murasaki →
1.68.6-9 →
armhf → 2020-02-26 08:42:57
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| murasaki 1.68.6-9 (armhf) Wed, 26 Feb 2020 08:12:39 +0000 |
+==============================================================================+
Package: murasaki
Version: 1.68.6-9
Source Version: 1.68.6-9
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-3f73b1b6-a0a3-4fb6-95b5-798c7a08b8b9' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.3 MB in 28s (875 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 320 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main murasaki 1.68.6-9 (dsc) [2237 B]
Get:2 http://172.17.0.1/private bullseye-staging/main murasaki 1.68.6-9 (tar) [308 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main murasaki 1.68.6-9 (diff) [10.3 kB]
Fetched 320 kB in 0s (2898 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/murasaki-6xnYUW/murasaki-1.68.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/murasaki-6xnYUW' 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-wc5M9d/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-wc5M9d/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-wc5M9d/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-wc5M9d/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-wc5M9d/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-wc5M9d/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-wc5M9d/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-wc5M9d/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2712 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:
libpam-cap netbase
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 31 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-wc5M9d/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 (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12256 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-compat (= 12), 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-compat (= 12), 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-wc5M9d/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-wc5M9d/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-wc5M9d/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-wc5M9d/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-wc5M9d/apt_archive ./ Sources [566 B]
Get:5 copy:/<<BUILDDIR>>/resolver-wc5M9d/apt_archive ./ Packages [646 B]
Fetched 2545 B in 1s (3299 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:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev binutils
binutils-arm-linux-gnueabihf binutils-common bsdmainutils cpp-8 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gcc-8 gcc-8-base gettext
gettext-base gfortran-8 groff-base ibverbs-providers icu-devtools
intltool-debian libarchive-zip-perl libbinutils 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 libctf0 libdebhelper-perl libedit2 libelf1 libevent-2.1-7
libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libfile-stripnondeterminism-perl libgcc-8-dev
libgfortran-8-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu63
libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 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 libssl1.1 libsub-override-perl
libterm-readkey-perl libtext-wrapper-perl libtinfo5 libtool libuchardet0
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0
m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
po-debconf sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican
| wordlist whois vacation gcc-8-locales dh-make gcc-8-doc gettext-doc
libasprintf-dev libgettextpo-dev gfortran-8-doc libcoarrays-dev groff
libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev
libboost-container1.67-dev libboost-context1.67-dev
libboost-contract1.67-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
krb5-doc krb5-user icu-doc libtool-doc openmpi-doc pciutils gcj-jdk m4-doc
apparmor less www-browser opencl-icd gfortran | fortran-compiler 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 krb5-locales libcoarrays-openmpi-dev xauth
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-8 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gcc-8 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
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libfile-stripnondeterminism-perl libgcc-8-dev
libgfortran-8-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu63
libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 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 libssl1.1 libsub-override-perl
libterm-readkey-perl libtext-wrapper-perl libtinfo5 libtool libuchardet0
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0
m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
po-debconf sbuild-build-depends-murasaki-dummy sensible-utils
The following packages will be upgraded:
binutils binutils-arm-linux-gnueabihf binutils-common gcc-8-base libbinutils
libctf0
6 upgraded, 102 newly installed, 0 to remove and 25 not upgraded.
Need to get 77.5 MB of archives.
