I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 16 08:38:56 -12 2024
I: pbuilder-time-stamp: 1718570336
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 [libmems_1.6.0+4725-9.dsc]
I: copying [./libmems_1.6.0+4725.orig.tar.xz]
I: copying [./libmems_1.6.0+4725-9.debian.tar.xz]
I: Extracting source
gpgv: Signature made Mon Nov 16 21:02:37 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 ./libmems_1.6.0+4725-9.dsc: no acceptable signature found
dpkg-source: info: extracting libmems in libmems-1.6.0+4725
dpkg-source: info: unpacking libmems_1.6.0+4725.orig.tar.xz
dpkg-source: info: unpacking libmems_1.6.0+4725-9.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 01_fix_ctors.patch
dpkg-source: info: applying 02_fix_a_Wformat.patch
dpkg-source: info: applying pkg-config-directive.patch
dpkg-source: info: applying 03_update_boost_m4_to_git_d9ff75.patch
dpkg-source: info: applying 04_add_dependend_libs_to_link_command.patch
dpkg-source: info: applying 05_gcc-6.patch
dpkg-source: info: applying boost1.62.patch
dpkg-source: info: applying drop-version-number.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/18907/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='18907'
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.SFeI9smE/pbuilderrc_Iwts --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.SFeI9smE/b1 --logfile b1/build.log libmems_1.6.0+4725-9.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 codethink11-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Jun 14 04:48 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/18907/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), d-shlibs, pkg-config, libgenome-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-dev
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.
pbuilder-satisfydepends-dummy depends on d-shlibs; however:
Package d-shlibs is not installed.
pbuilder-satisfydepends-dummy depends on pkg-config; however:
Package pkg-config is not installed.
pbuilder-satisfydepends-dummy depends on libgenome-dev; however:
Package libgenome-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however:
Package libboost-filesystem-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however:
Package libboost-iostreams-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however:
Package libboost-program-options-dev is not installed.
pbuilder-satisfydepends-dummy depends on libmuscle-dev; however:
Package libmuscle-dev 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} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgenome-dev{a} libgenome0{a} libicu-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libmuscle-dev{a} libmuscle1{a} libpipeline1{a} libpkgconf3{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{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, 54 newly installed, 0 to remove and 0 not upgraded.
Need to get 42.1 MB of archives. After unpacking 296 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 d-shlibs all 0.104 [18.6 kB]
Get: 17 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 18 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB]
Get: 19 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B]
Get: 22 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 23 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 24 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB]
Get: 25 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB]
Get: 26 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB]
Get: 27 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB]
Get: 28 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB]
Get: 29 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
Get: 32 http://deb.debian.org/debian bookworm/main arm64 icu-devtools arm64 72.1-3 [192 kB]
Get: 33 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-20 [9510 kB]
Get: 34 http://deb.debian.org/debian bookworm/main arm64 libboost-filesystem1.74.0 arm64 1.74.0+ds1-20 [254 kB]
Get: 35 http://deb.debian.org/debian bookworm/main arm64 libboost-system1.74.0 arm64 1.74.0+ds1-20 [218 kB]
Get: 36 http://deb.debian.org/debian bookworm/main arm64 libboost-system1.74-dev arm64 1.74.0+ds1-20 [219 kB]
Get: 37 http://deb.debian.org/debian bookworm/main arm64 libboost-filesystem1.74-dev arm64 1.74.0+ds1-20 [277 kB]
Get: 38 http://deb.debian.org/debian bookworm/main arm64 libboost-filesystem-dev arm64 1.74.0.3 [4368 B]
Get: 39 http://deb.debian.org/debian bookworm/main arm64 libboost-regex1.74.0 arm64 1.74.0+ds1-20 [448 kB]
Get: 40 http://deb.debian.org/debian bookworm/main arm64 libicu-dev arm64 72.1-3 [10.2 MB]
Get: 41 http://deb.debian.org/debian bookworm/main arm64 libboost-regex1.74-dev arm64 1.74.0+ds1-20 [525 kB]
Get: 42 http://deb.debian.org/debian bookworm/main arm64 libboost-iostreams1.74-dev arm64 1.74.0+ds1-20 [247 kB]
Get: 43 http://deb.debian.org/debian bookworm/main arm64 libboost-iostreams-dev arm64 1.74.0.3 [4316 B]
Get: 44 http://deb.debian.org/debian bookworm/main arm64 libboost-program-options1.74.0 arm64 1.74.0+ds1-20 [317 kB]
Get: 45 http://deb.debian.org/debian bookworm/main arm64 libboost-program-options1.74-dev arm64 1.74.0+ds1-20 [354 kB]
Get: 46 http://deb.debian.org/debian bookworm/main arm64 libboost-program-options-dev arm64 1.74.0.3 [4340 B]
Get: 47 http://deb.debian.org/debian bookworm/main arm64 libgenome0 arm64 1.3.11+svn20110227.4616-5 [104 kB]
Get: 48 http://deb.debian.org/debian bookworm/main arm64 libgenome-dev arm64 1.3.11+svn20110227.4616-5 [178 kB]
Get: 49 http://deb.debian.org/debian bookworm/main arm64 libmuscle1 arm64 3.7+4565-7 [232 kB]
Get: 50 http://deb.debian.org/debian bookworm/main arm64 libmuscle-dev arm64 3.7+4565-7 [293 kB]
Get: 51 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB]
Get: 52 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB]
Get: 53 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB]
Get: 54 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB]
Fetched 42.1 MB in 1s (28.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
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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.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
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Unpacking groff-base (1.22.4-10) ...
