murasaki →
1.68.6-7+b1 →
armhf → 2018-10-10 11:11:01
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| murasaki 1.68.6-7+b1 (armhf) Wed, 10 Oct 2018 11:00:43 +0000 |
+==============================================================================+
Package: murasaki
Version: 1.68.6-7+b1
Source Version: 1.68.6-7
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-85adf697-d77b-4a6a-8ee7-5ed663b02822' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.8 MB]
Fetched 23.9 MB in 16s (1494 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'murasaki' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/murasaki.git
Please use:
git clone https://salsa.debian.org/med-team/murasaki.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 319 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main murasaki 1.68.6-7 (dsc) [2233 B]
Get:2 http://172.17.0.1/private buster-staging/main murasaki 1.68.6-7 (tar) [308 kB]
Get:3 http://172.17.0.1/private buster-staging/main murasaki 1.68.6-7 (diff) [8564 B]
Fetched 319 kB in 0s (652 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/murasaki-AFy6Cf/murasaki-1.68.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/murasaki-AFy6Cf' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-IDQ5wN/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-IDQ5wN/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (11.0 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 81 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15689 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev
Filtered Build-Depends: debhelper (>= 11~), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev
dpkg-deb: building package 'sbuild-build-depends-murasaki-dummy' in '/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive/sbuild-build-depends-murasaki-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-murasaki-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ Sources [565 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ Packages [646 B]
Fetched 2544 B in 0s (13.6 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install murasaki build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd libsasl2-modules openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-8 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file g++-8 gcc-8 gcc-8-base
gettext gettext-base gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base
ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libasan5
libatomic1 libboost-filesystem-dev libboost-filesystem1.62-dev
libboost-filesystem1.62.0 libboost-iostreams-dev libboost-iostreams1.62-dev
libboost-iostreams1.62.0 libboost-regex-dev libboost-regex1.62-dev
libboost-regex1.62.0 libboost-system1.62-dev libboost-system1.62.0
libboost1.62-dev libbsd0 libcc1-0 libcroco3 libcrypto++-dev libcrypto++6
libedit2 libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libfreetype6 libgcc-8-dev libgcc1
libgfortran5 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin
libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgomp1 libgraphite2-3
libgraphite2-dev libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0
libharfbuzz-icu0 libharfbuzz0b libhwloc-dev libhwloc-plugins libhwloc5
libibverbs-dev libibverbs1 libicu-dev libicu-le-hb-dev libicu-le-hb0
libicu60 libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpdec2 libnl-3-200
libnl-route-3-200 libopenmpi-dev libopenmpi3 libpciaccess0 libpcre16-3
libpcre3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpmix2
libpstreams-dev libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib
libsigsegv2 libssl1.0.2 libstdc++-8-dev libstdc++6 libterm-readkey-perl
libtext-wrapper-perl libtool libubsan1 libxml2 m4 man-db mime-support
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3.6 python3.6-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-8-locales dh-make gcc-8-doc libstdc++6-8-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg gettext-doc
libasprintf-dev libgettextpo-dev groff libboost1.62-doc
libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev
libboost-coroutine1.62-dev libboost-date-time1.62-dev
libboost-exception1.62-dev libboost-fiber1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-serialization1.62-dev
libboost-signals1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev libglib2.0-doc
libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils libgraphite2-utils
krb5-doc krb5-user libhwloc-contrib-plugins icu-doc libtool-doc openmpi-doc
pciutils libstdc++-8-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser opencl-icd gfortran keychain libpam-ssh
monkeysphere ssh-askpass libmail-box-perl python3-doc python3-tk
python3-venv python3.6-venv python3.6-doc binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl shared-mime-info xdg-user-dirs
javascript-common krb5-locales libcoarrays-openmpi-dev xauth
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base ibverbs-providers
icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev
libboost-filesystem1.62-dev libboost-filesystem1.62.0 libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-regex-dev
libboost-regex1.62-dev libboost-regex1.62.0 libboost-system1.62-dev
libboost-system1.62.0 libboost1.62-dev libbsd0 libcroco3 libcrypto++-dev
libcrypto++6 libedit2 libelf1 libevent-2.1-6 libevent-core-2.1-6
libevent-pthreads-2.1-6 libfile-stripnondeterminism-perl libfreetype6
libgfortran5 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin
libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3
libgraphite2-dev libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0
libharfbuzz-icu0 libharfbuzz0b libhwloc-dev libhwloc-plugins libhwloc5
libibverbs-dev libibverbs1 libicu-dev libicu-le-hb-dev libicu-le-hb0
libicu60 libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpdec2 libnl-3-200
libnl-route-3-200 libopenmpi-dev libopenmpi3 libpciaccess0 libpcre16-3
libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpmix2 libpstreams-dev
libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libsigsegv2
libssl1.0.2 libterm-readkey-perl libtext-wrapper-perl libtool libxml2 m4
man-db mime-support ocl-icd-libopencl1 openmpi-bin openmpi-common
openssh-client pkg-config po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3.6 python3.6-minimal
sbuild-build-depends-murasaki-dummy zlib1g-dev
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libpcre3 libstdc++-8-dev libstdc++6 libubsan1
14 upgraded, 113 newly installed, 0 to remove and 67 not upgraded.