After this operation, 381 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-wc5M9d/apt_archive ./ sbuild-build-depends-murasaki-dummy 0.invalid.0 [932 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gcc-8-base armhf 8.3.0-29+rpi1 [194 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-1 [79.2 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.1p1-5 [713 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libctf0 armhf 2.34-3+rpi1 [34.9 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf binutils-arm-linux-gnueabihf armhf 2.34-3+rpi1 [1712 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libbinutils armhf 2.34-3+rpi1 [310 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf binutils armhf 2.34-3+rpi1 [59.0 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf binutils-common armhf 2.34-3+rpi1 [2063 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf cpp-8 armhf 8.3.0-29+rpi1 [6793 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libgcc-8-dev armhf 8.3.0-29+rpi1 [595 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf gcc-8 armhf 8.3.0-29+rpi1 [7252 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-13 [513 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.9 [183 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-2 [1138 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.9 [994 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-25+rpi1 [231 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-8-dev armhf 8.3.0-29+rpi1 [249 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf gfortran-8 armhf 8.3.0-29+rpi1 [7210 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 28.0-1 [47.6 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 28.0-1 [24.2 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 63.2-2 [163 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-17 [8389 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libboost-system1.67.0 armhf 1.67.0-17 [229 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libboost-filesystem1.67.0 armhf 1.67.0-17 [255 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libboost-system1.67-dev armhf 1.67.0-17 [231 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libboost-filesystem1.67-dev armhf 1.67.0-17 [261 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libboost-filesystem-dev armhf 1.67.0.2+b11 [4284 B]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.67.0 armhf 1.67.0-17 [452 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 63.2-2 [8846 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.67-dev armhf 1.67.0-17 [555 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.67.0 armhf 1.67.0-17 [246 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.67-dev armhf 1.67.0-17 [254 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams-dev armhf 1.67.0.2+b11 [4236 B]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex-dev armhf 1.67.0.2+b11 [4516 B]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libcrypto++6 armhf 5.6.4-9 [754 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libcrypto++-dev armhf 5.6.4-9 [1385 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.11-stable-1 [165 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.11-stable-1 [124 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.11-stable-1 [98.7 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.11-stable-1 [54.7 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.11-stable-1 [59.7 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.11-stable-1 [279 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-13 [388 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libhwloc15 armhf 2.1.0+dfsg-3+rpi1 [112 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-13 [159 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.1.0+dfsg-3+rpi1 [173 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.8-1 [298 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.8-1 [691 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libxnvctrl0 armhf 440.59-1 [25.0 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-3 [35.9 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.1.0+dfsg-3+rpi1 [18.6 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 28.0-1 [199 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.3.1~dfsg-3 [332 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 3.1.4-1+b1 [370 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.0.2-5+rpi1 [1679 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 4.0.2-5+rpi1 [168 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 4.0.2-5+rpi1 [185 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.0.2-5+rpi1 [905 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libpstreams-dev all 1.0.1-2 [129 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libterm-readkey-perl armhf 2.38-1+b1 [26.5 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libtext-wrapper-perl all 1.05-2 [11.0 kB]
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Unpacking sbuild-build-depends-murasaki-dummy (0.invalid.0) ...
Setting up libboost1.67-dev:armhf (1.67.0-17) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libpciaccess0:armhf (0.14-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libmagic-mgc (1:5.38-4) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.4-2) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1d-2) ...
Setting up libdebhelper-perl (12.9) ...
Setting up binutils-common:armhf (2.34-3+rpi1) ...
Setting up libmagic1:armhf (1:5.38-4) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-4) ...
Setting up libtext-wrapper-perl (1.05-2) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libx11-data (2:1.6.8-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libevent-core-2.1-7:armhf (2.1.11-stable-1) ...
Setting up libevent-2.1-7:armhf (2.1.11-stable-1) ...
Setting up gcc-8-base:armhf (8.3.0-29+rpi1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up icu-devtools (63.2-2) ...
Setting up libboost-iostreams1.67.0:armhf (1.67.0-17) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up libltdl7:armhf (2.4.6-13) ...
Setting up libgcc-8-dev:armhf (8.3.0-29+rpi1) ...
Setting up libgfortran5:armhf (9.2.1-25+rpi1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up ocl-icd-libopencl1:armhf (2.2.12-3) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up openmpi-common (4.0.2-5+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libjs-jquery (3.3.1~dfsg-3) ...
Setting up libboost-system1.67.0:armhf (1.67.0-17) ...
Setting up libterm-readkey-perl (2.38-1+b1) ...
Setting up libbinutils:armhf (2.34-3+rpi1) ...
Setting up cpp-8 (8.3.0-29+rpi1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libicu-dev:armhf (63.2-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.11-stable-1) ...
Setting up libcrypto++6 (5.6.4-9) ...
