murasaki →
1.68.6-8+b8 →
armhf → 2019-01-08 11:17:06
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| murasaki 1.68.6-8+b8 (armhf) Tue, 08 Jan 2019 10:43:56 +0000 |
+==============================================================================+
Package: murasaki
Version: 1.68.6-8+b8
Source Version: 1.68.6-8
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-fee168a9-8cd9-47fa-9123-dbc164252389' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.5 MB in 29s (834 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'murasaki' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/murasaki.git
Please use:
git clone https://salsa.debian.org/med-team/murasaki.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 319 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main murasaki 1.68.6-8 (dsc) [2233 B]
Get:2 http://172.17.0.1/private buster-staging/main murasaki 1.68.6-8 (tar) [308 kB]
Get:3 http://172.17.0.1/private buster-staging/main murasaki 1.68.6-8 (diff) [8620 B]
Fetched 319 kB in 0s (1153 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/murasaki-mJmq8b/murasaki-1.68.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/murasaki-mJmq8b' 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-c2nz4M/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-c2nz4M/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-c2nz4M/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-c2nz4M/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (3064 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 dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (5250 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15815 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev
Filtered Build-Depends: debhelper (>= 11~), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev
dpkg-deb: building package 'sbuild-build-depends-murasaki-dummy' in '/<<BUILDDIR>>/resolver-c2nz4M/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-c2nz4M/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ Sources [565 B]
Get:5 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ Packages [643 B]
Fetched 2541 B in 1s (3655 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 dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-8 groff-base ibverbs-providers icu-devtools intltool-debian
libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.67-dev
libboost-filesystem1.67.0 libboost-iostreams-dev libboost-iostreams1.67-dev
libboost-iostreams1.67.0 libboost-regex-dev libboost-regex1.67-dev
libboost-regex1.67.0 libboost-system1.67-dev libboost-system1.67.0
libboost1.67-dev libbsd0 libcroco3 libcrypto++-dev libcrypto++6 libedit2
libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libgfortran-8-dev libgfortran5 libglib2.0-0
libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1
libicu-dev libicu63 libjs-jquery libltdl-dev libltdl7 libmagic-mgc libmagic1
libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libpstreams-dev libsigsegv2
libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libxml2 m4
man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-8-doc
libgfortran5-dbg libcoarrays-dev groff libboost1.67-doc
libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev
libboost-context1.67-dev libboost-coroutine1.67-dev
libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-graph1.67-dev libboost-graph-parallel1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-serialization1.67-dev
libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libhwloc-contrib-plugins icu-doc libtool-doc openmpi-doc pciutils gcj-jdk
m4-doc apparmor less www-browser opencl-icd gfortran keychain libpam-ssh
monkeysphere ssh-askpass libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs javascript-common libcoarrays-openmpi-dev xauth
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-8 groff-base ibverbs-providers icu-devtools intltool-debian
libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.67-dev
libboost-filesystem1.67.0 libboost-iostreams-dev libboost-iostreams1.67-dev
libboost-iostreams1.67.0 libboost-regex-dev libboost-regex1.67-dev
libboost-regex1.67.0 libboost-system1.67-dev libboost-system1.67.0
libboost1.67-dev libbsd0 libcroco3 libcrypto++-dev libcrypto++6 libedit2
libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libgfortran-8-dev libgfortran5 libglib2.0-0
libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1
libicu-dev libicu63 libjs-jquery libltdl-dev libltdl7 libmagic-mgc libmagic1
libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libpstreams-dev libsigsegv2
libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libxml2 m4
man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
po-debconf sbuild-build-depends-murasaki-dummy
0 upgraded, 79 newly installed, 0 to remove and 5 not upgraded.
Need to get 52.3 MB/52.4 MB of archives.
