0.23.1-1_i386.deb ...
Unpacking gettext-base (0.23.1-1) ...
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Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
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Preparing to unpack .../06-groff-base_1.23.0-7_i386.deb ...
Unpacking groff-base (1.23.0-7) ...
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Unpacking bsdextrautils (2.40.4-5) ...
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Unpacking libpipeline1:i386 (1.5.8-1) ...
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Unpacking man-db (2.13.0-1) ...
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Unpacking m4 (1.4.19-5) ...
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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) ...
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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) ...
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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 <emollier@debian.org>
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 <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
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'