murasaki →
1.68.6-13+b6 →
armhf → 2024-02-07 22:57:17
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| murasaki 1.68.6-13+b6 (armhf) Wed, 07 Feb 2024 22:43:16 +0000 |
+==============================================================================+
Package: murasaki
Version: 1.68.6-13+b6
Source Version: 1.68.6-13
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-90c60970-fcfb-48b6-a532-d6e9ce74a690' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.4 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.1 MB]
Fetched 29.5 MB in 10s (3001 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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 4266 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main murasaki 1.68.6-13 (dsc) [2792 B]
Get:2 http://172.17.4.1/private trixie-staging/main murasaki 1.68.6-13 (tar) [3944 kB]
Get:3 http://172.17.4.1/private trixie-staging/main murasaki 1.68.6-13 (tar) [308 kB]
Get:4 http://172.17.4.1/private trixie-staging/main murasaki 1.68.6-13 (diff) [11.2 kB]
Fetched 4266 kB in 0s (8751 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/murasaki-N6GnhK/murasaki-1.68.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/murasaki-N6GnhK' 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-MRfBOL/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-MRfBOL/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-MRfBOL/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (6746 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:
krb5-locales libpam-cap netbase sensible-utils sgml-base util-linux-extra
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 14 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-MRfBOL/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 (80.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12880 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 (= 13), 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 (= 13), 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-MRfBOL/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-MRfBOL/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ Sources [564 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ Packages [644 B]
Fetched 2541 B in 0s (13.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install murasaki build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-13 groff-base ibverbs-providers icu-devtools intltool-debian
libarchive-zip-perl libboost-atomic1.83-dev libboost-atomic1.83.0
libboost-filesystem-dev libboost-filesystem1.83-dev
libboost-filesystem1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev
libboost-iostreams1.83.0 libboost-regex-dev libboost-regex1.83-dev
libboost-regex1.83.0 libboost-system1.83-dev libboost-system1.83.0
libboost1.83-dev libbsd0 libcbor0.10 libcrypto++-dev libcrypto++8
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 libfabric1 libfido2-1
libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1
libicu-dev libicu72 libjs-jquery libjs-jquery-ui libltdl-dev libltdl7
libmagic-mgc libmagic1 libmunge2 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpstreams-dev librdmacm1
libsub-override-perl libterm-readkey-perl libtext-wrapper-perl 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 zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev gfortran-13-doc libcoarrays-dev groff
libboost1.83-doc libboost-chrono1.83-dev libboost-container1.83-dev
libboost-context1.83-dev libboost-contract1.83-dev
libboost-coroutine1.83-dev libboost-date-time1.83-dev
libboost-exception1.83-dev libboost-fiber1.83-dev
libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-json1.83-dev
libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev
libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev
libboost-numpy1.83-dev libboost-program-options1.83-dev
libboost-python1.83-dev libboost-random1.83-dev
libboost-serialization1.83-dev libboost-stacktrace1.83-dev
libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev
libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev
libboost1.83-tools-dev libmpfrc++-dev libntl-dev icu-doc
libjs-jquery-ui-docs 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 javascript-common
libcoarrays-openmpi-dev xauth libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-13 groff-base ibverbs-providers icu-devtools intltool-debian
libarchive-zip-perl libboost-atomic1.83-dev libboost-atomic1.83.0
libboost-filesystem-dev libboost-filesystem1.83-dev
libboost-filesystem1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev
libboost-iostreams1.83.0 libboost-regex-dev libboost-regex1.83-dev
libboost-regex1.83.0 libboost-system1.83-dev libboost-system1.83.0
libboost1.83-dev libbsd0 libcbor0.10 libcrypto++-dev libcrypto++8
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 libfabric1 libfido2-1
libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1
libicu-dev libicu72 libjs-jquery libjs-jquery-ui libltdl-dev libltdl7
libmagic-mgc libmagic1 libmunge2 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpstreams-dev librdmacm1
libsub-override-perl libterm-readkey-perl libtext-wrapper-perl 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 zlib1g-dev
0 upgraded, 100 newly installed, 0 to remove and 14 not upgraded.
Need to get 67.2 MB of archives.
