I: pbuilder: network access will be disabled during build
I: Current time: Fri Apr 21 16:58:18 -12 2023
I: pbuilder-time-stamp: 1682139498
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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: Copying source file
I: copying [clustalw_2.1+lgpl-7.dsc]
I: copying [./clustalw_2.1+lgpl.orig.tar.gz]
I: copying [./clustalw_2.1+lgpl-7.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun Nov 15 20:43:21 2020 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./clustalw_2.1+lgpl-7.dsc: no acceptable signature found
dpkg-source: info: extracting clustalw in clustalw-2.1+lgpl
dpkg-source: info: unpacking clustalw_2.1+lgpl.orig.tar.gz
dpkg-source: info: unpacking clustalw_2.1+lgpl-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying spelling.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/18533/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
DISTRIBUTION='bookworm'
HOME='/var/lib/jenkins'
HOST_ARCH='arm64'
IFS='
'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
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='18533'
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.q4dhrcI9/pbuilderrc_fTcm --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.q4dhrcI9/b1 --logfile b1/build.log clustalw_2.1+lgpl-7.dsc'
SUDO_GID='117'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
USERNAME='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.16:3128'
I: uname -a
Linux codethink12-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Apr 20 22:25 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/18533/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: arm64
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 ... 19616 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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{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 18.3 MB of archives. After unpacking 74.4 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB]
Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB]
Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB]
Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB]
Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB]
Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB]
Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB]
Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB]
Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB]
Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB]
Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB]
Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB]
Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
Fetched 18.3 MB in 0s (45.9 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 19616 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
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Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:arm64.
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Unpacking libmagic1:arm64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ...
Unpacking file (1:5.44-3) ...
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Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.7-1) ...
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Unpacking m4 (1.4.19-3) ...
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Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
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Unpacking autotools-dev (20220109.1) ...
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Unpacking debhelper (13.11.4) ...
Setting up libpipeline1:arm64 (1.5.7-1) ...
Setting up libicu72:arm64 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libmagic1:arm64 (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-12) ...
Setting up autoconf (2.71-3) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:arm64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:arm64 (0.188-2.1) ...
Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-5) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.4) ...
Processing triggers for libc-bin (2.36-9) ...
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/clustalw-2.1+lgpl/ && 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 > ../clustalw_2.1+lgpl-7_source.changes
dpkg-buildpackage: info: source package clustalw
dpkg-buildpackage: info: source version 2.1+lgpl-7
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
configure.ac:40: warning: The macro `AC_CANONICAL_SYSTEM' is obsolete.
configure.ac:40: You should run autoupdate.
./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from...
configure.ac:40: the top level
configure.ac:90: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete.
configure.ac:90: You should run autoupdate.
./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from...
configure.ac:90: the top level
configure.ac:94: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:94: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:94: the top level
configure.ac:111: warning: 'AM_CONFIG_HEADER': this macro is obsolete.
configure.ac:111: You should use the 'AC_CONFIG_HEADERS' macro instead.
./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from...
aclocal.m4:745: AM_CONFIG_HEADER is expanded from...
configure.ac:111: the top level
configure.ac:133: warning: AC_OUTPUT should be used without arguments.
configure.ac:133: You should run autoupdate.
configure.ac:79: installing './compile'
src/Makefile.am:21: warning: source file './pairwise/FullPairwiseAlign.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least one source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However, this
automake: behavior may change in a future Automake major version, with object
automake: files being placed in the same subdirectory as the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
src/Makefile.am:21: warning: source file './pairwise/FastPairwiseAlign.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/MSFFileParser.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/FileReader.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/PIRFileParser.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/RSFFileParser.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/GDEFileParser.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/InFileStream.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/ClustalFileParser.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/PearsonFileParser.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/FileParser.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './fileInput/EMBLFileParser.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/UPGMA/RootedClusterTree.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/UPGMA/UPGMAAlgorithm.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/UPGMA/Node.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/UPGMA/RootedGuideTree.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/UPGMA/RootedTreeOutput.