murasaki →
1.68.6-6+b5 →
armhf → 2017-10-13 11:47:24
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| murasaki 1.68.6-6+b5 (armhf) Fri, 13 Oct 2017 11:22:19 +0000 |
+==============================================================================+
Package: murasaki
Version: 1.68.6-6+b5
Source Version: 1.68.6-6
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-da7c2e4e-1d23-441a-a7f0-81950b3b2cb9' 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 [10.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.1 MB]
Fetched 22.4 MB in 8s (2786 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://anonscm.debian.org/git/debian-med/murasaki.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/murasaki.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 317 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main murasaki 1.68.6-6 (dsc) [2213 B]
Get:2 http://172.17.0.1/private buster-staging/main murasaki 1.68.6-6 (tar) [308 kB]
Get:3 http://172.17.0.1/private buster-staging/main murasaki 1.68.6-6 (diff) [6920 B]
Fetched 317 kB in 0s (1059 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/murasaki-JlGhtE/murasaki-1.68.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/murasaki-JlGhtE' 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-x1UmnC/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-x1UmnC/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-x1UmnC/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-x1UmnC/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (7906 B/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 libreadline5 libsasl2-modules libssl1.1 openssl
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 35 not upgraded.
Need to get 770 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 770 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15082 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 (>= 9), 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 (>= 9), 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-x1UmnC/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-x1UmnC/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ Sources [560 B]
Get:5 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ Packages [642 B]
Fetched 2535 B in 0s (9973 B/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 libreadline5 libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-7 debhelper
dh-autoreconf dh-strip-nondeterminism file g++-7 gcc-7 gcc-7-base gettext
gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl
libasan4 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 libcilkrts5 libcroco3 libcrypto++-dev
libcrypto++6 libfile-stripnondeterminism-perl libgcc-7-dev libgcc1
libgfortran4 libglib2.0-0 libgomp1 libhwloc-dev libhwloc-plugins libhwloc5
libibverbs-dev libibverbs1 libicu-dev libicu57 libjs-jquery libltdl-dev
libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi2 libpciaccess0 libpipeline1 libpstreams-dev libsigsegv2
libstdc++-7-dev libstdc++6 libterm-readkey-perl libtext-wrapper-perl
libtimedate-perl libtool libubsan0 libxml2 m4 man-db ocl-icd-libopencl1
openmpi-common po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-7-locales dh-make gcc-7-doc libstdc++6-7-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan4-dbg liblsan0-dbg
libtsan0-dbg libubsan0-dbg libcilkrts5-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 libhwloc-contrib-plugins
icu-doc libtool-doc openmpi-doc pciutils libstdc++-7-doc gfortran
| fortran95-compiler gcj-jdk m4-doc less www-browser opencl-icd
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs javascript-common openmpi-bin libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
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 libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0
libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1
libicu-dev libicu57 libjs-jquery libltdl-dev libltdl7 libmagic-mgc libmagic1
libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi2 libpciaccess0
libpipeline1 libpstreams-dev libsigsegv2 libterm-readkey-perl
libtext-wrapper-perl libtimedate-perl libtool libxml2 m4 man-db
ocl-icd-libopencl1 openmpi-common po-debconf
sbuild-build-depends-murasaki-dummy
The following packages will be upgraded:
cpp-7 g++-7 gcc-7 gcc-7-base libasan4 libatomic1 libcc1-0 libcilkrts5
libgcc-7-dev libgcc1 libgomp1 libstdc++-7-dev libstdc++6 libubsan0
14 upgraded, 65 newly installed, 0 to remove and 21 not upgraded.
Need to get 68.6 MB of archives.
After this operation, 15.1 MB disk space will be freed.