Need to get 69.1 MB/78.3 MB of archives.
After this operation, 321 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IDQ5wN/apt_archive ./ sbuild-build-depends-murasaki-dummy 0.invalid.0 [924 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.2.0-7+rpi1 [30.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-7+rpi1 [187 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-7+rpi1 [36.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-7+rpi1 [63.9 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-7+rpi1 [8096 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-7+rpi1 [318 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-7+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-7+rpi1 [5939 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-7+rpi1 [1562 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-7+rpi1 [594 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-7+rpi1 [5844 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-7+rpi1 [5473 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-7+rpi1 [325 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2 [1161 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.6-1 [565 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.6-1 [1383 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.6-1 [36.4 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.6-1 [1638 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.6-1 [234 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.6-1 [19.8 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.6-1 [47.5 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpcre3 armhf 2:8.39-11+rpi1 [313 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2o-1 [888 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20180525-1 [70.6 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.3 [12.2 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.16.1-1 [59.3 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.16.1-1 [117 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.16.1-1 [268 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.16.1-1 [135 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf openssh-client armhf 1:7.8p1-1 [673 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-4 [547 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.043-1 [20.2 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.043-1 [12.1 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.9.0-1+rpi1 [877 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.4.1 [989 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.58.0-1 [78.2 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.58.0-1 [143 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.9.0-1+rpi1 [657 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.9.0-1+rpi1 [665 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 20.0-1 [43.2 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf ibverbs-providers armhf 20.0-1 [19.9 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-10 [7003 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libboost-system1.62.0 armhf 1.62.0+dfsg-10 [32.7 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libboost-filesystem1.62.0 armhf 1.62.0+dfsg-10 [58.0 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libboost-system1.62-dev armhf 1.62.0+dfsg-10 [33.9 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libboost-filesystem1.62-dev armhf 1.62.0+dfsg-10 [62.4 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libboost-filesystem-dev armhf 1.62.0.1+b8 [3732 B]
Get:78 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-10 [232 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.9.0-1+rpi1 [650 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.58.1-2 [1105 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.58.1-2 [114 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.6-1 [79.1 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.6-1 [144 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.58.1-2 [151 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-11+rpi1 [234 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-11+rpi1 [227 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-11+rpi1 [150 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-11+rpi1 [565 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.58.1-2 [1237 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.12-1 [22.6 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.9.0-1+rpi1 [944 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-10 [325 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-10 [49.9 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-10 [57.8 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b8 [3694 B]
Get:99 http://172.17.0.1/private buster-staging/main armhf libcrypto++6 armhf 5.6.4-8 [750 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libcrypto++-dev armhf 5.6.4-8 [1354 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-7+rpi1 [205 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-4 [387 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.11-2+rpi1 [86.0 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-4 [159 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.11-2+rpi1 [142 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.11-2+rpi1 [16.0 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 20.0-1 [108 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libpmix2 armhf 3.0.2-2 [344 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libopenmpi3 armhf 3.1.2-4+rpi1 [2068 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 3.1.2-4+rpi1 [162 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf openmpi-bin armhf 3.1.2-4+rpi1 [194 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 3.1.2-4+rpi1 [954 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf libpstreams-dev all 1.0.1-2 [129 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libterm-readkey-perl armhf 2.37-1+b1 [26.6 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libtext-wrapper-perl all 1.05-2 [11.0 kB]
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update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: error: no alternatives for mpi