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/Tree.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/ClusterTree.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/TreeInterface.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/UnRootedClusterTree.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/ClusterTreeOutput.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/RandomGenerator.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/NJTree.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './tree/AlignmentSteps.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './interface/InteractiveMenu.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './interface/CommandLineParser.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './substitutionMatrix/SubMatrix.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './multipleAlign/Iteration.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './multipleAlign/MSA.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './multipleAlign/MyersMillerProfileAlign.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './multipleAlign/ProfileStandard.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './multipleAlign/ProfileWithSub.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './multipleAlign/ProfileBase.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './multipleAlign/LowScoreSegProfile.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './general/OutputFile.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './general/UserParameters.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './general/Utility.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './general/InvalidCombination.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './general/DebugLog.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './general/ClustalWResources.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './general/VectorOutOfRange.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './general/SymMatrix.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './general/Stats.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './Help.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './alignment/Alignment.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './alignment/AlignmentOutput.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './alignment/ObjectiveScore.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './alignment/Sequence.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './Clustal.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
src/Makefile.am:21: warning: source file './main.cpp' is in a subdirectory,
src/Makefile.am:21: but option 'subdir-objects' is disabled
dh_auto_configure
./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking target system type... aarch64-unknown-linux-gnu
building for linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make sets $(MAKE)... (cached) yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking for ranlib... ranlib
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for _Bool... no
checking for stdbool.h that conforms to C99... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for GNU libc compatible malloc... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating m4/Makefile
config.status: creating src/Makefile
config.status: creating src/clustalw_version.h
config.status: creating src/config.h
config.status: executing depfiles commands
dh_auto_build
make -j8
make[1]: Entering directory '/build/clustalw-2.1+lgpl'
Making all in m4
make[2]: Entering directory '/build/clustalw-2.1+lgpl/m4'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/build/clustalw-2.1+lgpl/m4'
Making all in src
make[2]: Entering directory '/build/clustalw-2.1+lgpl/src'
make all-recursive
make[3]: Entering directory '/build/clustalw-2.1+lgpl/src'
make[4]: Entering directory '/build/clustalw-2.1+lgpl/src'
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo './'`./fileInput/RSFFileParser.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo './'`./fileInput/GDEFileParser.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo './'`./fileInput/InFileStream.cpp
In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./pairwise/../alignment/Alignment.h:42,
from ./pairwise/PairwiseAlignBase.h:10,
from ./pairwise/FastPairwiseAlign.h:9,
from ./pairwise/FastPairwiseAlign.cpp:10:
./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./fileInput/../alignment/Alignment.h:42,
from ./fileInput/FileReader.h:12,
from ./fileInput/FileReader.cpp:29:
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./fileInput/FileReader.h:11:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)':
./fileInput/FileReader.cpp:155:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
155 | auto_ptr<FileParser> fileParser; // Means we dont need to delete it!
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./pairwise/../alignment/Alignment.h:42,
from ./pairwise/PairwiseAlignBase.h:10,
from ./pairwise/FullPairwiseAlign.h:9,
from ./pairwise/FullPairwiseAlign.cpp:9:
./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./fileInput/FileReader.cpp: At global scope:
./fileInput/FileReader.cpp:426:42: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
426 | void FileReader::checkInfile(int *nseqs, auto_ptr<FileParser>& fileParser)
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo './'`./fileInput/EMBLFileParser.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp
./fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()':
./fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
37 | register int i;
| ^
./fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
38 | register char c;
| ^
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp
In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./tree/UPGMA/../../alignment/Alignment.h:42,
from ./tree/UPGMA/RootedGuideTree.h:17,
from ./tree/UPGMA/UPGMAAlgorithm.h:8,
from ./tree/UPGMA/UPGMAAlgorithm.cpp:4:
./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
23 | auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree,
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./tree/UPGMA/UPGMAAlgorithm.h:10:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
51 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
27 | auto_ptr<AlignmentSteps> UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp
In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./tree/UPGMA/../../alignment/Alignment.h:42,
from ./tree/UPGMA/../ClusterTree.h:20,
from ./tree/UPGMA/RootedClusterTree.h:8,
from ./tree/UPGMA/RootedClusterTree.cpp:9:
./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Tree.o `test -f './tree/Tree.cpp' || echo './'`./tree/Tree.cpp
In file included from ./tree/UPGMA/../ClusterTree.h:23:
./tree/UPGMA/../../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./tree/UPGMA/../ClusterTree.h:16:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/UPGMA/../ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::DistMatrix> quickDistMat;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