Setting up libctf0:armhf (2.34-3+rpi1) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-2) ...
Setting up libgfortran-8-dev:armhf (8.3.0-29+rpi1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.11-stable-1) ...
Setting up libxcb1:armhf (1.13.1-2) ...
Setting up libboost-regex1.67.0:armhf (1.67.0-17) ...
Setting up libtool (2.4.6-13) ...
Setting up libboost-regex1.67-dev:armhf (1.67.0-17) ...
Setting up libedit2:armhf (3.1-20191231-1) ...
Setting up libcrypto++-dev (5.6.4-9) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.11-stable-1) ...
Setting up m4 (1.4.18-4) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libevent-dev (2.1.11-stable-1) ...
Setting up libhwloc15:armhf (2.1.0+dfsg-3+rpi1) ...
Setting up libpstreams-dev (1.0.1-2) ...
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.6.3-2) ...
Setting up dwz (0.13-5) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-4) ...
Setting up libx11-6:armhf (2:1.6.8-1) ...
Setting up libboost-filesystem1.67.0:armhf (1.67.0-17) ...
Setting up libboost-system1.67-dev:armhf (1.67.0-17) ...
Setting up libboost-regex-dev:armhf (1.67.0.2+b11) ...
Setting up binutils-arm-linux-gnueabihf (2.34-3+rpi1) ...
Setting up libboost-iostreams1.67-dev:armhf (1.67.0-17) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libibverbs1:armhf (28.0-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libboost-filesystem1.67-dev:armhf (1.67.0-17) ...
Setting up ibverbs-providers:armhf (28.0-1) ...
Setting up openssh-client (1:8.1p1-5) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up binutils (2.34-3+rpi1) ...
Setting up libboost-iostreams-dev:armhf (1.67.0.2+b11) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libxnvctrl0:armhf (440.59-1) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-13) ...
Setting up libhwloc-dev:armhf (2.1.0+dfsg-3+rpi1) ...
Setting up libboost-filesystem-dev:armhf (1.67.0.2+b11) ...
Setting up gcc-8 (8.3.0-29+rpi1) ...
Setting up gfortran-8 (8.3.0-29+rpi1) ...
Setting up po-debconf (1.0.21) ...
Setting up libibverbs-dev:armhf (28.0-1) ...
Setting up libhwloc-plugins:armhf (2.1.0+dfsg-3+rpi1) ...
Setting up libpmix2:armhf (3.1.4-1+b1) ...
Setting up libopenmpi3:armhf (4.0.2-5+rpi1) ...
Setting up openmpi-bin (4.0.2-5+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.0.2-5+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up debhelper (12.9) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-murasaki-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-9+rpi1) ...
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_2.34-3+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-25+rpi1 gcc-8_8.3.0-29+rpi1 gcc-9_9.2.1-25+rpi1 libc6-dev_2.29-9+rpi1 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.34-3+rpi1 binutils-arm-linux-gnueabihf_2.34-3+rpi1 binutils-common_2.34-3+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-8_8.3.0-29+rpi1 cpp-9_9.2.1-25+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dirmngr_2.2.19-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-25+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-3+b1 gcc-8_8.3.0-29+rpi1 gcc-8-base_8.3.0-29+rpi1 gcc-9_9.2.1-25+rpi1 gcc-9-base_9.2.1-25+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran-8_8.3.0-29+rpi1 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 ibverbs-providers_28.0-1 icu-devtools_63.2-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-25+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-25+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.34-3+rpi1 libblkid1_2.34-0.1 libboost-filesystem-dev_1.67.0.2+b11 libboost-filesystem1.67-dev_1.67.0-17 libboost-filesystem1.67.0_1.67.0-17 libboost-iostreams-dev_1.67.0.2+b11 libboost-iostreams1.67-dev_1.67.0-17 libboost-iostreams1.67.0_1.67.0-17 libboost-regex-dev_1.67.0.2+b11 libboost-regex1.67-dev_1.67.0-17 libboost-regex1.67.0_1.67.0-17 libboost-system1.67-dev_1.67.0-17 libboost-system1.67.0_1.67.0-17 libboost1.67-dev_1.67.0-17 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-9+rpi1 libc-dev-bin_2.29-9+rpi1 libc6_2.29-9+rpi1 libc6-dev_2.29-9+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-25+rpi1 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libcrypto++-dev_5.6.4-9 libcrypto++6_5.6.4-9 libctf-nobfd0_2.33.90.20200122-2+rpi1 libctf0_2.34-3+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.9 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libevent-2.1-7_2.1.11-stable-1 libevent-core-2.1-7_2.1.11-stable-1 libevent-dev_2.1.11-stable-1 libevent-extra-2.1-7_2.1.11-stable-1 libevent-openssl-2.1-7_2.1.11-stable-1 libevent-pthreads-2.1-7_2.1.11-stable-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-8-dev_8.3.0-29+rpi1 libgcc-9-dev_9.2.1-25+rpi1 libgcc1_1:9.2.1-25+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-8-dev_8.3.0-29+rpi1 libgfortran5_9.2.1-25+rpi1 libglib2.0-0_2.62.4-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-25+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libhwloc-dev_2.1.0+dfsg-3+rpi1 libhwloc-plugins_2.1.0+dfsg-3+rpi1 libhwloc15_2.1.0+dfsg-3+rpi1 libibverbs-dev_28.0-1 libibverbs1_28.0-1 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libjs-jquery_3.3.1~dfsg-3 libk5crypto3_1.17-6+b1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblocale-gettext-perl_1.07-4 libltdl-dev_2.4.6-13 libltdl7_2.4.6-13 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 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 libopenmpi-dev_4.0.2-5+rpi1 libopenmpi3_4.0.2-5+rpi1 libp11-kit0_0.23.18.1-2+b1 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpmix2_3.1.4-1+b1 libpstreams-dev_1.0.1-2 libreadline8_8.0-3 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.0+really3.30.1+fossil191229-1 libss2_1.45.5-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 libsub-override-perl_0.09-2 libsystemd0_244.1-1+rpi1 libtasn1-6_4.15.0-2 libterm-readkey-perl_2.38-1+b1 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtext-wrapper-perl_1.05-2 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libubsan1_9.2.1-25+rpi1 libuchardet0_0.0.6-3 libudev1_244.1-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.8-1+b2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.4+dfsg1-8 libxnvctrl0_440.59-1 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-1 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 ocl-icd-libopencl1_2.2.12-3 openmpi-bin_4.0.2-5+rpi1 openmpi-common_4.0.2-5+rpi1 openssh-client_1:8.1p1-5 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 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+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 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 Thu Feb 20 18:05:10 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-9.dsc
dpkg-source: info: extracting murasaki in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz
dpkg-source: info: unpacking murasaki_1.68.6-9.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
dpkg-source: info: applying fix_mpi.patch
Check disc space
----------------
Sufficient free space for build
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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-3f73b1b6-a0a3-4fb6-95b5-798c7a08b8b9
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 1.68.6-9
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
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 binary-arch
dh binary-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 -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 -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 -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 -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 -c msethash.cc
dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
40 | int last=0;
| ^~~~
dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
53 | int last=0;
| ^~~~
sequence.cc: In destructor 'Sequence::~Sequence()':
sequence.cc:377:123: warning: throw will always call terminate() [-Wterminate]
377 | 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]
1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/stl_tree.h:63,
from /usr/include/c++/9/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/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
208 | 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]
1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/stl_tree.h:63,
from /usr/include/c++/9/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/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
208 | struct pair
| ^~~~
sequence.cc: In destructor 'BitSequence::~BitSequence()':
sequence.cc:1394:133: warning: throw will always call terminate() [-Wterminate]
1394 | 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]
3332 | SeqPos shortest=0,shortlen=length(spaces[0]);
| ^~~~~~~~
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]
225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/stl_tree.h:63,
from /usr/include/c++/9/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/bits/stl_pair.h:208:12: note: 'struct std::pair<long int, long int>' declared here
208 | struct pair
| ^~~~
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]
1008 | bool revZero=false;
| ^~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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 -c ecohash.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc
In file included from /usr/include/c++/9/vector:72,
from murasaki.cc:31:
/usr/include/c++/9/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++/9/bits/vector.tcc:509:5: 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
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from murasaki.cc:31:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void MurasakiRuntime::prep()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _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 -c murasaki_mpi.cc
In file included from /usr/include/c++/9/vector:72,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/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++/9/bits/vector.tcc:509:5: 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
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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 -c arrayhash.cc
In file included from /usr/include/c++/9/vector:67,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/bits/stl_vector.h: In member function 'double HashMethod::fitnessCheck()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
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]
561 | int send_done;
| ^~~~~~~~~
murasaki_mpi.cc: In function 'word mpi_extract_checkSentQueue(std::vector<std::__cxx11::list<AnchorBlock*> >&, std::vector<std::_Rb_tree_iterator<std::pair<const int, int> > >&, std::multimap<int, int>&)':
murasaki_mpi.cc:1025:18: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated]
1025 | packetsLeft++;
| ^~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc
In file included from /usr/include/c++/9/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++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/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++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/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++/9/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
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/9/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++/9/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
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/9/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++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/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++/9/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
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc
In file included from /usr/include/c++/9/vector:72,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/bits/vector.tcc: In member function 'void BitSequence::compileHashFunc()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/c++/9/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++/9/bits/vector.tcc:509:5: 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
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/c++/9/bits/stl_vector.h: In function 'void mpi_types_init()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _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 -c openhash.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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 -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 -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 -c cgr.cc
binseq.cc: In member function 'bool SequenceBinary::save(std::string)':
binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
70 | }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]
158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region));
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/istream:38,
from /usr/include/c++/9/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/9/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
208 | 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]
160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region));
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/istream:38,
from /usr/include/c++/9/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/9/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
208 | 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]
162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region));
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/istream:38,