After this operation, 319 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-c2nz4M/apt_archive ./ sbuild-build-depends-murasaki-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-1 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-3 [1160 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20181209-1 [78.7 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf openssh-client armhf 1:7.9p1-4 [683 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.2-3 [1076 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-13+rpi1 [205 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libgfortran-8-dev armhf 8.2.0-13+rpi1 [248 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf gfortran-8 armhf 8.2.0-13+rpi1 [5816 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 21.0-1 [43.5 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf ibverbs-providers armhf 21.0-1 [20.1 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 63.1-5 [166 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-11 [8386 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libboost-system1.67.0 armhf 1.67.0-11 [228 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libboost-filesystem1.67.0 armhf 1.67.0-11 [254 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libboost-system1.67-dev armhf 1.67.0-11 [230 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libboost-filesystem1.67-dev armhf 1.67.0-11 [259 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libboost-filesystem-dev armhf 1.67.0.1+b1 [3960 B]
Get:50 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.67.0 armhf 1.67.0-11 [429 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 63.1-5 [8845 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.67-dev armhf 1.67.0-11 [527 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.67.0 armhf 1.67.0-11 [244 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.67-dev armhf 1.67.0-11 [252 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.67.0.1+b1 [3908 B]
Get:56 http://172.17.0.1/private buster-staging/main armhf libboost-regex-dev armhf 1.67.0.1+b1 [4192 B]
Get:57 http://172.17.0.1/private buster-staging/main armhf libcrypto++6 armhf 5.6.4-8 [750 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libcrypto++-dev armhf 5.6.4-8 [1354 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-6 [387 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.12-1+rpi1 [86.5 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-6 [159 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.12-1+rpi1 [142 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.7 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.12-1+rpi1 [15.9 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 21.0-1 [147 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libpmix2 armhf 3.0.2-2+b1 [344 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libopenmpi3 armhf 3.1.3-3+rpi1 [1805 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 3.1.3-3+rpi1 [164 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf openmpi-bin armhf 3.1.3-3+rpi1 [196 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 3.1.3-3+rpi1 [963 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libpstreams-dev all 1.0.1-2 [129 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libterm-readkey-perl armhf 2.37-1+b2 [26.4 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libtext-wrapper-perl all 1.05-2 [11.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libbsd0:armhf.
(Reading database ... 15815 files and directories currently installed.)
Preparing to unpack .../00-libbsd0_0.9.1-1_armhf.deb ...
Unpacking libbsd0:armhf (0.9.1-1) ...
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-13+rpi1 gcc-8_8.2.0-13+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-13+rpi1 dash_0.5.10.2-4 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.69 debhelper_12 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.145-4.1+b5 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-13+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-13+rpi1 gcc-8-base_8.2.0-13+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran-8_8.2.0-13+rpi1 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.1-3 groff-base_1.22.4-1 gzip_1.9-2.1 hostname_3.21 ibverbs-providers_21.0-1 icu-devtools_63.1-5 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.2-1 libacl1_2.2.52-3 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-13+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-13+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33-0.2 libboost-filesystem-dev_1.67.0.1+b1 libboost-filesystem1.67-dev_1.67.0-11 libboost-filesystem1.67.0_1.67.0-11 libboost-iostreams-dev_1.67.0.1+b1 libboost-iostreams1.67-dev_1.67.0-11 libboost-iostreams1.67.0_1.67.0-11 libboost-regex-dev_1.67.0.1+b1 libboost-regex1.67-dev_1.67.0-11 libboost-regex1.67.0_1.67.0-11 libboost-system1.67-dev_1.67.0-11 libboost-system1.67.0_1.67.0-11 libboost1.67-dev_1.67.0-11 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcap-ng0_0.7.9-1+b1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-13+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcrypto++-dev_5.6.4-8 libcrypto++6_5.6.4-8 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libedit2_3.1-20181209-1 libelf1_0.175-2 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-13+rpi1 libgcc1_1:8.2.0-13+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran-8-dev_8.2.0-13+rpi1 libgfortran5_8.2.0-13+rpi1 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2+rpi1 libgomp1_8.2.0-13+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgssapi-krb5-2_1.16.2-1 libhogweed4_3.4.1~rc1-1 libhwloc-dev_1.11.12-1+rpi1 libhwloc-plugins_1.11.12-1+rpi1 libhwloc5_1.11.12-1+rpi1 libibverbs-dev_21.0-1 libibverbs1_21.0-1 libicu-dev_63.1-5 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjs-jquery_3.2.1-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.2-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.2-1 libkrb5support0_1.16.2-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-1 libldap-common_2.4.47+dfsg-1 libltdl-dev_2.4.6-6 libltdl7_2.4.6-6 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-1 libnss-systemd_240-2+rpi1 libopenmpi-dev_3.1.3-3+rpi1 libopenmpi3_3.1.3-3+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_240-2+rpi1 libpam0g_1.1.8-3.8 libpciaccess0_0.14-1 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpmix2_3.0.2-2+b1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpstreams-dev_1.0.1-2 libreadline7_7.0-5 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-1 libsemanage1_2.8-1+b1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 libsystemd0_240-2+rpi1 libtasn1-6_4.13-3 libterm-readkey-perl_2.37-1+b2 libtext-wrapper-perl_1.05-2 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-13+rpi1 libuchardet0_0.0.6-3 libudev1_240-2+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33-0.2 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.5+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-3 mawk_1.3.3-17 mount_2.33-0.2 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 ocl-icd-libopencl1_2.2.12-2 openmpi-bin_3.1.3-3+rpi1 openmpi-common_3.1.3-3+rpi1 openssh-client_1:7.9p1-4 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-murasaki-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-2+rpi1 systemd-sysv_240-2+rpi1 sysvinit-utils_2.93-2 tar_1.30+dfsg-3+rpi1 tzdata_2018i-1 udev_240-2+rpi1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 8 11:59:15 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-8.dsc