22 | auto_ptr<AlignmentSteps> treeFromDistMatrix(RootedGuideTree* phyloTree,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./tree/UPGMA/RootedClusterTree.cpp:11:
./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
23 | auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
51 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
17 | auto_ptr<AlignmentSteps> RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/UPGMA/RootedClusterTree.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)':
./tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
21 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp
In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./tree/UPGMA/../../alignment/Alignment.h:42,
from ./tree/UPGMA/RootedGuideTree.h:17,
from ./tree/UPGMA/RootedGuideTree.cpp:10:
./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp
In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./tree/../alignment/Alignment.h:42,
from ./tree/Tree.h:13,
from ./tree/Tree.cpp:10:
./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./tree/UPGMA/../../alignment/Alignment.h:42,
from ./tree/UPGMA/RootedGuideTree.h:17,
from ./tree/UPGMA/RootedTreeOutput.h:15,
from ./tree/UPGMA/RootedTreeOutput.cpp:9:
./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp
./tree/Tree.h:26:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./tree/Tree.h:15:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/Tree.cpp:278:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
278 | auto_ptr<AlignmentSteps> Tree::createSets(int firstSeq, int lastSeq)
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/Tree.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::Tree::createSets(int, int)':
./tree/Tree.cpp:280:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
280 | auto_ptr<AlignmentSteps> progAlignSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo './'`./tree/RandomGenerator.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp
In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./tree/../alignment/Alignment.h:42,
from ./tree/ClusterTree.h:20,
from ./tree/ClusterTree.cpp:9:
./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./tree/ClusterTree.h:23:
./tree/../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./tree/ClusterTree.h:16:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::DistMatrix> quickDistMat;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp
In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./tree/../alignment/Alignment.h:42,
from ./tree/TreeInterface.h:19,
from ./tree/TreeInterface.cpp:15:
./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/TreeInterface.h:38:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
38 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./tree/TreeInterface.h:17:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:57:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
57 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:102:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
102 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:108:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
108 | auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:133:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
133 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:138:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
138 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:142:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
142 | auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./tree/ClusterTree.h:23,
from ./tree/UnRootedClusterTree.h:8,
from ./tree/TreeInterface.cpp:17:
./tree/../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::DistMatrix> quickDistMat;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./tree/TreeInterface.cpp:18:
./tree/Tree.h:26:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./tree/TreeInterface.cpp:23:
./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
22 | auto_ptr<AlignmentSteps> treeFromDistMatrix(RootedGuideTree* phyloTree,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp:31:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp:103:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
103 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp:195:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
195 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsFromDistMatNJ(std::vector<int>*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)':
./tree/TreeInterface.cpp:200:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
200 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp: At global scope:
./tree/TreeInterface.cpp:208:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
208 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::string*, std::vector<int>*, int, int, bool*)':
./tree/TreeInterface.cpp:214:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
214 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp: At global scope:
./tree/TreeInterface.cpp:439:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
439 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::string*, std::vector<int>*, int, int, bool*)':
./tree/TreeInterface.cpp:445:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
445 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp: At global scope:
./tree/TreeInterface.cpp:485:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
485 | auto_ptr<AlignmentSteps>
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::getWeightsAndStepsFromDistMatUPGMA(std::vector<int>*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)':
./tree/TreeInterface.cpp:490:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
490 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp: At global scope:
./tree/TreeInterface.cpp:503:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
503 | auto_ptr<AlignmentSteps> TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::TreeInterface::generateTreeFromDistMatUPGMA(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)':
./tree/TreeInterface.cpp:506:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
506 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./tree/../alignment/Alignment.h:42,
from ./tree/ClusterTree.h:20,
from ./tree/UnRootedClusterTree.h:8,
from ./tree/UnRootedClusterTree.cpp:9:
./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./tree/ClusterTree.h:23:
./tree/../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./tree/ClusterTree.h:16:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
70 | auto_ptr<clustalw::DistMatrix> quickDistMat;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./tree/../alignment/Alignment.h:42,
from ./tree/ClusterTreeOutput.h:11,
from ./tree/ClusterTreeOutput.cpp:9:
./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)':
./tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
164 | register int i;
| ^