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libboost-iostreams-dev:armhf (1.62.0.1+b8) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up sbuild-build-depends-murasaki-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.2.0-7+rpi1 gcc-8_8.2.0-7+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.2.0-7+rpi1 libstdc++6_8.2.0-7+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.2.0-7+rpi1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.4.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.043-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 g++_4:8.1.0-1+rpi1 g++-8_8.2.0-7+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-7+rpi1 gcc-8-base_8.2.0-7+rpi1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gir1.2-glib-2.0_1.58.0-1 gir1.2-harfbuzz-0.0_1.9.0-1+rpi1 gnupg_2.2.9-1+rpi1 gnupg-agent_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2 hostname_3.20 ibverbs-providers_20.0-1 icu-devtools_60.2-6 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.6.3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-7+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-7+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.31.1-2+rpi1 libblkid1_2.32.1-0.1 libboost-filesystem-dev_1.62.0.1+b8 libboost-filesystem1.62-dev_1.62.0+dfsg-10 libboost-filesystem1.62.0_1.62.0+dfsg-10 libboost-iostreams-dev_1.62.0.1+b8 libboost-iostreams1.62-dev_1.62.0+dfsg-10 libboost-iostreams1.62.0_1.62.0+dfsg-10 libboost-regex-dev_1.62.0.1+b8 libboost-regex1.62-dev_1.62.0+dfsg-10 libboost-regex1.62.0_1.62.0+dfsg-10 libboost-system1.62-dev_1.62.0+dfsg-10 libboost-system1.62.0_1.62.0+dfsg-10 libboost1.62-dev_1.62.0+dfsg-10 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-7+rpi1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcrypto++-dev_5.6.4-8 libcrypto++6_5.6.4-8 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libedit2_3.1-20180525-1 libelf1_0.170-0.5 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libexpat1_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.043-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.2.0-7+rpi1 libgcc1_1:8.2.0-7+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran5_8.2.0-7+rpi1 libgirepository-1.0-1_1.58.0-1 libglib2.0-0_2.58.1-2 libglib2.0-bin_2.58.1-2 libglib2.0-data_2.58.1-2 libglib2.0-dev_2.58.1-2 libglib2.0-dev-bin_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.2.0-7+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libgraphite2-dev_1.3.12-1 libgssapi-krb5-2_1.16.1-1 libharfbuzz-dev_1.9.0-1+rpi1 libharfbuzz-gobject0_1.9.0-1+rpi1 libharfbuzz-icu0_1.9.0-1+rpi1 libharfbuzz0b_1.9.0-1+rpi1 libhogweed4_3.4-1 libhwloc-dev_1.11.11-2+rpi1 libhwloc-plugins_1.11.11-2+rpi1 libhwloc5_1.11.11-2+rpi1 libibverbs-dev_20.0-1 libibverbs1_20.0-1 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjs-jquery_3.2.1-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 libltdl-dev_2.4.6-4 libltdl7_2.4.6-4 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnl-3-200_3.4.0-1 libnl-route-3-200_3.4.0-1 libnpth0_1.6-1 libnss-systemd_239-7 libopenmpi-dev_3.1.2-4+rpi1 libopenmpi3_3.1.2-4+rpi1 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_239-7 libpam0g_1.1.8-3.7 libpciaccess0_0.14-1 libpcre16-3_2:8.39-11+rpi1 libpcre3_2:8.39-11+rpi1 libpcre3-dev_2:8.39-11+rpi1 libpcre32-3_2:8.39-11+rpi1 libpcrecpp0v5_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpmix2_3.0.2-2 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpstreams-dev_1.0.1-2 libpython3-stdlib_3.6.6-1 libpython3.6-minimal_3.6.6-1 libpython3.6-stdlib_3.6.6-1 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssl1.0.2_1.0.2o-1 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.2.0-7+rpi1 libstdc++6_8.2.0-7+rpi1 libsystemd0_239-7 libtasn1-6_4.13-3 libterm-readkey-perl_2.37-1+b1 libtext-wrapper-perl_1.05-2 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-4 libubsan1_8.2.0-7+rpi1 libudev1_239-7 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mime-support_3.61 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 ocl-icd-libopencl1_2.2.12-1 openmpi-bin_3.1.2-4+rpi1 openmpi-common_3.1.2-4+rpi1 openssh-client_1:7.8p1-1 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python3_3.6.6-1 python3-distutils_3.6.6-1 python3-lib2to3_3.6.6-1 python3-minimal_3.6.6-1 python3.6_3.6.6-1 python3.6-minimal_3.6.6-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-murasaki-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-7 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Jul 14 14:02:44 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-7.dsc
dpkg-source: info: extracting murasaki in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz
dpkg-source: info: unpacking murasaki_1.68.6-7.debian.tar.xz
dpkg-source: info: applying use_proper_libboost_names.patch
dpkg-source: info: applying include_libpstream.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying man_syntax.patch
dpkg-source: info: applying freebsd.patch
dpkg-source: info: applying gcc-6.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.68.6-7+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-85adf697-d77b-4a6a-8ee7-5ed663b02822
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package murasaki
dpkg-buildpackage: info: source version 1.68.6-7+b1
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build murasaki-1.68.6
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf *.o *~ .*~ core
make -C src clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- USE_MPI=YES
make -j4 "INSTALL=install --strip-program=true" USE_MPI=YES
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C src all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c timing.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c msethash.cc
dinkymath.cc: In function 'std::__cxx11::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
dinkymath.cc: In function 'std::__cxx11::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
sequence.cc: In destructor 'Sequence::~Sequence()':
sequence.cc:377:123: warning: throw will always call terminate() [-Wterminate]
throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno));
^
sequence.cc:377:123: note: in C++11 destructors default to noexcept
sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)':
sequence.cc:1113:136: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
struct pair
^~~~
sequence.cc:1114:97: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
struct pair
^~~~
sequence.cc: In destructor 'BitSequence::~BitSequence()':
sequence.cc:1394:133: warning: throw will always call terminate() [-Wterminate]
throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno));
^
sequence.cc:1394:133: note: in C++11 destructors default to noexcept
sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
SeqPos shortest=0,shortlen=length(spaces[0]);
^~~~~~~~
murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
bool revZero=false;
^~~~~~~
In file included from sequence.h:44,
from murasaki.h:24,
from sequence.cc:28:
shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]':
shmvector.hh:282:5: required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]'
sequence.cc:1110:39: required from here
shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<long int, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: 'struct std::pair<long int, long int>' declared here
struct pair
^~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c options.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecohash.cc
In file included from /usr/include/c++/8/vector:69,
from murasaki.cc:31:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from murasaki.cc:31:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void MurasakiRuntime::prep()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecolist.cc
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const HashMethod&}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' {aka '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c arrayhash.cc
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {HashMethod}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' {aka '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >'} changed in GCC 7.1
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c seqread.cc
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_vector.h: In member function 'double HashMethod::fitnessCheck()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
murasaki_mpi.cc: In function 'void mpi_types_init()':
murasaki_mpi.cc:107:28: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.key,disp);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:107:28: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.key,disp);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:108:32: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.seqno,disp+1);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:108:32: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.seqno,disp+1);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:109:30: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.pos,disp+1);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:109:30: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.pos,disp+1);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:112:61: warning: 'int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations]
MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here
OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[],
^~~~~~~~~~~~~~~
murasaki_mpi.cc:112:61: warning: 'int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations]
MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here
OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[],
^~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)':
murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable]
int send_done;
^~~~~~~~~
murasaki_mpi.cc: In function 'word mpi_extract_checkSentQueue(std::vector<std::__cxx11::list<AnchorBlock*> >&, std::vector<std::_Rb_tree_iterator<std::pair<const int, int> > >&, std::multimap<int, int>&)':
murasaki_mpi.cc:1025:18: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated]
packetsLeft++;
^~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/vector.tcc: In member function 'void BitSequence::compileHashFunc()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c scoring.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c openhash.cc
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/c++/8/bits/stl_vector.h: In function 'void mpi_types_init()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c genopts.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c binseq.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-image.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr.cc
cgr.cc: In member function 'void Cgr::merge(Cgr&)':
cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
int redist=(unsigned long)(rez*rez)<=seedcount;
^~~~~~
cgr.cc: In member function 'bool Cgr::savePNG(std::__cxx11::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
int res;
^~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
int wordwidth=1;
^~~~~~~~~
binseq.cc: In member function 'bool SequenceBinary::save(std::__cxx11::string)':
binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
}catch(ofstream::failure e){
^
binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()':
binseq.cc:158:67: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
binseq.cc:160:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
binseq.cc:162:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c testeco.cc
In file included from /usr/include/c++/8/map:60,
from cgr-compare.cc:30:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from cgr-compare.cc:30:
/usr/include/c++/8/bits/stl_map.h: In function 'void doSubsets(CgrSet, std::__cxx11::list<std::vector<std::pair<PgmBuffer*, std::__cxx11::basic_string<char> > > >)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In function 'void doNwise(CgrSet, CgrSet, unsigned int)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
cgr-sample.cc: In function 'int main(int, char**)':
cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
bool repeatmask=false,save=false;
^~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-compare.cc
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:43: warning: left shift count >= width of type [-Wshift-count-overflow]
return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
^~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c alignments.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-or.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c geneparse.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-and.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-best.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c getsegments.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c mbfa.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
align-coverage.cc: In function 'int main(int, char**)':
align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
bool seqStats=true;
^~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, std::__cxx11::string)':
getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=]
}catch(bad_lexical_cast e){
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \
mv ${bin} ${bin}-mpi ; \
done
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf *.o *~ .*~ core
make -C src clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -- USE_MPI=NO
make -j4 "INSTALL=install --strip-program=true" USE_MPI=NO
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C src all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c timing.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c msethash.cc
dinkymath.cc: In function 'std::__cxx11::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
dinkymath.cc: In function 'std::__cxx11::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)':
sequence.cc:1113:136: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