dpkg-source: info: extracting murasaki in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz
dpkg-source: info: unpacking murasaki_1.68.6-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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 disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.68.6-8+b8
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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-fee168a9-8cd9-47fa-9123-dbc164252389
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package murasaki
dpkg-buildpackage: info: source version 1.68.6-8+b8
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf *.o *~ .*~ core
make -C src clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- USE_MPI=YES
make -j4 "INSTALL=install --strip-program=true" USE_MPI=YES
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C src all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c timing.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c msethash.cc
dinkymath.cc: In function 'std::__cxx11::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
dinkymath.cc: In function 'std::__cxx11::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
sequence.cc: In destructor 'Sequence::~Sequence()':
sequence.cc:377:123: warning: throw will always call terminate() [-Wterminate]
throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno));
^
sequence.cc:377:123: note: in C++11 destructors default to noexcept
sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)':
sequence.cc:1113:136: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
struct pair
^~~~
sequence.cc:1114:97: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
struct pair
^~~~
sequence.cc: In destructor 'BitSequence::~BitSequence()':
sequence.cc:1394:133: warning: throw will always call terminate() [-Wterminate]
throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno));
^
sequence.cc:1394:133: note: in C++11 destructors default to noexcept
sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
SeqPos shortest=0,shortlen=length(spaces[0]);
^~~~~~~~
murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
bool revZero=false;
^~~~~~~
In file included from sequence.h:44,
from murasaki.h:24,
from sequence.cc:28:
shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]':
shmvector.hh:282:5: required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]'
sequence.cc:1110:39: required from here
shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<long int, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'struct std::pair<long int, long int>' declared here
struct pair
^~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c options.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecohash.cc
In file included from /usr/include/c++/8/vector:69,
from murasaki.cc:31:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecolist.cc
In file included from /usr/include/c++/8/vector:64,
from murasaki.cc:31:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void MurasakiRuntime::prep()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const HashMethod&}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' {aka '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c arrayhash.cc
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {HashMethod}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' {aka '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >'} changed in GCC 7.1
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c seqread.cc
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_vector.h: In member function 'double HashMethod::fitnessCheck()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
murasaki_mpi.cc: In function 'void mpi_types_init()':
murasaki_mpi.cc:107:28: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.key,disp);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:107:28: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.key,disp);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:108:32: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.seqno,disp+1);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:108:32: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.seqno,disp+1);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:109:30: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.pos,disp+1);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:109:30: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.pos,disp+1);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:112:61: warning: 'int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations]
MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here
OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[],
^~~~~~~~~~~~~~~
murasaki_mpi.cc:112:61: warning: 'int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations]
MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type);
^
In file included from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here
OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[],
^~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
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;
^~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
murasaki_mpi.cc: In function 'word mpi_extract_checkSentQueue(std::vector<std::__cxx11::list<AnchorBlock*> >&, std::vector<std::_Rb_tree_iterator<std::pair<const int, int> > >&, std::multimap<int, int>&)':
murasaki_mpi.cc:1025:18: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated]
packetsLeft++;
^~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/vector.tcc: In member function 'void BitSequence::compileHashFunc()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c scoring.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c openhash.cc