Get:1 copy:/<<BUILDDIR>>/resolver-x1UmnC/apt_archive ./ sbuild-build-depends-murasaki-dummy 0.invalid.0 [842 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 7.2.0-8 [63.5 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf gcc-7-base armhf 7.2.0-8 [181 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:7.2.0-8 [38.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 7.2.0-8 [6726 B]
Get:6 http://172.17.0.1/private buster-staging/main armhf libasan4 armhf 7.2.0-8 [302 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libubsan0 armhf 7.2.0-8 [106 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libcilkrts5 armhf 7.2.0-8 [35.4 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf cpp-7 armhf 7.2.0-8 [5136 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 7.2.0-8 [30.2 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-7 armhf 7.2.0-8 [5593 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf gcc-7 armhf 7.2.0-8 [5457 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-7-dev armhf 7.2.0-8 [670 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libstdc++-7-dev armhf 7.2.0-8 [1499 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 7.2.0-8 [335 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-2 [95.8 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-4 [609 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.8 [973 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 57.1-6 [156 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4+b1 [7053 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libboost-system1.62.0 armhf 1.62.0+dfsg-4+b1 [32.4 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libboost-filesystem1.62.0 armhf 1.62.0+dfsg-4+b1 [58.3 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libboost-system1.62-dev armhf 1.62.0+dfsg-4+b1 [33.4 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libboost-filesystem1.62-dev armhf 1.62.0+dfsg-4+b1 [66.3 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libboost-filesystem-dev armhf 1.62.0.1+b8 [3732 B]
Get:52 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-4+b1 [232 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 57.1-6 [15.8 MB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-4+b1 [323 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-4+b1 [49.0 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-4+b1 [58.0 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b8 [3694 B]
Get:58 http://172.17.0.1/private buster-staging/main armhf libboost-regex-dev armhf 1.62.0.1+b8 [3960 B]
Get:59 http://172.17.0.1/private buster-staging/main armhf libcrypto++6 armhf 5.6.4-8 [750 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libcrypto++-dev armhf 5.6.4-8 [1354 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.2.0-8 [191 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-2 [386 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.8-1+rpi1 [85.6 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2 [159 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.8-1+rpi1 [140 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.13.4-1 [47.4 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf ocl-icd-libopencl1 armhf 2.2.11-1 [35.5 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.8-1+rpi1 [15.1 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libjs-jquery all 3.2.1-1 [154 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libnl-3-200 armhf 3.2.27-2 [53.7 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-200 armhf 3.2.27-2 [113 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpstreams-dev all 1.0.1-1 [129 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libterm-readkey-perl armhf 2.37-1+b1 [26.6 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libtext-wrapper-perl all 1.05-2 [11.0 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 1.2.1-2 [35.4 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 1.2.1-2 [104 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libopenmpi2 armhf 2.1.1-7+rpi1 [1744 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 2.1.1-7+rpi1 [154 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 2.1.1-7+rpi1 [1019 kB]
debconf: delaying package configuration, since apt-utils is not installed
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-3+rpi1 dpkg-dev_1.18.24 g++-7_7.2.0-8 gcc-7_7.2.0-8 libc6-dev_2.24-14 libstdc++-7-dev_7.2.0-8 libstdc++6_7.2.0-8 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch
Package versions: adduser_3.116 apt_1.5 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-3+rpi1 binutils-arm-linux-gnueabihf_2.29.1-3+rpi1 binutils-common_2.29.1-3+rpi1 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-8 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.8 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dirmngr_2.2.1-1 dmsetup_2:1.02.142-1 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.6-1 e2fsprogs_1.43.6-1 fakeroot_1.22-1 fdisk_2.29.2-5 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-8 gcc_4:7.2.0-1d1 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_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-8 gcc-7-base_7.2.0-8 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-1 gnupg-agent_2.2.1-1 gnupg-l10n_2.2.1-1 gnupg-utils_2.2.1-1 gpg_2.2.1-1 gpg-agent_2.2.1-1 gpg-wks-client_2.2.1-1 gpg-wks-server_2.2.1-1 gpgconf_2.2.1-1 gpgsm_2.2.1-1 gpgv_2.2.1-1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-6 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-11 libapt-pkg5.0_1.5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-8 libassuan0_2.4.3-3 libatomic1_7.2.0-8 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libbinutils_2.29.1-3+rpi1 libblkid1_2.29.2-5 libboost-filesystem-dev_1.62.0.1+b8 libboost-filesystem1.62-dev_1.62.0+dfsg-4+b1 libboost-filesystem1.62.0_1.62.0+dfsg-4+b1 libboost-iostreams-dev_1.62.0.1+b8 libboost-iostreams1.62-dev_1.62.0+dfsg-4+b1 libboost-iostreams1.62.0_1.62.0+dfsg-4+b1 libboost-regex-dev_1.62.0.1+b8 libboost-regex1.62-dev_1.62.0+dfsg-4+b1 libboost-regex1.62.0_1.62.0+dfsg-4+b1 libboost-system1.62-dev_1.62.0+dfsg-4+b1 libboost-system1.62.0_1.62.0+dfsg-4+b1 libboost1.62-dev_1.62.0+dfsg-4+b1 libbsd0_0.8.6-2 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-14 libc-dev-bin_2.24-14 libc6_2.24-14 libc6-dev_2.24-14 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.2.0-8 libcilkrts5_7.2.0-8 libcomerr2_1.43.6-1 libcroco3_0.6.12-1 libcrypto++-dev_5.6.4-8 libcrypto++6_5.6.4-8 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.16+really1.10.22-1 libdebconfclient0_0.230 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.18.24 libdrm-common_2.4.82-1+rpi1 