struct pair
^~~~
sequence.cc:1114:97: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
struct pair
^~~~
sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
SeqPos shortest=0,shortlen=length(spaces[0]);
^~~~~~~~
murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
bool revZero=false;
^~~~~~~
In file included from sequence.h:44,
from murasaki.h:24,
from sequence.cc:28:
shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]':
shmvector.hh:282:5: required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]'
sequence.cc:1110:39: required from here
shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<long int, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: 'struct std::pair<long int, long int>' declared here
struct pair
^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c options.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecohash.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecolist.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c arrayhash.cc
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const HashMethod&}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' {aka '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c seqread.cc
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {HashMethod}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' {aka '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >'} changed in GCC 7.1
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c scoring.cc
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_vector.h: In member function 'double HashMethod::fitnessCheck()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c openhash.cc
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/vector.tcc: In member function 'void BitSequence::compileHashFunc()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c genopts.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c binseq.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-image.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr.cc
binseq.cc: In member function 'bool SequenceBinary::save(std::__cxx11::string)':
binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
}catch(ofstream::failure e){
^
binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()':
binseq.cc:158:67: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
binseq.cc:160:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
binseq.cc:162:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:198:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
cgr.cc: In member function 'void Cgr::merge(Cgr&)':
cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
int redist=(unsigned long)(rez*rez)<=seedcount;
^~~~~~
cgr.cc: In member function 'bool Cgr::savePNG(std::__cxx11::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
int res;
^~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
int wordwidth=1;
^~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc
In file included from /usr/include/c++/8/map:60,
from cgr-compare.cc:30:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from cgr-compare.cc:30:
/usr/include/c++/8/bits/stl_map.h: In function 'void doSubsets(CgrSet, std::__cxx11::list<std::vector<std::pair<PgmBuffer*, std::__cxx11::basic_string<char> > > >)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In function 'void doNwise(CgrSet, CgrSet, unsigned int)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c testeco.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-compare.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c alignments.cc
cgr-sample.cc: In function 'int main(int, char**)':
cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
bool repeatmask=false,save=false;
^~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-or.cc
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:43: warning: left shift count >= width of type [-Wshift-count-overflow]
return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
^~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c geneparse.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-and.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-best.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c getsegments.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c mbfa.cc
align-coverage.cc: In function 'int main(int, char**)':
align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
bool seqStats=true;
^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, std::__cxx11::string)':
getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=]
}catch(bad_lexical_cast e){
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install -a
# using wildcards in install files is practical but it duplicates some files
find debian/murasaki/usr -name "*-mpi" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
debian/rules override_dh_link
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_link
mkdir -p debian/murasaki-mpi/usr/share/man/man1
for man in debian/murasaki/usr/share/man/man1/* ; do \
ln -s `basename ${man}`.gz debian/murasaki-mpi/usr/share/man/man1/`basename ${man} .1`-mpi.1.gz ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-random contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/geneparse-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-coverage contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/testeco contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-sample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/murasaki-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-and contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-image contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/mbfa-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/murasaki contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-random-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/mbfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/geneparse contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-best contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-or contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/murasaki-mpi/usr/bin/geneparse-mpi debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi debian/murasaki-mpi/usr/bin/murasaki-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi debian/murasaki-mpi/usr/bin/mbfa-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-random-mpi debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi were not linked against libmpi_cxx.so.40 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package murasaki-mpi: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: package murasaki-mpi: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-7+b1_armhf.deb'.
dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-7+b1_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-7+b1_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-7+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../murasaki_1.68.6-7+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build murasaki-1.68.6
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-10-10T11:10:48Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
murasaki_1.68.6-7+b1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Sat, 14 Jul 2018 15:54:27 +0200
Source: murasaki (1.68.6-7)
Binary: murasaki murasaki-mpi murasaki-common
Binary-Only: yes
Architecture: armhf
Version: 1.68.6-7+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
murasaki - homology detection tool across multiple large genomes
murasaki-common - homology detection tool across multiple large genomes (common fil
murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio
Changes:
murasaki (1.68.6-7+b1) buster-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
murasaki-dbgsym_1.68.6-7+b1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 14291016 bytes: control archive=1148 bytes.
887 bytes, 12 lines control
1378 bytes, 13 lines md5sums
Package: murasaki-dbgsym
Source: murasaki (1.68.6-7)
Version: 1.68.6-7+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 15126
Depends: murasaki (= 1.68.6-7+b1)
Section: debug
Priority: optional
Description: debug symbols for murasaki
Build-Ids: 04cffd0dfccf9568c907561f3394fd11352a7dbe 15967abed570f0c2868d3252767c2e6adf06d607 3a17b855de9889eb45edcc3e52c4165c0c53d5ce 48b471df55fdaded816d3205decc628eaa53790d 4bd53212106fdfdd1187f3cb9d18ba52b17f65ce 5ea99175e8ca4ec0b7bd30c0615531650723c502 861ef15a0e2f5d24b9a5d4f1f38399feecdbe578 b14c0bd5c8afc8e638ea93da048b90e2926cb473 bdac9cafc13a834191e20be76b591dc595768196 d2b1da78f6344c18a32721c41d618023fc3df7db d35c80d9a09c4427ca2d9d8fff39e74bf4f6ee88 dce38d88616841feaa96e57b7dcd851b4721b75d ecbcb05e28dbd828dd5e08d8e49e1e8c18d99bd1
drwxr-xr-x root/root 0 2018-07-14 13:54 ./
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/04/
-rw-r--r-- root/root 615704 2018-07-14 13:54 ./usr/lib/debug/.build-id/04/cffd0dfccf9568c907561f3394fd11352a7dbe.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/15/
-rw-r--r-- root/root 1237160 2018-07-14 13:54 ./usr/lib/debug/.build-id/15/967abed570f0c2868d3252767c2e6adf06d607.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/3a/
-rw-r--r-- root/root 943184 2018-07-14 13:54 ./usr/lib/debug/.build-id/3a/17b855de9889eb45edcc3e52c4165c0c53d5ce.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/48/
-rw-r--r-- root/root 571948 2018-07-14 13:54 ./usr/lib/debug/.build-id/48/b471df55fdaded816d3205decc628eaa53790d.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/4b/
-rw-r--r-- root/root 490188 2018-07-14 13:54 ./usr/lib/debug/.build-id/4b/d53212106fdfdd1187f3cb9d18ba52b17f65ce.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/5e/
-rw-r--r-- root/root 1606132 2018-07-14 13:54 ./usr/lib/debug/.build-id/5e/a99175e8ca4ec0b7bd30c0615531650723c502.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/86/
-rw-r--r-- root/root 1263064 2018-07-14 13:54 ./usr/lib/debug/.build-id/86/1ef15a0e2f5d24b9a5d4f1f38399feecdbe578.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/b1/
-rw-r--r-- root/root 3671704 2018-07-14 13:54 ./usr/lib/debug/.build-id/b1/4c0bd5c8afc8e638ea93da048b90e2926cb473.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/bd/
-rw-r--r-- root/root 1119420 2018-07-14 13:54 ./usr/lib/debug/.build-id/bd/ac9cafc13a834191e20be76b591dc595768196.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/d2/
-rw-r--r-- root/root 926768 2018-07-14 13:54 ./usr/lib/debug/.build-id/d2/b1da78f6344c18a32721c41d618023fc3df7db.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/d3/
-rw-r--r-- root/root 1161092 2018-07-14 13:54 ./usr/lib/debug/.build-id/d3/5c80d9a09c4427ca2d9d8fff39e74bf4f6ee88.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/dc/
-rw-r--r-- root/root 866788 2018-07-14 13:54 ./usr/lib/debug/.build-id/dc/e38d88616841feaa96e57b7dcd851b4721b75d.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/debug/.build-id/ec/
-rw-r--r-- root/root 986092 2018-07-14 13:54 ./usr/lib/debug/.build-id/ec/bcb05e28dbd828dd5e08d8e49e1e8c18d99bd1.debug
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-07-14 13:54 ./usr/share/doc/murasaki-dbgsym -> murasaki
murasaki-mpi-dbgsym_1.68.6-7+b1_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 15290084 bytes: control archive=1164 bytes.