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Unpacking bsdextrautils (2.38.1-5+b1) ...
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Unpacking m4 (1.4.19-3) ...
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Unpacking libicu72:arm64 (72.1-3) ...
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I: Building the package
I: Running cd /build/libmems-1.6.0+4725/ && 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 > ../libmems_1.6.0+4725-9_source.changes
dpkg-buildpackage: info: source package libmems
dpkg-buildpackage: info: source version 1.6.0+4725-9
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
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'.
libtoolize: copying file 'config/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:54: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated.
./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from...
aclocal.m4:429: AM_INIT_AUTOMAKE is expanded from...
configure.ac:54: the top level
configure.ac:66: warning: The macro `AM_PROG_LIBTOOL' is obsolete.
configure.ac:66: You should run autoupdate.
m4/libtool.m4:101: AM_PROG_LIBTOOL is expanded from...
configure.ac:66: the top level
configure.ac:70: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:70: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:70: the top level
configure.ac:92: warning: The macro `AC_LANG_CPLUSPLUS' is obsolete.
configure.ac:92: You should run autoupdate.
./lib/autoconf/c.m4:262: AC_LANG_CPLUSPLUS is expanded from...
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
m4/ac_cxx_namespaces.m4:12: AC_CXX_NAMESPACES is expanded from...
configure.ac:92: the top level
configure.ac:92: warning: The macro `AC_TRY_COMPILE' is obsolete.
configure.ac:92: You should run autoupdate.
./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from...
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
m4/ac_cxx_namespaces.m4:12: AC_CXX_NAMESPACES is expanded from...
configure.ac:92: the top level
configure.ac:122: warning: 'AM_CONFIG_HEADER': this macro is obsolete.
configure.ac:122: 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:122: the top level
configure.ac:128: warning: The macro `AC_HEADER_TIME' is obsolete.
configure.ac:128: You should run autoupdate.
./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from...
configure.ac:128: the top level
configure.ac:136: warning: AC_OUTPUT should be used without arguments.
configure.ac:136: You should run autoupdate.
configure.ac:54: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see:
configure.ac:54: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation
configure.ac:66: installing 'config/compile'
configure.ac:66: installing 'config/config.guess'
configure.ac:66: installing 'config/config.sub'
configure.ac:54: installing 'config/install-sh'
configure.ac:54: installing 'config/missing'
libMems/Makefile.am:48: warning: source file 'HomologyHMM/algebras.cc' is in a subdirectory,
libMems/Makefile.am:48: 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.