After this operation, 402 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-MRfBOL/apt_archive ./ sbuild-build-depends-murasaki-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-6 [81.4 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-3 [1358 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.8-1 [120 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libedit2 armhf 3.1-20230828-1 [76.0 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf libcbor0.10 armhf 0.10.2-1.1 [23.8 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libfido2-1 armhf 1.14.0-1 [67.7 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf openssh-client armhf 1:9.6p1-3 [802 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.13 [85.0 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:28 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.13 [889 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-9+rpi1 [247 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libgfortran-13-dev armhf 13.2.0-9+rpi1 [293 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf gfortran-13 armhf 13.2.0-9+rpi1 [7837 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libnl-3-200 armhf 3.7.0-0.3 [51.5 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.3 [149 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libibverbs1 armhf 48.0-1.1 [53.8 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf ibverbs-providers armhf 48.0-1.1 [28.1 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf icu-devtools armhf 72.1-4 [174 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libboost1.83-dev armhf 1.83.0-2 [10.6 MB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libboost-atomic1.83.0 armhf 1.83.0-2 [232 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libboost-atomic1.83-dev armhf 1.83.0-2 [233 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libboost-filesystem1.83.0 armhf 1.83.0-2 [270 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libboost-system1.83.0 armhf 1.83.0-2 [230 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libboost-system1.83-dev armhf 1.83.0-2 [231 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libboost-filesystem1.83-dev armhf 1.83.0-2 [279 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libboost-filesystem-dev armhf 1.83.0.2 [3340 B]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.83.0 armhf 1.83.0-2 [303 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libicu-dev armhf 72.1-4 [9956 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.83-dev armhf 1.83.0-2 [328 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.83.0 armhf 1.83.0-2 [249 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.83-dev armhf 1.83.0-2 [257 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams-dev armhf 1.83.0.2 [3292 B]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libboost-regex-dev armhf 1.83.0.2 [3580 B]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libcrypto++8 armhf 8.9.0-1+rpi1 [1035 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libcrypto++-dev armhf 8.9.0-1+rpi1 [1930 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-8 [160 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-8 [119 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-8 [97.3 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-8 [53.2 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-8 [58.3 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libevent-dev armhf 2.1.12-stable-8 [274 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf librdmacm1 armhf 48.0-1.1 [60.2 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libfabric1 armhf 1.17.0-3 [376 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libhwloc15 armhf 2.10.0-1 [131 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libnuma1 armhf 2.0.16-1 [18.4 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libnuma-dev armhf 2.0.16-1 [31.5 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libltdl7 armhf 2.4.7-7 [390 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libltdl-dev armhf 2.4.7-7 [161 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libhwloc-dev armhf 2.10.0-1 [204 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libpciaccess0 armhf 0.17-3 [49.1 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libx11-data all 2:1.8.7-1 [328 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.7-1 [729 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libxnvctrl0 armhf 525.125.06-1 [12.3 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf ocl-icd-libopencl1 armhf 2.3.2-1 [36.8 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libhwloc-plugins armhf 2.10.0-1 [16.1 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libnl-3-dev armhf 3.7.0-0.3 [89.7 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf libnl-route-3-dev armhf 3.7.0-0.3 [160 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libibverbs-dev armhf 48.0-1.1 [193 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libmunge2 armhf 0.5.15-3 [15.8 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libpmix2 armhf 5.0.1-4 [528 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libopenmpi3 armhf 4.1.6-5+rpi1 [1792 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf openmpi-common all 4.1.6-5+rpi1 [166 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg-3 [903 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libpmix-dev armhf 5.0.1-4 [3831 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf openmpi-bin armhf 4.1.6-5+rpi1 [193 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libopenmpi-dev armhf 4.1.6-5+rpi1 [923 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libpstreams-dev all 1.0.3-1 [134 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libterm-readkey-perl armhf 2.38-2+b2 [23.6 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libtext-wrapper-perl all 1.05-4 [10.3 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 67.2 MB in 7s (9441 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12880 files and directories currently installed.)
Preparing to unpack .../00-libuchardet0_0.0.8-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.8-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../01-groff-base_1.23.0-3_armhf.deb ...
Unpacking groff-base (1.23.0-3) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../02-bsdextrautils_2.39.3-6_armhf.deb ...
Unpacking bsdextrautils (2.39.3-6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.5.7-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.12.0-3_armhf.deb ...