899 bytes, 12 lines control
1378 bytes, 13 lines md5sums
Package: murasaki-mpi-dbgsym
Source: murasaki (1.68.6-7)
Version: 1.68.6-7+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 16125
Depends: murasaki-mpi (= 1.68.6-7+b1)
Section: debug
Priority: optional
Description: debug symbols for murasaki-mpi
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drwxr-xr-x root/root 0 2018-07-14 13:54 ./
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drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-07-14 13:54 ./usr/share/doc/murasaki-mpi-dbgsym -> murasaki-mpi
murasaki-mpi_1.68.6-7+b1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 377904 bytes: control archive=1564 bytes.
1411 bytes, 28 lines control
1203 bytes, 18 lines md5sums
Package: murasaki-mpi
Source: murasaki (1.68.6-7)
Version: 1.68.6-7+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2454
Depends: murasaki-common, libboost-filesystem1.62.0, libboost-iostreams1.62.0, libboost-regex1.62.0 (>= 1.62.0+dfsg-5.1), libboost-system1.62.0, libc6 (>= 2.4), libcrypto++6, libgcc1 (>= 1:3.5), libopenmpi3, libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Description: homology detection tool across multiple large genomes (MPI-version)
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
scale multiple genome global alignments. Supports unlimited length
gapped-seed patterns and unique TF-IDF based filtering.
.
Murasaki is an anchor alignment software, which is
* exteremely fast (17 CPU hours for whole Human x Mouse genome (with
40 nodes: 52 wall minutes))
* scalable (Arbitrarily parallelizable across multiple nodes using MPI.
Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
* unlimited pattern length
* repeat tolerant
* intelligent noise reduction
.
This package provides the MPI-enabled binary for murasaki. While this
will speed up operation on multi-processor machines it will slow down
on a single processor.
drwxr-xr-x root/root 0 2018-07-14 13:54 ./
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/bin/
-rwxr-xr-x root/root 186056 2018-07-14 13:54 ./usr/bin/geneparse-mpi
-rwxr-xr-x root/root 218760 2018-07-14 13:54 ./usr/bin/mbfa-mpi
-rwxr-xr-x root/root 568088 2018-07-14 13:54 ./usr/bin/murasaki-mpi
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/murasaki/
-rwxr-xr-x root/root 149096 2018-07-14 13:54 ./usr/lib/murasaki/align-and-mpi
-rwxr-xr-x root/root 157304 2018-07-14 13:54 ./usr/lib/murasaki/align-best-mpi
-rwxr-xr-x root/root 169616 2018-07-14 13:54 ./usr/lib/murasaki/align-compare-mpi
-rwxr-xr-x root/root 231048 2018-07-14 13:54 ./usr/lib/murasaki/align-coverage-mpi
-rwxr-xr-x root/root 149080 2018-07-14 13:54 ./usr/lib/murasaki/align-or-mpi
-rwxr-xr-x root/root 75340 2018-07-14 13:54 ./usr/lib/murasaki/cgr-compare-mpi
-rwxr-xr-x root/root 227012 2018-07-14 13:54 ./usr/lib/murasaki/cgr-image-mpi
-rwxr-xr-x root/root 7138 2010-08-24 14:18 ./usr/lib/murasaki/cgr-image.pl-mpi
-rwxr-xr-x root/root 79456 2018-07-14 13:54 ./usr/lib/murasaki/cgr-random-mpi
-rwxr-xr-x root/root 222892 2018-07-14 13:54 ./usr/lib/murasaki/cgr-sample-mpi
-rwxr-xr-x root/root 46604 2018-07-14 13:54 ./usr/lib/murasaki/testeco-mpi
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/doc/murasaki-mpi/
-rw-r--r-- root/root 249 2018-07-14 13:54 ./usr/share/doc/murasaki-mpi/README.test
-rw-r--r-- root/root 222 2018-07-14 13:54 ./usr/share/doc/murasaki-mpi/changelog.Debian.armhf.gz
-rw-r--r-- root/root 818 2018-07-14 13:54 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz
-rw-r--r-- root/root 2221 2018-07-14 13:54 ./usr/share/doc/murasaki-mpi/copyright
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/man/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2018-07-14 13:54 ./usr/share/man/man1/geneparse-mpi.1.gz -> geneparse.1.gz
lrwxrwxrwx root/root 0 2018-07-14 13:54 ./usr/share/man/man1/mbfa-mpi.1.gz -> mbfa.1.gz
lrwxrwxrwx root/root 0 2018-07-14 13:54 ./usr/share/man/man1/murasaki-mpi.1.gz -> murasaki.1.gz
murasaki_1.68.6-7+b1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 360144 bytes: control archive=1500 bytes.