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp
In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./interface/../fileInput/../alignment/Alignment.h:42,
from ./interface/../fileInput/FileReader.h:12,
from ./interface/../Clustal.h:18,
from ./interface/InteractiveMenu.h:15,
from ./interface/InteractiveMenu.cpp:23:
./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./interface/../fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./interface/../fileInput/FileReader.h:11:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./interface/../Clustal.h:20:
./interface/../alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp
./interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()':
./interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1190 | system(lin1.c_str());
| ~~~~~~^~~~~~~~~~~~~~
In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./interface/../fileInput/../alignment/Alignment.h:42,
from ./interface/../fileInput/FileReader.h:12,
from ./interface/../Clustal.h:18,
from ./interface/CommandLineParser.h:18,
from ./interface/CommandLineParser.cpp:13:
./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./interface/../fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./interface/../fileInput/FileReader.h:11:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./interface/../Clustal.h:20:
./interface/../alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp
In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./multipleAlign/../alignment/Alignment.h:42,
from ./multipleAlign/ProfileBase.h:14,
from ./multipleAlign/MSA.h:10,
from ./multipleAlign/MSA.cpp:16:
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./multipleAlign/../alignment/Alignment.h:42,
from ./multipleAlign/Iteration.h:8,
from ./multipleAlign/Iteration.cpp:13:
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./multipleAlign/../alignment/Alignment.h:42,
from ./multipleAlign/ProfileAlignAlgorithm.h:10,
from ./multipleAlign/MyersMillerProfileAlign.h:10,
from ./multipleAlign/MyersMillerProfileAlign.cpp:10:
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./multipleAlign/Iteration.cpp:17:
./multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
38 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./multipleAlign/../tree/TreeInterface.h:17:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
57 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
102 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
108 | auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
133 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
138 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
142 | auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./substitutionMatrix/SubMatrix.cpp:15:
./substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./multipleAlign/../alignment/Alignment.h:42,
from ./multipleAlign/ProfileStandard.h:9,
from ./multipleAlign/ProfileStandard.cpp:9:
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
./multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | tmpnam (buffer);
| ~~~~~~~^~~~~~~~
In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./multipleAlign/../alignment/Alignment.h:42,
from ./multipleAlign/ProfileWithSub.h:9,
from ./multipleAlign/ProfileWithSub.cpp:9:
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp
In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./multipleAlign/../alignment/Alignment.h:42,
from ./multipleAlign/ProfileBase.h:14,
from ./multipleAlign/ProfileBase.cpp:9:
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./multipleAlign/../alignment/Alignment.h:42,
from ./multipleAlign/LowScoreSegProfile.h:13,
from ./multipleAlign/LowScoreSegProfile.cpp:9:
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./general/OutputFile.cpp:9:
./general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
26 | std::auto_ptr<std::ofstream> file;
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./general/OutputFile.h:8:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp
./general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)':
./general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
475 | register int i;
| ^
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo './'`./general/SymMatrix.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp
./general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)':
./general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
53 | register int p;
| ^
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp
./general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)':
./general/Utility.cpp:183:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
183 | fgets(line, MAXLINE, stdin);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
./general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)':
./general/Utility.cpp:221:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
221 | fgets(line, MAXLINE, stdin);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo './'`./alignment/Alignment.cpp
./general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const':
./general/ClustalWResources.cpp:105:14: warning: writing 2 bytes into a region of size 1 [-Wstringop-overflow=]
105 | delim[0] = DIRDELIM;
| ~~~~~~~~~^~~~~~~~~~
./general/ClustalWResources.cpp:104:10: note: destination object 'delim' of size 1
104 | char delim[1];
| ^~~~~
In file included from ./general/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./general/../alignment/Alignment.h:42,
from ./general/Stats.cpp:15:
./general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o `test -f './main.cpp' || echo './'`./main.cpp
In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8,
from ./alignment/Alignment.h:42,
from ./alignment/Alignment.cpp:25:
./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()':
./alignment/Alignment.cpp:47:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
47 | register int sl; /* which have code = gap_pos2 */
| ^~
./alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()':
./alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
122 | register int sl; /* which have code = gap_pos2 */
| ^~
./alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()':
./alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
617 | register int sl;
| ^~
In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8,
from ./alignment/Alignment.h:42,
from ./alignment/AlignmentOutput.h:24,
from ./alignment/AlignmentOutput.cpp:27:
./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./alignment/AlignmentOutput.h:20:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.cpp:512:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
512 | bool AlignmentOutput::openExplicitFile(auto_ptr<ofstream>& outFile, string fileName)
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.cpp:535:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
535 | string AlignmentOutput::openOutputFile(auto_ptr<ofstream>& outFile, string prompt,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8,