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/c++/8/bits/stl_vector.h: In function 'void mpi_types_init()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c genopts.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c binseq.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-image.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr.cc
binseq.cc: In member function 'bool SequenceBinary::save(std::__cxx11::string)':
binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
}catch(ofstream::failure e){
^
binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()':
binseq.cc:158:67: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
binseq.cc:160:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
binseq.cc:162:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
cgr.cc: In member function 'void Cgr::merge(Cgr&)':
cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
int redist=(unsigned long)(rez*rez)<=seedcount;
^~~~~~
cgr.cc: In member function 'bool Cgr::savePNG(std::__cxx11::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
int res;
^~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
int wordwidth=1;
^~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc
In file included from /usr/include/c++/8/map:60,
from cgr-compare.cc:30:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from cgr-compare.cc:30:
/usr/include/c++/8/bits/stl_map.h: In function 'void doSubsets(CgrSet, std::__cxx11::list<std::vector<std::pair<PgmBuffer*, std::__cxx11::basic_string<char> > > >)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
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
/usr/include/c++/8/bits/stl_map.h: In function 'void doNwise(CgrSet, CgrSet, unsigned int)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
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
cgr-sample.cc: In function 'int main(int, char**)':
cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
bool repeatmask=false,save=false;
^~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c alignments.cc
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:43: warning: left shift count >= width of type [-Wshift-count-overflow]
return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
^~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-or.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c geneparse.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-and.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-best.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c getsegments.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c mbfa.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
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
align-coverage.cc: In function 'int main(int, char**)':
align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
bool seqStats=true;
^~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, std::__cxx11::string)':
getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=]
}catch(bad_lexical_cast e){
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \
mv ${bin} ${bin}-mpi ; \
done
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf *.o *~ .*~ core
make -C src clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -- USE_MPI=NO
make -j4 "INSTALL=install --strip-program=true" USE_MPI=NO
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C src all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c timing.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c msethash.cc
dinkymath.cc: In function 'std::__cxx11::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
dinkymath.cc: In function 'std::__cxx11::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)':
sequence.cc:1113:136: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
struct pair
^~~~
sequence.cc:1114:97: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
struct pair
^~~~
sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
SeqPos shortest=0,shortlen=length(spaces[0]);
^~~~~~~~
murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
bool revZero=false;
^~~~~~~
In file included from sequence.h:44,
from murasaki.h:24,
from sequence.cc:28:
shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]':
shmvector.hh:282:5: required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]'
sequence.cc:1110:39: required from here
shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<long int, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/stl_tree.h:63,
from /usr/include/c++/8/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'struct std::pair<long int, long int>' declared here
struct pair
^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c options.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecohash.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecolist.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c arrayhash.cc
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const HashMethod&}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' {aka '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c seqread.cc
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {HashMethod}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' {aka '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >'} changed in GCC 7.1
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c scoring.cc
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_vector.h: In member function 'double HashMethod::fitnessCheck()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c openhash.cc
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/vector.tcc: In member function 'void BitSequence::compileHashFunc()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c genopts.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c binseq.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-image.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr.cc
binseq.cc: In member function 'bool SequenceBinary::save(std::__cxx11::string)':
binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
}catch(ofstream::failure e){
^
binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()':
binseq.cc:158:67: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
binseq.cc:160:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
binseq.cc:162:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region));
^
In file included from /usr/include/c++/8/bits/stl_algobase.h:64,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits<std::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
struct pair
^~~~
cgr.cc: In member function 'void Cgr::merge(Cgr&)':
cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
int redist=(unsigned long)(rez*rez)<=seedcount;
^~~~~~
cgr.cc: In member function 'bool Cgr::savePNG(std::__cxx11::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