1210 bytes, 24 lines control
1265 bytes, 20 lines md5sums
Package: murasaki
Source: murasaki (1.68.6-7)
Version: 1.68.6-7+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2377
Depends: murasaki-common, libboost-filesystem1.62.0, libboost-iostreams1.62.0, libboost-regex1.62.0 (>= 1.62.0+dfsg-5.1), libboost-system1.62.0, libc6 (>= 2.4), libcrypto++6, libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Description: homology detection tool across multiple large genomes
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
scale multiple genome global alignments. Supports unlimited length
gapped-seed patterns and unique TF-IDF based filtering.
.
Murasaki is an anchor alignment software, which is
* exteremely fast (17 CPU hours for whole Human x Mouse genome (with
40 nodes: 52 wall minutes))
* scalable (Arbitrarily parallelizable across multiple nodes using MPI.
Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
* unlimited pattern length
* repeat tolerant
* intelligent noise reduction
drwxr-xr-x root/root 0 2018-07-14 13:54 ./
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/bin/
-rwxr-xr-x root/root 186056 2018-07-14 13:54 ./usr/bin/geneparse
-rwxr-xr-x root/root 218760 2018-07-14 13:54 ./usr/bin/mbfa
-rwxr-xr-x root/root 482056 2018-07-14 13:54 ./usr/bin/murasaki
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drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/lib/murasaki/
-rwxr-xr-x root/root 149096 2018-07-14 13:54 ./usr/lib/murasaki/align-and
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-rwxr-xr-x root/root 169616 2018-07-14 13:54 ./usr/lib/murasaki/align-compare
-rwxr-xr-x root/root 231048 2018-07-14 13:54 ./usr/lib/murasaki/align-coverage
-rwxr-xr-x root/root 149080 2018-07-14 13:54 ./usr/lib/murasaki/align-or
-rwxr-xr-x root/root 75340 2018-07-14 13:54 ./usr/lib/murasaki/cgr-compare
-rwxr-xr-x root/root 227012 2018-07-14 13:54 ./usr/lib/murasaki/cgr-image
-rwxr-xr-x root/root 79456 2018-07-14 13:54 ./usr/lib/murasaki/cgr-random
-rwxr-xr-x root/root 222892 2018-07-14 13:54 ./usr/lib/murasaki/cgr-sample
-rwxr-xr-x root/root 46604 2018-07-14 13:54 ./usr/lib/murasaki/testeco
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/doc/murasaki/
-rw-r--r-- root/root 249 2018-07-14 13:54 ./usr/share/doc/murasaki/README.test
-rw-r--r-- root/root 222 2018-07-14 13:54 ./usr/share/doc/murasaki/changelog.Debian.armhf.gz
-rw-r--r-- root/root 818 2018-07-14 13:54 ./usr/share/doc/murasaki/changelog.Debian.gz
-rw-r--r-- root/root 2221 2018-07-14 13:54 ./usr/share/doc/murasaki/copyright
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/man/
drwxr-xr-x root/root 0 2018-07-14 13:54 ./usr/share/man/man1/
-rw-r--r-- root/root 2518 2018-07-14 13:54 ./usr/share/man/man1/geneparse.1.gz
-rw-r--r-- root/root 2721 2018-07-14 13:54 ./usr/share/man/man1/mbfa.1.gz
-rw-r--r-- root/root 10887 2018-07-14 13:54 ./usr/share/man/man1/murasaki.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 207104
Build-Time: 240
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 340
Job: murasaki_1.68.6-7
Machine Architecture: armhf
Package: murasaki
Package-Time: 605
Source-Version: 1.68.6-7
Space: 207104
Status: successful
Version: 1.68.6-7+b1
--------------------------------------------------------------------------------
Finished at 2018-10-10T11:10:48Z
Build needed 00:10:05, 207104k disk space