libdrm2_2.4.82-1+rpi1 libfakeroot_1.22-1 libfdisk1_2.29.2-5 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-7-dev_7.2.0-8 libgcc1_1:7.2.0-8 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libgfortran4_7.2.0-8 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.15-2 libgomp1_7.2.0-8 libgpg-error0_1.27-3 libhogweed4_3.3-2 libhwloc-dev_1.11.8-1+rpi1 libhwloc-plugins_1.11.8-1+rpi1 libhwloc5_1.11.8-1+rpi1 libibverbs-dev_1.2.1-2 libibverbs1_1.2.1-2 libicu-dev_57.1-6 libicu57_57.1-6 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2 libisl15_0.18-1 libjs-jquery_3.2.1-1 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.29.2-5 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnl-3-200_3.2.27-2 libnl-route-3-200_3.2.27-2 libnpth0_1.5-2 libopenmpi-dev_2.1.1-7+rpi1 libopenmpi2_2.1.1-7+rpi1 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpciaccess0_0.13.4-1 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.0-8 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.32-3 libprocps6_2:3.3.12-3 libpstreams-dev_1.0.1-1 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.29.2-5 libsqlite3-0_3.20.1-1 libss2_1.43.6-1 libssl1.1_1.1.0f-5 libstdc++-7-dev_7.2.0-8 libstdc++6_7.2.0-8 libsystemd0_234-3 libtasn1-6_4.12-2.1 libterm-readkey-perl_2.37-1+b1 libtext-wrapper-perl_1.05-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-8 libudev1_234-3 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-5 libxml2_2.9.4+dfsg1-4 linux-base_4.5 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch login_1:4.4-4.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-5 mountall_2.54 multiarch-support_2.24-14 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 ocl-icd-libopencl1_2.2.11-1 openmpi-common_2.1.1-7+rpi1 openssl_1.1.0f-5 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-8 perl-base_5.26.0-8 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-8 pinentry-curses_1.0.0-2 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-murasaki-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017b-2 udev_234-3 util-linux_2.29.2-5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Jul 12 07:30:27 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-6.dsc
dpkg-source: info: extracting murasaki in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz
dpkg-source: info: unpacking murasaki_1.68.6-6.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 1.68.6-6+b5
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-da7c2e4e-1d23-441a-a7f0-81950b3b2cb9
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package murasaki
dpkg-buildpackage: info: source version 1.68.6-6+b5
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 -j1 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_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- USE_MPI=YES
make -j1 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
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 /usr/include/c++/7/vector:69:0,
from murasaki.cc:31:
/usr/include/c++/7/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++/7/bits/vector.tcc:458:5: 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++/7/vector:64:0,
from murasaki.cc:31:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void MurasakiRuntime::prep()':
/usr/include/c++/7/bits/stl_vector.h:712:18: 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++/7/bits/stl_vector.h:712:18: 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 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
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;
^~~~
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
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 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]);
^~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/7/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++/7/bits/vector.tcc:458:5: 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++/7/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++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/7/bits/stl_vector.h: In member function 'double HashMethod::fitnessCheck()':
/usr/include/c++/7/bits/stl_vector.h:712:18: 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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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
/usr/include/c++/7/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
/usr/include/c++/7/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++/7/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++/7/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++/7/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
In file included from /usr/include/c++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/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++/7/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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/vector:69:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/7/bits/vector.tcc: In member function 'void BitSequence::compileHashFunc()':
/usr/include/c++/7/bits/vector.tcc:105:21: 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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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++/7/vector:64:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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 msethash.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 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
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
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
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:29:0:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1202:20: 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:29:0:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1202:20: 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:29:0:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1202:20: 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:29:0:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1819:20: note: declared here
OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[],
^~~~~~~~~~~~~~~
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++;
^~
In file included from /usr/include/c++/7/vector:69:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/c++/7/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++/7/bits/vector.tcc:458:5: 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++/7/vector:64:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/c++/7/bits/stl_vector.h: In function 'void mpi_types_init()':