libMems/Makefile.am:48: warning: source file 'HomologyHMM/homology.cc' is in a subdirectory,
libMems/Makefile.am:48: but option 'subdir-objects' is disabled
libMems/Makefile.am:48: warning: source file 'HomologyHMM/homologymain.cc' is in a subdirectory,
libMems/Makefile.am:48: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/asyncio.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/alinuxaio.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/aPOSIXaio.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/alibc.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/awin32aio.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/buffer.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/util.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/sorting.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/dmsort.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/timing.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am:51: warning: source file 'dmSML/sml.c' is in a subdirectory,
libMems/Makefile.am:51: but option 'subdir-objects' is disabled
libMems/Makefile.am: installing 'config/depcomp'
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
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checking whether build environment is sane... yes
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checking whether make sets $(MAKE)... yes
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checking for C++ compiler default output file name... a.out
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checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking whether ln -s works... yes
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking how to print strings... printf
checking for gcc... gcc
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 dependency style of gcc... none
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checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
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checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
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checking for sys/stat.h... yes
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checking for sys/time.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for egrep... (cached) /usr/bin/grep -E
checking for Boost headers version >= 1.34.0... yes
checking for Boost's header version... 1_74
checking whether the compiler implements namespaces... yes
checking for the toolset name used by Boost for g++... configure: WARNING: could not figure out which toolset name to use for g++
checking for boost/system/error_code.hpp... yes
checking for the Boost system library... yes
checking for boost/filesystem/path.hpp... yes
checking for the Boost filesystem library... (cached) yes
checking for boost/program_options.hpp... yes
checking for the Boost program_options library... (cached) yes
checking for boost/iostreams/device/file_descriptor.hpp... yes
checking for the Boost iostreams library... (cached) yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for DEPS... yes
checking for sys/types.h... (cached) yes
checking for sys/aio.h... no
checking for aio.h... yes
checking for features.h... yes
checking for pthread_mutex_unlock in -lpthread... yes
checking for aio_write in -lrt... yes
checking for doxygen... no
configure: WARNING: doxygen not found - will not generate any doxygen documentation
checking for perl... /usr/bin/perl
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking how to run the C preprocessor... gcc -E
checking whether gcc needs -traditional... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating libMems/Makefile
config.status: creating libMems.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
dh_auto_build
make -j8
make[1]: Entering directory '/build/libmems-1.6.0+4725'
make all-recursive
make[2]: Entering directory '/build/libmems-1.6.0+4725'
Making all in libMems
make[3]: Entering directory '/build/libmems-1.6.0+4725/libMems'
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAFileSML.lo DNAFileSML.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchFinder.lo MatchFinder.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAMemorySML.lo DNAMemorySML.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileSML.lo FileSML.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemHash.lo MemHash.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchHashEntry.lo MatchHashEntry.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Interval.lo Interval.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -fPIC -DPIC -o .libs/Interval.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IntervalList.lo IntervalList.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o twister.lo twister.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -fPIC -DPIC -o .libs/twister.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -o twister.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gnAlignedSequences.lo gnAlignedSequences.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -o MemHash.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -o Interval.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -o FileSML.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchList.lo MatchList.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Aligner.lo Aligner.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Islands.lo Islands.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o