Unpacking man-db (2.12.0-3) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../05-libmagic-mgc_1%3a5.45-2_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../06-libmagic1_1%3a5.45-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.45-2) ...
Selecting previously unselected package file.
Preparing to unpack .../07-file_1%3a5.45-2_armhf.deb ...
Unpacking file (1:5.45-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../08-gettext-base_0.21-14_armhf.deb ...
Unpacking gettext-base (0.21-14) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../09-libbsd0_0.11.8-1_armhf.deb ...
Unpacking libbsd0:armhf (0.11.8-1) ...
Selecting previously unselected package libedit2:armhf.
Preparing to unpack .../10-libedit2_3.1-20230828-1_armhf.deb ...
Unpacking libedit2:armhf (3.1-20230828-1) ...
Selecting previously unselected package libcbor0.10:armhf.
Preparing to unpack .../11-libcbor0.10_0.10.2-1.1_armhf.deb ...
Unpacking libcbor0.10:armhf (0.10.2-1.1) ...
Selecting previously unselected package libfido2-1:armhf.
Preparing to unpack .../12-libfido2-1_1.14.0-1_armhf.deb ...
Unpacking libfido2-1:armhf (1.14.0-1) ...
Selecting previously unselected package openssh-client.
Preparing to unpack .../13-openssh-client_1%3a9.6p1-3_armhf.deb ...
Unpacking openssh-client (1:9.6p1-3) ...
Selecting previously unselected package m4.
Preparing to unpack .../14-m4_1.4.19-4_armhf.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../15-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../16-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../17-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../18-autopoint_0.21-14_all.deb ...
Unpacking autopoint (0.21-14) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../19-libdebhelper-perl_13.13_all.deb ...
Unpacking libdebhelper-perl (13.13) ...
Selecting previously unselected package libtool.
Preparing to unpack .../20-libtool_2.4.7-7_all.deb ...
Unpacking libtool (2.4.7-7) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../21-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../22-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../23-libsub-override-perl_0.10-1_all.deb ...
Unpacking libsub-override-perl (0.10-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../24-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../25-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../26-libelf1_0.188-2.1+rpi1_armhf.deb ...
Unpacking libelf1:armhf (0.188-2.1+rpi1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../27-dwz_0.15-1_armhf.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../28-libicu72_72.1-4_armhf.deb ...
Unpacking libicu72:armhf (72.1-4) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../29-libxml2_2.9.14+dfsg-1.3_armhf.deb ...
Unpacking libxml2:armhf (2.9.14+dfsg-1.3) ...
Selecting previously unselected package gettext.
Preparing to unpack .../30-gettext_0.21-14_armhf.deb ...
Unpacking gettext (0.21-14) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../31-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../32-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../33-debhelper_13.13_all.deb ...
Unpacking debhelper (13.13) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../34-libgfortran5_13.2.0-9+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (13.2.0-9+rpi1) ...
Selecting previously unselected package libgfortran-13-dev:armhf.
Preparing to unpack .../35-libgfortran-13-dev_13.2.0-9+rpi1_armhf.deb ...
Unpacking libgfortran-13-dev:armhf (13.2.0-9+rpi1) ...
Selecting previously unselected package gfortran-13.
Preparing to unpack .../36-gfortran-13_13.2.0-9+rpi1_armhf.deb ...
Unpacking gfortran-13 (13.2.0-9+rpi1) ...
Selecting previously unselected package libnl-3-200:armhf.
Preparing to unpack .../37-libnl-3-200_3.7.0-0.3_armhf.deb ...
Unpacking libnl-3-200:armhf (3.7.0-0.3) ...
Selecting previously unselected package libnl-route-3-200:armhf.
Preparing to unpack .../38-libnl-route-3-200_3.7.0-0.3_armhf.deb ...
Unpacking libnl-route-3-200:armhf (3.7.0-0.3) ...
Selecting previously unselected package libibverbs1:armhf.
Preparing to unpack .../39-libibverbs1_48.0-1.1_armhf.deb ...
Unpacking libibverbs1:armhf (48.0-1.1) ...
Selecting previously unselected package ibverbs-providers:armhf.
Preparing to unpack .../40-ibverbs-providers_48.0-1.1_armhf.deb ...
Unpacking ibverbs-providers:armhf (48.0-1.1) ...