/usr/include/c++/7/bits/stl_vector.h:712:18: 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 arrayhash.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 seqread.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 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
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 -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
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;
^~~~~~~~~
cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::__cxx11::string)':
cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
~~~~~~~^~~~~~~
cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
~~~~~~~^~~~~~~
cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
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
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 -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 -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 -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 -c cgr-sample.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;
^~~~~~~~~~
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 -c testeco.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 -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 -c align-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 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -c align-coverage.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;
^~~~~~~~
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 -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 -o ../getsegments getsegments.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 -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 ../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
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 -j1 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
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;
^~~~~~~
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
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;
^~~~
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
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]);
^~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/7/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++/7/bits/vector.tcc:458:5: 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++/7/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++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/7/bits/stl_vector.h: In member function 'double HashMethod::fitnessCheck()':
/usr/include/c++/7/bits/stl_vector.h:712:18: 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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/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++/7/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++/7/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++/7/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++/7/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++/7/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
/usr/include/c++/7/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
/usr/include/c++/7/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++/7/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++/7/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++/7/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
In file included from /usr/include/c++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/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++/7/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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/vector:69:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/7/bits/vector.tcc: In member function 'void BitSequence::compileHashFunc()':
/usr/include/c++/7/bits/vector.tcc:105:21: 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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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++/7/vector:64:0,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++/7/algorithm:62:0,
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++/7/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++/7/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++/7/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 msethash.cc
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
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
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
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
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 -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 -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
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;
^~~~~~~~~
cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::__cxx11::string)':
cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
~~~~~~~^~~~~~~
cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
~~~~~~~^~~~~~~
cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
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 -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 -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
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 -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 -c cgr-sample.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 -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 -c testeco.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 -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 -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
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 -c align-or.cc
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 -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 -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 -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 -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 -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 -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 -c align-coverage.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 ../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 -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 -o ../getsegments getsegments.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 -c mbfa.cc
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