In file included from /usr/include/c++/12/ext/hash_map:60,
from ../libMems/HomologyHMM/dptables.h:43,
from ../libMems/HomologyHMM/homology.h:27,
from ../libMems/Islands.h:25,
from Aligner.cpp:10:
/usr/include/c++/12/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
In file included from /usr/include/c++/12/ext/hash_map:60,
from ../libMems/HomologyHMM/dptables.h:43,
from ../libMems/HomologyHMM/homology.h:27,
from ../libMems/Islands.h:25,
from Islands.cpp:13:
/usr/include/c++/12/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskedMemHash.lo MaskedMemHash.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -o MatchList.o >/dev/null 2>&1
In file included from ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GappedAlignment.lo GappedAlignment.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o
In file included from ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MuscleInterface.lo MuscleInterface.cpp
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/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatchList.lo RepeatMatchList.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1
In file included from /usr/include/c++/12/ext/hash_map:60,
from ../libMems/HomologyHMM/dptables.h:43,
from ../libMems/HomologyHMM/homology.h:27,
from ../libMems/Islands.h:25,
from ../libMems/ProgressiveAligner.h:21,
from Backbone.cpp:13:
/usr/include/c++/12/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1
In file included from ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -o Islands.o >/dev/null 2>&1
In file included from /usr/include/c++/12/ext/hash_map:60,
from ../libMems/HomologyHMM/dptables.h:43,
from ../libMems/HomologyHMM/homology.h:27,
from ../libMems/Islands.h:25,
from ../libMems/ProgressiveAligner.h:21,
from ProgressiveAligner.cpp:14:
/usr/include/c++/12/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o
In file included from ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o
In file included from /usr/include/c++/12/ext/hash_map:60,
from ../libMems/HomologyHMM/dptables.h:43,
from ../libMems/HomologyHMM/homology.h:27,
from ../libMems/Islands.h:25,
from ../libMems/ProgressiveAligner.h:21,
from GreedyBreakpointElimination.cpp:7:
/usr/include/c++/12/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o algebras.lo `test -f 'HomologyHMM/algebras.cc' || echo './'`HomologyHMM/algebras.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o
In file included from HomologyHMM/algebras.cc:27:
HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1
In file included from ../libMems/HomologyHMM/homology.h:28:
../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo './'`HomologyHMM/homology.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o
In file included from /usr/include/c++/12/ext/hash_map:60,
from HomologyHMM/dptables.h:43,
from HomologyHMM/homology.h:27,
from HomologyHMM/homology.cc:24:
/usr/include/c++/12/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo './'`HomologyHMM/homologymain.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o
In file included from /usr/include/c++/12/ext/hash_map:60,
from HomologyHMM/dptables.h:43,
from HomologyHMM/homology.h:27,
from HomologyHMM/homologymain.cc:21:
/usr/include/c++/12/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
In file included from HomologyHMM/homology.h:28:
HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
HomologyHMM/homology.cc: In function 'Algebra<BFloatMethods> Forward(HomologyDPTable**, Params, char*, int)':
HomologyHMM/homology.cc:319:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
319 | register double iTempResult[1];
| ^~~~~~~~~~~
HomologyHMM/homology.cc:321:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
321 | register bfloat iTempProb[1];
| ^~~~~~~~~
HomologyHMM/homology.cc: In function 'Algebra<BFloatMethods> Backward(HomologyBaumWelch&, HomologyDPTable*, HomologyDPTable**, Params, char*, int)':
HomologyHMM/homology.cc:417:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
417 | register double iTempResult[1];
| ^~~~~~~~~~~
HomologyHMM/homology.cc:419:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
419 | register bfloat iTempProb[3];
| ^~~~~~~~~
HomologyHMM/homology.cc: In function 'Algebra<BFloatMethods> Viterbi_recurse(HomologyDPTable**, Params, char*, int)':
HomologyHMM/homology.cc:565:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
565 | register double iTempResult[1];
| ^~~~~~~~~~~
HomologyHMM/homology.cc:567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
567 | register bfloat iTempProb[1];
| ^~~~~~~~~
HomologyHMM/homology.cc: In function 'Path& Viterbi_trace(HomologyDPTable*, Params, char*, int)':