int res;
^~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
int wordwidth=1;
^~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc
In file included from /usr/include/c++/8/map:60,
from cgr-compare.cc:30:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from cgr-compare.cc:30:
/usr/include/c++/8/bits/stl_map.h: In function 'void doSubsets(CgrSet, std::__cxx11::list<std::vector<std::pair<PgmBuffer*, std::__cxx11::basic_string<char> > > >)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In function 'void doNwise(CgrSet, CgrSet, unsigned int)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c testeco.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-compare.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c alignments.cc
cgr-sample.cc: In function 'int main(int, char**)':
cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
bool repeatmask=false,save=false;
^~~~~~~~~~
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:43: warning: left shift count >= width of type [-Wshift-count-overflow]
return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
^~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c 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 -c geneparse.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-and.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-best.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c getsegments.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c mbfa.cc
align-coverage.cc: In function 'int main(int, char**)':
align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
bool seqStats=true;
^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, std::__cxx11::string)':
getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=]
}catch(bad_lexical_cast e){
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install -a
# using wildcards in install files is practical but it duplicates some files
find debian/murasaki/usr -name "*-mpi" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installman -a
mkdir -p debian/murasaki-mpi/usr/share/man/man1
for man in debian/murasaki/usr/share/man/man1/*.1 ; do \
cp -a ${man} debian/murasaki-mpi/usr/share/man/man1/`basename ${man} .1`-mpi.1 ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/testeco contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/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/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/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/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-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/cgr-image contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/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/usr/lib/murasaki/cgr-sample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/mbfa-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/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/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-or contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/geneparse-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/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/testeco-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/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/bin/murasaki-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-and contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-coverage 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/usr/lib/murasaki/testeco debian/murasaki/usr/bin/geneparse debian/murasaki/usr/lib/murasaki/align-compare debian/murasaki/usr/bin/murasaki debian/murasaki/usr/lib/murasaki/cgr-image debian/murasaki/usr/lib/murasaki/cgr-sample debian/murasaki/usr/lib/murasaki/align-best debian/murasaki/usr/lib/murasaki/align-or debian/murasaki/usr/lib/murasaki/cgr-compare debian/murasaki/usr/bin/mbfa debian/murasaki/usr/lib/murasaki/cgr-random debian/murasaki/usr/lib/murasaki/align-and debian/murasaki/usr/lib/murasaki/align-coverage were not linked against libboost_system.so.1.67.0 (they use none of the library's symbols)
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-mpi/usr/lib/murasaki/align-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/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-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: package could avoid a useless dependency if debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi debian/murasaki-mpi/usr/bin/mbfa-mpi debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi debian/murasaki-mpi/usr/bin/geneparse-mpi debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi debian/murasaki-mpi/usr/bin/murasaki-mpi debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-random-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi were not linked against libmpi_cxx.so.40 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi debian/murasaki-mpi/usr/bin/mbfa-mpi debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi debian/murasaki-mpi/usr/bin/geneparse-mpi debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi debian/murasaki-mpi/usr/bin/murasaki-mpi debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-random-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi were not linked against libboost_system.so.1.67.0 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-8+b8_armhf.deb'.
dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-8+b8_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-8+b8_armhf.deb'.
dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-8+b8_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../murasaki_1.68.6-8+b8_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-01-08T11:16:53Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
murasaki_1.68.6-8+b8_armhf.changes:
-----------------------------------
Format: 1.8
Date: Mon, 08 Oct 2018 12:49:39 +0200
Source: murasaki (1.68.6-8)
Binary: murasaki murasaki-mpi murasaki-common
Binary-Only: yes
Architecture: armhf
Version: 1.68.6-8+b8
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <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 (1.68.6-8+b8) 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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d733c0590bfff5acdc0a3e259c0dc011 397100 science optional murasaki-mpi_1.68.6-8+b8_armhf.deb
be059e0f641cb3d5c39337bad1561a08 7274 science optional murasaki_1.68.6-8+b8_armhf.buildinfo
364604ea655c3af5719ada5de560cb5e 364624 science optional murasaki_1.68.6-8+b8_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
murasaki-dbgsym_1.68.6-8+b8_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 14704264 bytes: control archive=1148 bytes.