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/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-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/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/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-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-random 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/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/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/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/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/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/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-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/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-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/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/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/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/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-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/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-and-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/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-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-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: package could avoid a useless dependency if debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi debian/murasaki-mpi/usr/bin/geneparse-mpi debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-random-mpi debian/murasaki-mpi/usr/bin/murasaki-mpi debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi debian/murasaki-mpi/usr/bin/mbfa-mpi debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi were not linked against libmpi_cxx.so.20 (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' in '../murasaki_1.68.6-6+b5_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-6+b5_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-6+b5_armhf.deb'.
dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-6+b5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../murasaki_1.68.6-6+b5_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 2017-10-13T11:47:19Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
murasaki_1.68.6-6+b5_armhf.changes:
-----------------------------------
Format: 1.8
Date: Thu, 30 Jun 2016 09:15:01 +0000
Source: murasaki (1.68.6-6)
Binary: murasaki murasaki-mpi murasaki-common
Binary-Only: yes
Architecture: armhf
Version: 1.68.6-6+b5
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 (1.68.6-6+b5) 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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552b63379f19c4d28726077c40af71b9 6595 science optional murasaki_1.68.6-6_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
murasaki-dbgsym_1.68.6-6+b5_armhf.deb
-------------------------------------
new debian package, version 2.0.
size 10942444 bytes: control archive=1115 bytes.
887 bytes, 12 lines control
1378 bytes, 13 lines md5sums
Package: murasaki-dbgsym
Source: murasaki (1.68.6-6)
Version: 1.68.6-6+b5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 11816
Depends: murasaki (= 1.68.6-6+b5)
Section: debug
Priority: optional
Description: debug symbols for murasaki
Build-Ids: 07aab6985399bfab21c33f64ec9646455e9a37cc 4266c97eec4282cce0945b9401b692e5d41c7b9a 7ab4a016ffd8534d92f4da81acc071deaf01c6e6 7d0154334ab6b7f1252ab45401585ba31fd13497 7e645d2ba975cf3e73ffd44d94abfe5c3d234020 8da05a06684772502c970f15b7aeca626945c015 b5bde7ef934e258609acc903e18cbfe3738317af b6d1a78bc9e1e37558853dd32767e447d4edf5e9 c14c69b94c64bbf12310aff334fd798f492daf50 cb8256860f179c3741491997b3c36e71cf6a17cf ccda5ce68c817468bb8307ecb9bd74602113773c d7a828b447c9bb9cb085b88c0bf691bd004a9149 fa0637917971070e80249c2d83d2cf1e18f8083b
drwxr-xr-x root/root 0 2016-06-30 09:15 ./
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/07/
-rw-r--r-- root/root 459108 2016-06-30 09:15 ./usr/lib/debug/.build-id/07/aab6985399bfab21c33f64ec9646455e9a37cc.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/42/
-rw-r--r-- root/root 767552 2016-06-30 09:15 ./usr/lib/debug/.build-id/42/66c97eec4282cce0945b9401b692e5d41c7b9a.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/7a/
-rw-r--r-- root/root 933344 2016-06-30 09:15 ./usr/lib/debug/.build-id/7a/b4a016ffd8534d92f4da81acc071deaf01c6e6.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/7d/
-rw-r--r-- root/root 476072 2016-06-30 09:15 ./usr/lib/debug/.build-id/7d/0154334ab6b7f1252ab45401585ba31fd13497.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/7e/
-rw-r--r-- root/root 756632 2016-06-30 09:15 ./usr/lib/debug/.build-id/7e/645d2ba975cf3e73ffd44d94abfe5c3d234020.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/8d/
-rw-r--r-- root/root 849536 2016-06-30 09:15 ./usr/lib/debug/.build-id/8d/a05a06684772502c970f15b7aeca626945c015.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/b5/
-rw-r--r-- root/root 1244220 2016-06-30 09:15 ./usr/lib/debug/.build-id/b5/bde7ef934e258609acc903e18cbfe3738317af.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/b6/
-rw-r--r-- root/root 800528 2016-06-30 09:15 ./usr/lib/debug/.build-id/b6/d1a78bc9e1e37558853dd32767e447d4edf5e9.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/c1/
-rw-r--r-- root/root 2781728 2016-06-30 09:15 ./usr/lib/debug/.build-id/c1/4c69b94c64bbf12310aff334fd798f492daf50.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/cb/
-rw-r--r-- root/root 943780 2016-06-30 09:15 ./usr/lib/debug/.build-id/cb/8256860f179c3741491997b3c36e71cf6a17cf.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/cc/
-rw-r--r-- root/root 661652 2016-06-30 09:15 ./usr/lib/debug/.build-id/cc/da5ce68c817468bb8307ecb9bd74602113773c.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/d7/
-rw-r--r-- root/root 974808 2016-06-30 09:15 ./usr/lib/debug/.build-id/d7/a828b447c9bb9cb085b88c0bf691bd004a9149.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/debug/.build-id/fa/
-rw-r--r-- root/root 422476 2016-06-30 09:15 ./usr/lib/debug/.build-id/fa/0637917971070e80249c2d83d2cf1e18f8083b.debug
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/doc/murasaki-dbgsym -> murasaki
murasaki-mpi-dbgsym_1.68.6-6+b5_armhf.deb
-----------------------------------------
new debian package, version 2.0.
size 11776700 bytes: control archive=1120 bytes.
899 bytes, 12 lines control
1378 bytes, 13 lines md5sums
Package: murasaki-mpi-dbgsym
Source: murasaki (1.68.6-6)
Version: 1.68.6-6+b5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 12635
Depends: murasaki-mpi (= 1.68.6-6+b5)
Section: debug
Priority: optional
Description: debug symbols for murasaki-mpi
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drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi-dbgsym -> murasaki-mpi
murasaki-mpi_1.68.6-6+b5_armhf.deb
----------------------------------
new debian package, version 2.0.
size 381320 bytes: control archive=1495 bytes.