HomologyHMM/homology.cc:673:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
673 | register double iTempResult[1];
| ^~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -o Aligner.o >/dev/null 2>&1
In file included from HomologyHMM/homology.h:28:
HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o
dmSML/aPOSIXaio.c: In function 'QueryLastCompletePAIO':
dmSML/aPOSIXaio.c:115:28: warning: passing argument 1 of 'aio_suspend' from incompatible pointer type [-Wincompatible-pointer-types]
115 | rval = aio_suspend(request_array, 1, &zero_wait);
| ^~~~~~~~~~~~~
| |
| struct aiocb **
In file included from /usr/include/features.h:489,
from /usr/include/aarch64-linux-gnu/sys/types.h:25,
from ../libMems/dmSML/asyncio.h:24,
from ../libMems/dmSML/aPOSIXaio.h:8,
from dmSML/aPOSIXaio.c:5:
/usr/include/aio.h:202:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **'
202 | extern int __REDIRECT_NTH (aio_suspend,
| ^~~~~~~~~~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o
dmSML/util.c: In function 'removeFile':
dmSML/util.c:126:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
126 | rm_cmd = Fmt( "/bin/rm -fv %s", filename );
| ^
dmSML/util.c:128:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
128 | rm_cmd = Fmt( "/bin/rm -f %s", filename );
| ^
dmSML/util.c:129:16: warning: implicit declaration of function 'system' [-Wimplicit-function-declaration]
129 | return system( rm_cmd );
| ^~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -o timing.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -o Backbone.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/aarch64-linux-gnu RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o .libs/RepeatHash.o .libs/DNAFileSML.o .libs/MatchFinder.o .libs/DNAMemorySML.o .libs/MemorySML.o .libs/SortedMerList.o .libs/FileSML.o .libs/MemHash.o .libs/MatchHashEntry.o .libs/Interval.o .libs/IntervalList.o .libs/twister.o .libs/gnAlignedSequences.o .libs/MatchList.o .libs/Aligner.o .libs/Islands.o .libs/MaskedMemHash.o .libs/GappedAlignment.o .libs/MuscleInterface.o .libs/PhyloTree.o .libs/RepeatMatchList.o .libs/RepeatMatch.o .libs/Backbone.o .libs/PairwiseMatchFinder.o .libs/ProgressiveAligner.o .libs/SuperInterval.o .libs/GreedyBreakpointElimination.o .libs/algebras.o .libs/homology.o .libs/homologymain.o .libs/asyncio.o .libs/alinuxaio.o .libs/aPOSIXaio.o .libs/alibc.o .libs/awin32aio.o .libs/buffer.o .libs/util.o .libs/sorting.o .libs/dmsort.o .libs/timing.o .libs/sml.o -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -O2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libMems.so.1 -o .libs/libMems.so.1.0.0
libtool: link: (cd ".libs" && rm -f "libMems.so.1" && ln -s "libMems.so.1.0.0" "libMems.so.1")
libtool: link: (cd ".libs" && rm -f "libMems.so" && ln -s "libMems.so.1.0.0" "libMems.so")
libtool: link: ar cr .libs/libMems.a RepeatHash.o DNAFileSML.o MatchFinder.o DNAMemorySML.o MemorySML.o SortedMerList.o FileSML.o MemHash.o MatchHashEntry.o Interval.o IntervalList.o twister.o gnAlignedSequences.o MatchList.o Aligner.o Islands.o MaskedMemHash.o GappedAlignment.o MuscleInterface.o PhyloTree.o RepeatMatchList.o RepeatMatch.o Backbone.o PairwiseMatchFinder.o ProgressiveAligner.o SuperInterval.o GreedyBreakpointElimination.o algebras.o homology.o homologymain.o asyncio.o alinuxaio.o aPOSIXaio.o alibc.o awin32aio.o buffer.o util.o sorting.o dmsort.o timing.o sml.o
libtool: link: ranlib .libs/libMems.a
libtool: link: ( cd ".libs" && rm -f "libMems.la" && ln -s "../libMems.la" "libMems.la" )
make[3]: Leaving directory '/build/libmems-1.6.0+4725/libMems'
make[3]: Entering directory '/build/libmems-1.6.0+4725'
make[3]: Leaving directory '/build/libmems-1.6.0+4725'
make[2]: Leaving directory '/build/libmems-1.6.0+4725'
make[1]: Leaving directory '/build/libmems-1.6.0+4725'
dh_auto_test
make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1
make[1]: Entering directory '/build/libmems-1.6.0+4725'
Making check in libMems
make[2]: Entering directory '/build/libmems-1.6.0+4725/libMems'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/libmems-1.6.0+4725/libMems'
make[2]: Entering directory '/build/libmems-1.6.0+4725'
make[2]: Leaving directory '/build/libmems-1.6.0+4725'
make[1]: Leaving directory '/build/libmems-1.6.0+4725'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
make -j1 install DESTDIR=/build/libmems-1.6.0\+4725/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/libmems-1.6.0+4725'
Making install in libMems
make[2]: Entering directory '/build/libmems-1.6.0+4725/libMems'
make[3]: Entering directory '/build/libmems-1.6.0+4725/libMems'
/usr/bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu'
/bin/bash ../libtool --mode=install /usr/bin/install -c libMems.la '/build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libMems.so.1.0.0 /build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu/libMems.so.1.0.0
libtool: install: (cd /build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libMems.so.1.0.0 libMems.so.1 || { rm -f libMems.so.1 && ln -s libMems.so.1.0.0 libMems.so.1; }; })