887 bytes, 12 lines control
1378 bytes, 13 lines md5sums
Package: murasaki-dbgsym
Source: murasaki (1.68.6-8)
Version: 1.68.6-8+b8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 15570
Depends: murasaki (= 1.68.6-8+b8)
Section: debug
Priority: optional
Description: debug symbols for murasaki
Build-Ids: 22bab94abbe775964a424ef48dddcc653e17e59b 4e41ae9bc9d62fea010207027a5474341a7f1505 502185f9fd9b8fd4a92c73019abba66d19dcad63 5f3a4c1299d7de4e1bca623a834c6e54f2dc9a3b 822228f8448138afe70ceb31353006fa12119370 840fd253af41ab9fca4a7c5590ddbf3f30825302 88c1ad7370da3c33dcb33ba5f3b9f48145ccd574 8f7e34be003d1e0f3b77b76d915a3eb78177a382 94c4d6d42c3a699d88055ccb34026e2b8ad6bf51 9f6459b8956297f2b3f8f476e9e888c58f54c57f deaf809981d3b033fed52954606467c67cfd7e60 e822bd1596103e630d825fe32b554892156baabe e9573f4ec26511a1500e5fd9e1438f603cae2f99
drwxr-xr-x root/root 0 2018-10-08 10:49 ./
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root 1664808 2018-10-08 10:49 ./usr/lib/debug/.build-id/22/bab94abbe775964a424ef48dddcc653e17e59b.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/4e/
-rw-r--r-- root/root 945332 2018-10-08 10:49 ./usr/lib/debug/.build-id/4e/41ae9bc9d62fea010207027a5474341a7f1505.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/50/
-rw-r--r-- root/root 1005740 2018-10-08 10:49 ./usr/lib/debug/.build-id/50/2185f9fd9b8fd4a92c73019abba66d19dcad63.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/5f/
-rw-r--r-- root/root 498240 2018-10-08 10:49 ./usr/lib/debug/.build-id/5f/3a4c1299d7de4e1bca623a834c6e54f2dc9a3b.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/82/
-rw-r--r-- root/root 1193744 2018-10-08 10:49 ./usr/lib/debug/.build-id/82/2228f8448138afe70ceb31353006fa12119370.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/84/
-rw-r--r-- root/root 961392 2018-10-08 10:49 ./usr/lib/debug/.build-id/84/0fd253af41ab9fca4a7c5590ddbf3f30825302.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/88/
-rw-r--r-- root/root 1166576 2018-10-08 10:49 ./usr/lib/debug/.build-id/88/c1ad7370da3c33dcb33ba5f3b9f48145ccd574.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/8f/
-rw-r--r-- root/root 1290988 2018-10-08 10:49 ./usr/lib/debug/.build-id/8f/7e34be003d1e0f3b77b76d915a3eb78177a382.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/94/
-rw-r--r-- root/root 1312932 2018-10-08 10:49 ./usr/lib/debug/.build-id/94/c4d6d42c3a699d88055ccb34026e2b8ad6bf51.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/9f/
-rw-r--r-- root/root 3762208 2018-10-08 10:49 ./usr/lib/debug/.build-id/9f/6459b8956297f2b3f8f476e9e888c58f54c57f.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/de/
-rw-r--r-- root/root 619392 2018-10-08 10:49 ./usr/lib/debug/.build-id/de/af809981d3b033fed52954606467c67cfd7e60.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/e8/
-rw-r--r-- root/root 916536 2018-10-08 10:49 ./usr/lib/debug/.build-id/e8/22bd1596103e630d825fe32b554892156baabe.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/debug/.build-id/e9/
-rw-r--r-- root/root 575496 2018-10-08 10:49 ./usr/lib/debug/.build-id/e9/573f4ec26511a1500e5fd9e1438f603cae2f99.debug
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-10-08 10:49 ./usr/share/doc/murasaki-dbgsym -> murasaki
murasaki-mpi-dbgsym_1.68.6-8+b8_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 15730480 bytes: control archive=1156 bytes.