1390 bytes, 28 lines control
1203 bytes, 18 lines md5sums
Package: murasaki-mpi
Source: murasaki (1.68.6-6)
Version: 1.68.6-6+b5
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, libboost-system1.62.0, libc6 (>= 2.4), libcrypto++6, libgcc1 (>= 1:3.5), libopenmpi2, 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 2016-06-30 09:15 ./
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/bin/
-rwxr-xr-x root/root 181960 2016-06-30 09:15 ./usr/bin/geneparse-mpi
-rwxr-xr-x root/root 218760 2016-06-30 09:15 ./usr/bin/mbfa-mpi
-rwxr-xr-x root/root 572184 2016-06-30 09:15 ./usr/bin/murasaki-mpi
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/murasaki/
-rwxr-xr-x root/root 149096 2016-06-30 09:15 ./usr/lib/murasaki/align-and-mpi
-rwxr-xr-x root/root 153208 2016-06-30 09:15 ./usr/lib/murasaki/align-best-mpi
-rwxr-xr-x root/root 169616 2016-06-30 09:15 ./usr/lib/murasaki/align-compare-mpi
-rwxr-xr-x root/root 231048 2016-06-30 09:15 ./usr/lib/murasaki/align-coverage-mpi
-rwxr-xr-x root/root 144984 2016-06-30 09:15 ./usr/lib/murasaki/align-or-mpi
-rwxr-xr-x root/root 75340 2016-06-30 09:15 ./usr/lib/murasaki/cgr-compare-mpi
-rwxr-xr-x root/root 227012 2016-06-30 09:15 ./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 83552 2016-06-30 09:15 ./usr/lib/murasaki/cgr-random-mpi
-rwxr-xr-x root/root 222892 2016-06-30 09:15 ./usr/lib/murasaki/cgr-sample-mpi
-rwxr-xr-x root/root 50700 2016-06-30 09:15 ./usr/lib/murasaki/testeco-mpi
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/
-rw-r--r-- root/root 249 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/README.test
-rw-r--r-- root/root 221 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/changelog.Debian.armhf.gz
-rw-r--r-- root/root 708 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz
-rw-r--r-- root/root 2221 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/copyright
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/man/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/man/man1/geneparse-mpi.1.gz -> geneparse.1.gz
lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/man/man1/mbfa-mpi.1.gz -> mbfa.1.gz
lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/man/man1/murasaki-mpi.1.gz -> murasaki.1.gz
murasaki_1.68.6-6+b5_armhf.deb
------------------------------
new debian package, version 2.0.
size 363724 bytes: control archive=1439 bytes.
1189 bytes, 24 lines control
1265 bytes, 20 lines md5sums
Package: murasaki
Source: murasaki (1.68.6-6)
Version: 1.68.6-6+b5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2381
Depends: murasaki-common, libboost-filesystem1.62.0, libboost-iostreams1.62.0, libboost-regex1.62.0, 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 2016-06-30 09:15 ./
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/bin/
-rwxr-xr-x root/root 181960 2016-06-30 09:15 ./usr/bin/geneparse
-rwxr-xr-x root/root 218760 2016-06-30 09:15 ./usr/bin/mbfa
-rwxr-xr-x root/root 490248 2016-06-30 09:15 ./usr/bin/murasaki
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/lib/murasaki/
-rwxr-xr-x root/root 149096 2016-06-30 09:15 ./usr/lib/murasaki/align-and
-rwxr-xr-x root/root 153208 2016-06-30 09:15 ./usr/lib/murasaki/align-best
-rwxr-xr-x root/root 169616 2016-06-30 09:15 ./usr/lib/murasaki/align-compare
-rwxr-xr-x root/root 231048 2016-06-30 09:15 ./usr/lib/murasaki/align-coverage
-rwxr-xr-x root/root 144984 2016-06-30 09:15 ./usr/lib/murasaki/align-or
-rwxr-xr-x root/root 75340 2016-06-30 09:15 ./usr/lib/murasaki/cgr-compare
-rwxr-xr-x root/root 227012 2016-06-30 09:15 ./usr/lib/murasaki/cgr-image
-rwxr-xr-x root/root 83552 2016-06-30 09:15 ./usr/lib/murasaki/cgr-random
-rwxr-xr-x root/root 222892 2016-06-30 09:15 ./usr/lib/murasaki/cgr-sample
-rwxr-xr-x root/root 50700 2016-06-30 09:15 ./usr/lib/murasaki/testeco
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/murasaki/
-rw-r--r-- root/root 249 2016-06-30 09:15 ./usr/share/doc/murasaki/README.test
-rw-r--r-- root/root 221 2016-06-30 09:15 ./usr/share/doc/murasaki/changelog.Debian.armhf.gz
-rw-r--r-- root/root 708 2016-06-30 09:15 ./usr/share/doc/murasaki/changelog.Debian.gz
-rw-r--r-- root/root 2221 2016-06-30 09:15 ./usr/share/doc/murasaki/copyright
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/man/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/man/man1/
-rw-r--r-- root/root 2518 2016-06-30 09:15 ./usr/share/man/man1/geneparse.1.gz
-rw-r--r-- root/root 2721 2016-06-30 09:15 ./usr/share/man/man1/mbfa.1.gz
-rw-r--r-- root/root 10888 2016-06-30 09:15 ./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: 162392
Build-Time: 1114
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 370
Job: murasaki_1.68.6-6
Machine Architecture: armhf
Package: murasaki
Package-Time: 1500
Source-Version: 1.68.6-6
Space: 162392
Status: successful
Version: 1.68.6-6+b5
--------------------------------------------------------------------------------
Finished at 2017-10-13T11:47:19Z
Build needed 00:25:00, 162392k disk space