libtool: install: (cd /build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libMems.so.1.0.0 libMems.so || { rm -f libMems.so && ln -s libMems.so.1.0.0 libMems.so; }; })
libtool: install: /usr/bin/install -c .libs/libMems.lai /build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu/libMems.la
libtool: install: /usr/bin/install -c .libs/libMems.a /build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu/libMems.a
libtool: install: chmod 644 /build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu/libMems.a
libtool: install: ranlib /build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu/libMems.a
libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu'
/usr/bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems/dmSML'
/usr/bin/install -c -m 644 dmSML/asyncio.h dmSML/alinuxaio.h dmSML/aPOSIXaio.h dmSML/alibc.h dmSML/awin32aio.h dmSML/buffer.h dmSML/util.h dmSML/sorting.h dmSML/dmsort.h dmSML/timing.h dmSML/sml.h '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems/dmSML'
/usr/bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems/HomologyHMM'
/usr/bin/install -c -m 644 HomologyHMM/homology.h HomologyHMM/dptables.h HomologyHMM/algebras.h HomologyHMM/parameters.h '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems/HomologyHMM'
/usr/bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems'
/usr/bin/install -c -m 644 RepeatHash.h MatchHashEntry.h DNAFileSML.h MemorySML.h MatchProjectionAdapter.h DNAMemorySML.h MatchFinder.h SortedMerList.h IntervalList.h FileSML.h gnAlignedSequences.h Interval.h MemHash.h AbstractMatch.h SlotAllocator.h Aligner.h Match.h MatchList.h Matrix.h NumericMatrix.h Islands.h MaskedMemHash.h SeedMasks.h GappedAlignment.h MuscleInterface.h GappedAligner.h PhyloTree.h SparseAbstractMatch.h DenseAbstractMatch.h RepeatMatch.h UngappedLocalAlignment.h AbstractGappedAlignment.h CompactGappedAlignment.h HybridAbstractMatch.h twister.h SubstitutionMatrix.h RepeatMatchList.h Backbone.h ProgressiveAligner.h PairwiseMatchAdapter.h '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems'
/usr/bin/install -c -m 644 PairwiseMatchFinder.h SeedOccurrenceList.h TreeUtilities.h SuperInterval.h GreedyBreakpointElimination.h LCB.h DistanceMatrix.h Scoring.h configuration.h Memory.h Files.h gnRAWSequence.h '/build/libmems-1.6.0+4725/debian/tmp/usr/include/libMems'
make[3]: Leaving directory '/build/libmems-1.6.0+4725/libMems'
make[2]: Leaving directory '/build/libmems-1.6.0+4725/libMems'
make[2]: Entering directory '/build/libmems-1.6.0+4725'
make[3]: Entering directory '/build/libmems-1.6.0+4725'
make[3]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 libMems.pc '/build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
make[3]: Leaving directory '/build/libmems-1.6.0+4725'
make[2]: Leaving directory '/build/libmems-1.6.0+4725'
make[1]: Leaving directory '/build/libmems-1.6.0+4725'
debian/rules override_dh_install
make[1]: Entering directory '/build/libmems-1.6.0+4725'
dh_install
d-shlibmove --commit \
--multiarch \
--devunversioned \
--exclude-la \
--override s/libGenome0-dev/libgenome-dev/ \
--override s/libMUSCLE1-dev/libmuscle-dev/ \
--movedev debian/tmp/usr/include usr \
--movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/aarch64-linux-gnu/pkgconfig \
debian/tmp/usr/lib/*/*.so
Library package automatic movement utility
--> libboost-filesystem1.74-dev package exists.
--> libboost-iostreams1.74-dev package exists.
--> libgenome-dev package exists.
--> libmuscle-dev package exists.
set -e
install -d -m 755 debian/libmems-dev/usr/lib/aarch64-linux-gnu
install -d -m 755 debian/libmems1/usr/lib/aarch64-linux-gnu
mv debian/tmp/usr/lib/aarch64-linux-gnu/libMems.a debian/libmems-dev/usr/lib/aarch64-linux-gnu
mv debian/tmp/usr/lib/aarch64-linux-gnu/libMems.so debian/libmems-dev/usr/lib/aarch64-linux-gnu
mv /build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu/libMems.so.1 debian/libmems1/usr/lib/aarch64-linux-gnu
mv /build/libmems-1.6.0+4725/debian/tmp/usr/lib/aarch64-linux-gnu/libMems.so.1.0.0 debian/libmems1/usr/lib/aarch64-linux-gnu
PKGDEV=libmems-dev
PKGSHL=libmems1
install -d -m 755 debian/libmems-dev/usr
mv debian/tmp/usr/include debian/libmems-dev/usr
install -d -m 755 debian/libmems-dev/usr/lib/aarch64-linux-gnu/pkgconfig
mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libmems-dev/usr/lib/aarch64-linux-gnu/pkgconfig
find debian -name "lib*.la" -delete
make[1]: Leaving directory '/build/libmems-1.6.0+4725'
dh_installdocs
dh_installchangelogs
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 'libmems-dev' in '../libmems-dev_1.6.0+4725-9_arm64.deb'.
dpkg-deb: building package 'libmems1-dbgsym' in '../libmems1-dbgsym_1.6.0+4725-9_arm64.deb'.
dpkg-deb: building package 'libmems1' in '../libmems1_1.6.0+4725-9_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../libmems_1.6.0+4725-9_arm64.buildinfo
dpkg-genchanges --build=binary -O../libmems_1.6.0+4725-9_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/18907 and its subdirectories
I: Current time: Sun Jun 16 08:55:53 -12 2024
I: pbuilder-time-stamp: 1718571353