899 bytes, 12 lines control
1378 bytes, 13 lines md5sums
Package: murasaki-mpi-dbgsym
Source: murasaki (1.68.6-8)
Version: 1.68.6-8+b8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 16565
Depends: murasaki-mpi (= 1.68.6-8+b8)
Section: debug
Priority: optional
Description: debug symbols for murasaki-mpi
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lrwxrwxrwx root/root 0 2018-10-08 10:49 ./usr/share/doc/murasaki-mpi-dbgsym -> murasaki-mpi
murasaki-mpi_1.68.6-8+b8_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 397100 bytes: control archive=1644 bytes.
1406 bytes, 28 lines control
1413 bytes, 21 lines md5sums
Package: murasaki-mpi
Source: murasaki (1.68.6-8)
Version: 1.68.6-8+b8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2484
Depends: murasaki-common, libboost-filesystem1.67.0, libboost-iostreams1.67.0, libboost-regex1.67.0 (>= 1.67.0-10), libboost-system1.67.0, libc6 (>= 2.28), libcrypto++6, libgcc1 (>= 1:3.5), libopenmpi3, libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Description: homology detection tool across multiple large genomes (MPI-version)
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
scale multiple genome global alignments. Supports unlimited length
gapped-seed patterns and unique TF-IDF based filtering.
.
Murasaki is an anchor alignment software, which is
* exteremely fast (17 CPU hours for whole Human x Mouse genome (with
40 nodes: 52 wall minutes))
* scalable (Arbitrarily parallelizable across multiple nodes using MPI.
Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
* unlimited pattern length
* repeat tolerant
* intelligent noise reduction
.
This package provides the MPI-enabled binary for murasaki. While this
will speed up operation on multi-processor machines it will slow down
on a single processor.
drwxr-xr-x root/root 0 2018-10-08 10:49 ./
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/bin/
-rwxr-xr-x root/root 186056 2018-10-08 10:49 ./usr/bin/geneparse-mpi
-rwxr-xr-x root/root 218760 2018-10-08 10:49 ./usr/bin/mbfa-mpi
-rwxr-xr-x root/root 572184 2018-10-08 10:49 ./usr/bin/murasaki-mpi
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/murasaki/
-rwxr-xr-x root/root 149096 2018-10-08 10:49 ./usr/lib/murasaki/align-and-mpi
-rwxr-xr-x root/root 157304 2018-10-08 10:49 ./usr/lib/murasaki/align-best-mpi
-rwxr-xr-x root/root 169616 2018-10-08 10:49 ./usr/lib/murasaki/align-compare-mpi
-rwxr-xr-x root/root 235144 2018-10-08 10:49 ./usr/lib/murasaki/align-coverage-mpi
-rwxr-xr-x root/root 149080 2018-10-08 10:49 ./usr/lib/murasaki/align-or-mpi
-rwxr-xr-x root/root 75340 2018-10-08 10:49 ./usr/lib/murasaki/cgr-compare-mpi
-rwxr-xr-x root/root 231108 2018-10-08 10:49 ./usr/lib/murasaki/cgr-image-mpi
-rwxr-xr-x root/root 7138 2010-08-24 14:18 ./usr/lib/murasaki/cgr-image.pl-mpi
-rwxr-xr-x root/root 79456 2018-10-08 10:49 ./usr/lib/murasaki/cgr-random-mpi
-rwxr-xr-x root/root 226988 2018-10-08 10:49 ./usr/lib/murasaki/cgr-sample-mpi
-rwxr-xr-x root/root 46604 2018-10-08 10:49 ./usr/lib/murasaki/testeco-mpi
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/doc/murasaki-mpi/
-rw-r--r-- root/root 249 2018-10-08 10:49 ./usr/share/doc/murasaki-mpi/README.test
-rw-r--r-- root/root 223 2018-10-08 10:49 ./usr/share/doc/murasaki-mpi/changelog.Debian.armhf.gz
-rw-r--r-- root/root 889 2018-10-08 10:49 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz
-rw-r--r-- root/root 2221 2018-10-08 10:49 ./usr/share/doc/murasaki-mpi/copyright
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/man/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/man/man1/
-rw-r--r-- root/root 2518 2018-10-08 10:49 ./usr/share/man/man1/geneparse-mpi.1.gz
-rw-r--r-- root/root 2721 2018-10-08 10:49 ./usr/share/man/man1/mbfa-mpi.1.gz
-rw-r--r-- root/root 10887 2018-10-08 10:49 ./usr/share/man/man1/murasaki-mpi.1.gz
murasaki_1.68.6-8+b8_armhf.deb
------------------------------
new Debian package, version 2.0.
size 364624 bytes: control archive=1500 bytes.