from /usr/include/c++/9/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/9/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
208 | 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]
140 | int redist=(unsigned long)(rez*rez)<=seedcount;
| ^~~~~~
cgr.cc: In member function 'bool Cgr::savePNG(std::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
288 | int res;
| ^~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
435 | 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 -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 -c cgr-random.cc
cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)':
cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
557 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
485 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /usr/include/c++/9/map:60,
from cgr-compare.cc:30:
/usr/include/c++/9/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++/9/bits/stl_tree.h:2452:7: 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
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from cgr-compare.cc:30:
/usr/include/c++/9/bits/stl_map.h: In function 'void setCmp(CgrSet&)':
/usr/include/c++/9/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
499 | __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 -c cgr-sample.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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]
54 | 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 -c alignments.cc
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:43: warning: left shift count >= width of type [-Wshift-count-overflow]
29 | 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 -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 -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 -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 -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 -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 -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 -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]
148 | bool seqStats=true;
| ^~~~~~~~
getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, std::string)':
getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=]
153 | }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 -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
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 -c murasaki.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c timing.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c dinkymath.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c sequence.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c msethash.cc
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]
1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]);
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/stl_tree.h:63,
from /usr/include/c++/9/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/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
208 | 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]
1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/stl_tree.h:63,
from /usr/include/c++/9/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/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
208 | struct pair
| ^~~~
dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
40 | int last=0;
| ^~~~
dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
53 | int last=0;
| ^~~~
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]
3332 | 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]
1008 | 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]
225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/stl_tree.h:63,
from /usr/include/c++/9/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/bits/stl_pair.h:208:12: note: 'struct std::pair<long int, long int>' declared here
208 | struct pair
| ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c options.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecohash.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecolist.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc
In file included from /usr/include/c++/9/vector:72,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/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++/9/bits/vector.tcc:509:5: 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
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c seqread.cc
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.cc
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
In file included from /usr/include/c++/9/vector:67,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/bits/stl_vector.h: In member function 'double HashMethod::fitnessCheck()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c openhash.cc
In file included from /usr/include/c++/9/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++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/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++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/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++/9/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
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/9/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++/9/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
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/9/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++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/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++/9/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
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c genopts.cc
In file included from /usr/include/c++/9/vector:72,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/bits/vector.tcc: In member function 'void BitSequence::compileHashFunc()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from scoring.h:27,
from sequence.h:31,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c binseq.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-image.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr.cc
binseq.cc: In member function 'bool SequenceBinary::save(std::string)':
binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
70 | }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]
158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region));
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/istream:38,
from /usr/include/c++/9/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/9/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
208 | 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]
160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region));
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/istream:38,
from /usr/include/c++/9/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/9/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