from ./alignment/ObjectiveScore.h:15,
from ./alignment/ObjectiveScore.cpp:10:
./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
from ./fileInput/../alignment/Alignment.h:42,
from ./fileInput/FileReader.h:12,
from ./Clustal.h:18,
from ./Clustal.cpp:27:
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./fileInput/FileReader.h:11:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./Clustal.h:20:
./alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./Clustal.cpp:33:
./tree/TreeInterface.h:38:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
38 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:57:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
57 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:102:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
102 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:108:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
108 | auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:133:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
133 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:138:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
138 | auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./tree/TreeInterface.h:142:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
142 | auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8,
from ./alignment/Alignment.h:42,
from ./main.cpp:10:
./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
96 | void printInFormat(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
97 | void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
| ^~~~~~~~~~~~~~
./Clustal.cpp: In member function 'void clustalw::Clustal::align(std::string*, bool)':
./Clustal.cpp:162:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
162 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./Clustal.cpp: In member function 'void clustalw::Clustal::doAlignUseOldTree(std::string*)':
./Clustal.cpp:837:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
837 | auto_ptr<AlignmentSteps> progSteps;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./main.cpp:16:
./fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
42 | void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
| ^~~~~~~~
In file included from /usr/include/c++/12/memory:76,
from ./fileInput/FileReader.h:11:
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./interface/../Clustal.h:20,
from ./interface/InteractiveMenu.h:15,
from ./main.cpp:17:
./interface/../alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
68 | bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
69 | string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | auto_ptr<ofstream> clustalOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
76 | auto_ptr<ofstream> gcgOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
77 | auto_ptr<ofstream> nbrfOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
78 | auto_ptr<ofstream> phylipOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
79 | auto_ptr<ofstream> gdeOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
80 | auto_ptr<ofstream> nexusOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./interface/../alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
81 | auto_ptr<ofstream> fastaOutFile;
| ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/clustalw-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o clustalw2 FullPairwiseAlign.o FastPairwiseAlign.o MSFFileParser.o FileReader.o PIRFileParser.o RSFFileParser.o GDEFileParser.o InFileStream.o ClustalFileParser.o PearsonFileParser.o FileParser.o EMBLFileParser.o RootedClusterTree.o UPGMAAlgorithm.o Node.o RootedGuideTree.o RootedTreeOutput.o Tree.o ClusterTree.o TreeInterface.o UnRootedClusterTree.o ClusterTreeOutput.o RandomGenerator.o NJTree.o AlignmentSteps.o InteractiveMenu.o CommandLineParser.o SubMatrix.o Iteration.o MSA.o MyersMillerProfileAlign.o ProfileStandard.o ProfileWithSub.o ProfileBase.o LowScoreSegProfile.o OutputFile.o UserParameters.o Utility.o InvalidCombination.o DebugLog.o ClustalWResources.o VectorOutOfRange.o SymMatrix.o Stats.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o Clustal.o main.o
/usr/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
./src/./multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
make[4]: Leaving directory '/build/clustalw-2.1+lgpl/src'
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dh_auto_test
make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1
make[1]: Entering directory '/build/clustalw-2.1+lgpl'
Making check in m4
make[2]: Entering directory '/build/clustalw-2.1+lgpl/m4'
make[2]: Nothing to be done for 'check'.
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Making check in src
make[2]: Entering directory '/build/clustalw-2.1+lgpl/src'
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create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/clustalw/
make -j8 install DESTDIR=/build/clustalw-2.1\+lgpl/debian/clustalw AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/clustalw-2.1+lgpl'
Making install in m4
make[2]: Entering directory '/build/clustalw-2.1+lgpl/m4'
make[3]: Entering directory '/build/clustalw-2.1+lgpl/m4'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Leaving directory '/build/clustalw-2.1+lgpl/m4'
make[2]: Leaving directory '/build/clustalw-2.1+lgpl/m4'
Making install in src
make[2]: Entering directory '/build/clustalw-2.1+lgpl/src'
make[3]: Entering directory '/build/clustalw-2.1+lgpl/src'
make[4]: Entering directory '/build/clustalw-2.1+lgpl/src'
make[4]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/clustalw-2.1+lgpl/debian/clustalw/usr/bin'
/usr/bin/install -c clustalw2 '/build/clustalw-2.1+lgpl/debian/clustalw/usr/bin'
make[4]: Leaving directory '/build/clustalw-2.1+lgpl/src'
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make[1]: Leaving directory '/build/clustalw-2.1+lgpl'
debian/rules override_dh_install
make[1]: Entering directory '/build/clustalw-2.1+lgpl'
dh_install
# We have to ask upstream if it is important for them that the binary is named clustalw2
mv /build/clustalw-2.1+lgpl/debian/clustalw/usr/bin/clustalw2 /build/clustalw-2.1+lgpl/debian/clustalw/usr/bin/clustalw
make[1]: Leaving directory '/build/clustalw-2.1+lgpl'
dh_installdocs
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/build/clustalw-2.1+lgpl'
dh_installchangelogs debian/CHANGELOG.upstream
make[1]: Leaving directory '/build/clustalw-2.1+lgpl'
dh_installexamples
dh_installman
dh_installmenu
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'clustalw-dbgsym' in '../clustalw-dbgsym_2.1+lgpl-7_arm64.deb'.
dpkg-deb: building package 'clustalw' in '../clustalw_2.1+lgpl-7_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../clustalw_2.1+lgpl-7_arm64.buildinfo
dpkg-genchanges --build=binary -O../clustalw_2.1+lgpl-7_arm64.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/18533 and its subdirectories
I: Current time: Fri Apr 21 16:59:56 -12 2023
I: pbuilder-time-stamp: 1682139596