1205 bytes, 24 lines control
1265 bytes, 20 lines md5sums
Package: murasaki
Source: murasaki (1.68.6-8)
Version: 1.68.6-8+b8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2397
Depends: murasaki-common, libboost-filesystem1.67.0, libboost-iostreams1.67.0, libboost-regex1.67.0 (>= 1.67.0-10), libboost-system1.67.0, libc6 (>= 2.28), libcrypto++6, libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Description: homology detection tool across multiple large genomes
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
scale multiple genome global alignments. Supports unlimited length
gapped-seed patterns and unique TF-IDF based filtering.
.
Murasaki is an anchor alignment software, which is
* exteremely fast (17 CPU hours for whole Human x Mouse genome (with
40 nodes: 52 wall minutes))
* scalable (Arbitrarily parallelizable across multiple nodes using MPI.
Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
* unlimited pattern length
* repeat tolerant
* intelligent noise reduction
drwxr-xr-x root/root 0 2018-10-08 10:49 ./
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/bin/
-rwxr-xr-x root/root 186056 2018-10-08 10:49 ./usr/bin/geneparse
-rwxr-xr-x root/root 218760 2018-10-08 10:49 ./usr/bin/mbfa
-rwxr-xr-x root/root 490248 2018-10-08 10:49 ./usr/bin/murasaki
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/lib/murasaki/
-rwxr-xr-x root/root 149096 2018-10-08 10:49 ./usr/lib/murasaki/align-and
-rwxr-xr-x root/root 157304 2018-10-08 10:49 ./usr/lib/murasaki/align-best
-rwxr-xr-x root/root 169616 2018-10-08 10:49 ./usr/lib/murasaki/align-compare
-rwxr-xr-x root/root 235144 2018-10-08 10:49 ./usr/lib/murasaki/align-coverage
-rwxr-xr-x root/root 149080 2018-10-08 10:49 ./usr/lib/murasaki/align-or
-rwxr-xr-x root/root 75340 2018-10-08 10:49 ./usr/lib/murasaki/cgr-compare
-rwxr-xr-x root/root 231108 2018-10-08 10:49 ./usr/lib/murasaki/cgr-image
-rwxr-xr-x root/root 79456 2018-10-08 10:49 ./usr/lib/murasaki/cgr-random
-rwxr-xr-x root/root 226988 2018-10-08 10:49 ./usr/lib/murasaki/cgr-sample
-rwxr-xr-x root/root 46604 2018-10-08 10:49 ./usr/lib/murasaki/testeco
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/doc/murasaki/
-rw-r--r-- root/root 249 2018-10-08 10:49 ./usr/share/doc/murasaki/README.test
-rw-r--r-- root/root 223 2018-10-08 10:49 ./usr/share/doc/murasaki/changelog.Debian.armhf.gz
-rw-r--r-- root/root 889 2018-10-08 10:49 ./usr/share/doc/murasaki/changelog.Debian.gz
-rw-r--r-- root/root 2221 2018-10-08 10:49 ./usr/share/doc/murasaki/copyright
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/man/
drwxr-xr-x root/root 0 2018-10-08 10:49 ./usr/share/man/man1/
-rw-r--r-- root/root 2518 2018-10-08 10:49 ./usr/share/man/man1/geneparse.1.gz
-rw-r--r-- root/root 2721 2018-10-08 10:49 ./usr/share/man/man1/mbfa.1.gz
-rw-r--r-- root/root 10887 2018-10-08 10:49 ./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: 213012
Build-Time: 1009
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 916
Job: murasaki_1.68.6-8
Machine Architecture: armhf
Package: murasaki
Package-Time: 1977
Source-Version: 1.68.6-8
Space: 213012
Status: successful
Version: 1.68.6-8+b8
--------------------------------------------------------------------------------
Finished at 2019-01-08T11:16:53Z
Build needed 00:32:57, 213012k disc space