208 | 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]
162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region));
| ^
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/istream:38,
from /usr/include/c++/9/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/9/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
208 | 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]
140 | int redist=(unsigned long)(rez*rez)<=seedcount;
| ^~~~~~
cgr.cc: In member function 'bool Cgr::savePNG(std::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
288 | int res;
| ^~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
435 | int wordwidth=1;
| ^~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-compare.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-random.cc
cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)':
cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
557 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
485 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /usr/include/c++/9/map:60,
from cgr-compare.cc:30:
/usr/include/c++/9/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++/9/bits/stl_tree.h:2452:7: 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
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from cgr-compare.cc:30:
/usr/include/c++/9/bits/stl_map.h: In function 'void setCmp(CgrSet&)':
/usr/include/c++/9/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
499 | __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 -c cgr-sample.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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]
54 | 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]
29 | 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 -c alignments.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-or.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-and.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-best.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-coverage.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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]
148 | bool seqStats=true;
| ^~~~~~~~
getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, std::string)':
getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=]
153 | }catch(bad_lexical_cast e){
| ^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
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
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_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/murasaki contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/geneparse-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-sample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-coverage contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/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/testeco contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-random-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-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/cgr-image-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-random contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/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/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/usr/lib/murasaki/cgr-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/murasaki-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/geneparse contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-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-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/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-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-mpi/usr/lib/murasaki/align-and-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/mbfa-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
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_1.68.6-9_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-9_armhf.deb'.
dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-9_armhf.deb'.
dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-9_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../murasaki_1.68.6-9_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 2020-02-26T08:42:44Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
murasaki_1.68.6-9_armhf.changes:
--------------------------------
Format: 1.8
Date: Thu, 20 Feb 2020 21:11:15 +0530
Source: murasaki
Binary: murasaki murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym
Architecture: armhf
Version: 1.68.6-9
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
murasaki - homology detection tool across multiple large genomes
murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio
Closes: 951643
Changes:
murasaki (1.68.6-9) unstable; urgency=medium
.
* Team Upload.
.
[ Steffen Moeller ]
* d/u/metadata: yamllint
.
[ Nilesh Patra ]
* Fix syntax with new MPI version
Closes: #951643
* Drop compat, switch to debhelper-compat
* Add "Rules-Requires-Root: no"
* Switch to https
* Fix License locations, switch to https
* Update spellings patch
* Bump standards version to 4.5.0
.
[ Andreas Tille ]
* Remove trailing whitespace in debian/rules (routine-update)
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
murasaki-dbgsym_1.68.6-9_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 9573836 bytes: control archive=1188 bytes.
870 bytes, 12 lines control
1466 bytes, 14 lines md5sums
Package: murasaki-dbgsym
Source: murasaki
Version: 1.68.6-9
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10524
Depends: murasaki (= 1.68.6-9)
Section: debug
Priority: optional
Description: debug symbols for murasaki
Build-Ids: 29f7061b5921410f2b2f94cf5e849c70e7bedd08 303f4045fbf4f1a5797a0eeb885b24e5ba3790e6 3973ab061814d413bd87fe84a2de32aee470d242 3a262039fab3cf60bf5e7e57bf660045aa219a17 40424798df194d1ccd6f5eb4f6c6841a294f171e 71e1b47a9b562babfdc33ee18b5410c86a61b2ff 8fa4cccab49ecaf7849273f0bac155d7ac688d89 b6359c4140f05c2023bb78f36b180822aeaf1b08 bb90f66a9a9746ee9061f418764e2609f163c244 cabb6c7740f1a23a869c770dd83481eddc5d8697 ce6b4b606c9882b5150c4db9eb56a2383e7e0d1d ce88f8c93b6bc1bfb1bc97689fa55265243d1d6a d86edb47c88c1ff3ee3fb5cadfa356e45a8d2014
drwxr-xr-x root/root 0 2020-02-20 15:41 ./
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/
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-rw-r--r-- root/root 760752 2020-02-20 15:41 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/murasaki.debug
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/share/
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-02-20 15:41 ./usr/share/doc/murasaki-dbgsym -> murasaki
murasaki-mpi-dbgsym_1.68.6-9_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 10207132 bytes: control archive=1200 bytes.
882 bytes, 12 lines control
1470 bytes, 14 lines md5sums
Package: murasaki-mpi-dbgsym
Source: murasaki
Version: 1.68.6-9
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 11155
Depends: murasaki-mpi (= 1.68.6-9)
Section: debug
Priority: optional
Description: debug symbols for murasaki-mpi
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-rw-r--r-- root/root 779808 2020-02-20 15:41 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/murasaki-mpi.debug
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/share/
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-02-20 15:41 ./usr/share/doc/murasaki-mpi-dbgsym -> murasaki-mpi
murasaki-mpi_1.68.6-9_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 413204 bytes: control archive=1600 bytes.
1357 bytes, 28 lines control
1326 bytes, 20 lines md5sums
Package: murasaki-mpi
Source: murasaki
Version: 1.68.6-9
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2632
Depends: murasaki-common, libboost-filesystem1.67.0, libboost-iostreams1.67.0, libboost-regex1.67.0-icu63, libc6 (>= 2.29), libgcc1 (>= 1:3.5), libopenmpi3 (>= 4.0.2), 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 2020-02-20 15:41 ./
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/bin/
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-rw-r--r-- root/root 249 2020-02-20 15:41 ./usr/share/doc/murasaki-mpi/README.test
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-rw-r--r-- root/root 2225 2020-02-20 15:41 ./usr/share/doc/murasaki-mpi/copyright
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/share/man/
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/share/man/man1/
-rw-r--r-- root/root 2518 2020-02-20 15:41 ./usr/share/man/man1/geneparse-mpi.1.gz
-rw-r--r-- root/root 2721 2020-02-20 15:41 ./usr/share/man/man1/mbfa-mpi.1.gz
-rw-r--r-- root/root 10888 2020-02-20 15:41 ./usr/share/man/man1/murasaki-mpi.1.gz
murasaki_1.68.6-9_armhf.deb
---------------------------
new Debian package, version 2.0.
size 377364 bytes: control archive=1452 bytes.
1128 bytes, 23 lines control
1182 bytes, 19 lines md5sums
Package: murasaki
Version: 1.68.6-9
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2537
Depends: murasaki-common, libboost-filesystem1.67.0, libboost-iostreams1.67.0, libboost-regex1.67.0-icu63, libc6 (>= 2.29), 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 2020-02-20 15:41 ./
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/bin/
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drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/share/doc/murasaki/
-rw-r--r-- root/root 249 2020-02-20 15:41 ./usr/share/doc/murasaki/README.test
-rw-r--r-- root/root 1125 2020-02-20 15:41 ./usr/share/doc/murasaki/changelog.Debian.gz
-rw-r--r-- root/root 2225 2020-02-20 15:41 ./usr/share/doc/murasaki/copyright
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/share/man/
drwxr-xr-x root/root 0 2020-02-20 15:41 ./usr/share/man/man1/
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-rw-r--r-- root/root 2721 2020-02-20 15:41 ./usr/share/man/man1/mbfa.1.gz
-rw-r--r-- root/root 10888 2020-02-20 15:41 ./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: 201780
Build-Time: 1059
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 697
Job: murasaki_1.68.6-9
Machine Architecture: armhf
Package: murasaki
Package-Time: 1805
Source-Version: 1.68.6-9
Space: 201780
Status: successful
Version: 1.68.6-9
--------------------------------------------------------------------------------
Finished at 2020-02-26T08:42:44Z
Build needed 00:30:05, 201780k disc space