Selecting previously unselected package icu-devtools.
Preparing to unpack .../41-icu-devtools_72.1-4_armhf.deb ...
Unpacking icu-devtools (72.1-4) ...
Selecting previously unselected package libboost1.83-dev:armhf.
Preparing to unpack .../42-libboost1.83-dev_1.83.0-2_armhf.deb ...
Unpacking libboost1.83-dev:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-atomic1.83.0:armhf.
Preparing to unpack .../43-libboost-atomic1.83.0_1.83.0-2_armhf.deb ...
Unpacking libboost-atomic1.83.0:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-atomic1.83-dev:armhf.
Preparing to unpack .../44-libboost-atomic1.83-dev_1.83.0-2_armhf.deb ...
Unpacking libboost-atomic1.83-dev:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-filesystem1.83.0:armhf.
Preparing to unpack .../45-libboost-filesystem1.83.0_1.83.0-2_armhf.deb ...
Unpacking libboost-filesystem1.83.0:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-system1.83.0:armhf.
Preparing to unpack .../46-libboost-system1.83.0_1.83.0-2_armhf.deb ...
Unpacking libboost-system1.83.0:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-system1.83-dev:armhf.
Preparing to unpack .../47-libboost-system1.83-dev_1.83.0-2_armhf.deb ...
Unpacking libboost-system1.83-dev:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-filesystem1.83-dev:armhf.
Preparing to unpack .../48-libboost-filesystem1.83-dev_1.83.0-2_armhf.deb ...
Unpacking libboost-filesystem1.83-dev:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-filesystem-dev:armhf.
Preparing to unpack .../49-libboost-filesystem-dev_1.83.0.2_armhf.deb ...
Unpacking libboost-filesystem-dev:armhf (1.83.0.2) ...
Selecting previously unselected package libboost-regex1.83.0:armhf.
Preparing to unpack .../50-libboost-regex1.83.0_1.83.0-2_armhf.deb ...
Unpacking libboost-regex1.83.0:armhf (1.83.0-2) ...
Selecting previously unselected package libicu-dev:armhf.
Preparing to unpack .../51-libicu-dev_72.1-4_armhf.deb ...
Unpacking libicu-dev:armhf (72.1-4) ...
Selecting previously unselected package libboost-regex1.83-dev:armhf.
Preparing to unpack .../52-libboost-regex1.83-dev_1.83.0-2_armhf.deb ...
Unpacking libboost-regex1.83-dev:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-iostreams1.83.0:armhf.
Preparing to unpack .../53-libboost-iostreams1.83.0_1.83.0-2_armhf.deb ...
Unpacking libboost-iostreams1.83.0:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-iostreams1.83-dev:armhf.
Preparing to unpack .../54-libboost-iostreams1.83-dev_1.83.0-2_armhf.deb ...
Unpacking libboost-iostreams1.83-dev:armhf (1.83.0-2) ...
Selecting previously unselected package libboost-iostreams-dev:armhf.
Preparing to unpack .../55-libboost-iostreams-dev_1.83.0.2_armhf.deb ...
Unpacking libboost-iostreams-dev:armhf (1.83.0.2) ...
Selecting previously unselected package libboost-regex-dev:armhf.
Preparing to unpack .../56-libboost-regex-dev_1.83.0.2_armhf.deb ...
Unpacking libboost-regex-dev:armhf (1.83.0.2) ...
Selecting previously unselected package libcrypto++8:armhf.
Preparing to unpack .../57-libcrypto++8_8.9.0-1+rpi1_armhf.deb ...
Unpacking libcrypto++8:armhf (8.9.0-1+rpi1) ...
Selecting previously unselected package libcrypto++-dev:armhf.
Preparing to unpack .../58-libcrypto++-dev_8.9.0-1+rpi1_armhf.deb ...
Unpacking libcrypto++-dev:armhf (8.9.0-1+rpi1) ...
Selecting previously unselected package libevent-2.1-7:armhf.
Preparing to unpack .../59-libevent-2.1-7_2.1.12-stable-8_armhf.deb ...
Unpacking libevent-2.1-7:armhf (2.1.12-stable-8) ...
Selecting previously unselected package libevent-core-2.1-7:armhf.
Preparing to unpack .../60-libevent-core-2.1-7_2.1.12-stable-8_armhf.deb ...
Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-8) ...
Selecting previously unselected package libevent-extra-2.1-7:armhf.
Preparing to unpack .../61-libevent-extra-2.1-7_2.1.12-stable-8_armhf.deb ...
Unpacking libevent-extra-2.1-7:armhf (2.1.12-stable-8) ...
Selecting previously unselected package libevent-pthreads-2.1-7:armhf.
Preparing to unpack .../62-libevent-pthreads-2.1-7_2.1.12-stable-8_armhf.deb ...
Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-8) ...
Selecting previously unselected package libevent-openssl-2.1-7:armhf.
Preparing to unpack .../63-libevent-openssl-2.1-7_2.1.12-stable-8_armhf.deb ...
Unpacking libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ...
Selecting previously unselected package libevent-dev.
Preparing to unpack .../64-libevent-dev_2.1.12-stable-8_armhf.deb ...
Unpacking libevent-dev (2.1.12-stable-8) ...
Selecting previously unselected package librdmacm1:armhf.
Preparing to unpack .../65-librdmacm1_48.0-1.1_armhf.deb ...
Unpacking librdmacm1:armhf (48.0-1.1) ...
Selecting previously unselected package libfabric1:armhf.
Preparing to unpack .../66-libfabric1_1.17.0-3_armhf.deb ...
Unpacking libfabric1:armhf (1.17.0-3) ...
Selecting previously unselected package libhwloc15:armhf.
Preparing to unpack .../67-libhwloc15_2.10.0-1_armhf.deb ...
Unpacking libhwloc15:armhf (2.10.0-1) ...
Selecting previously unselected package libnuma1:armhf.
Preparing to unpack .../68-libnuma1_2.0.16-1_armhf.deb ...
Unpacking libnuma1:armhf (2.0.16-1) ...
Selecting previously unselected package libnuma-dev:armhf.
Preparing to unpack .../69-libnuma-dev_2.0.16-1_armhf.deb ...
Unpacking libnuma-dev:armhf (2.0.16-1) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../70-libltdl7_2.4.7-7_armhf.deb ...
Unpacking libltdl7:armhf (2.4.7-7) ...
Selecting previously unselected package libltdl-dev:armhf.
Preparing to unpack .../71-libltdl-dev_2.4.7-7_armhf.deb ...
Unpacking libltdl-dev:armhf (2.4.7-7) ...
Selecting previously unselected package libhwloc-dev:armhf.
Preparing to unpack .../72-libhwloc-dev_2.10.0-1_armhf.deb ...
Unpacking libhwloc-dev:armhf (2.10.0-1) ...
Selecting previously unselected package libpciaccess0:armhf.
Preparing to unpack .../73-libpciaccess0_0.17-3_armhf.deb ...
Unpacking libpciaccess0:armhf (0.17-3) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../74-libxau6_1%3a1.0.9-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../75-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../76-libxcb1_1.15-1_armhf.deb ...
Unpacking libxcb1:armhf (1.15-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../77-libx11-data_2%3a1.8.7-1_all.deb ...
Unpacking libx11-data (2:1.8.7-1) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../78-libx11-6_2%3a1.8.7-1_armhf.deb ...
Unpacking libx11-6:armhf (2:1.8.7-1) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../79-libxext6_2%3a1.3.4-1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.4-1) ...
Selecting previously unselected package libxnvctrl0:armhf.
Preparing to unpack .../80-libxnvctrl0_525.125.06-1_armhf.deb ...
Unpacking libxnvctrl0:armhf (525.125.06-1) ...
Selecting previously unselected package ocl-icd-libopencl1:armhf.
Preparing to unpack .../81-ocl-icd-libopencl1_2.3.2-1_armhf.deb ...
Unpacking ocl-icd-libopencl1:armhf (2.3.2-1) ...
Selecting previously unselected package libhwloc-plugins:armhf.
Preparing to unpack .../82-libhwloc-plugins_2.10.0-1_armhf.deb ...
Unpacking libhwloc-plugins:armhf (2.10.0-1) ...
Selecting previously unselected package libnl-3-dev:armhf.
Preparing to unpack .../83-libnl-3-dev_3.7.0-0.3_armhf.deb ...
Unpacking libnl-3-dev:armhf (3.7.0-0.3) ...
Selecting previously unselected package libnl-route-3-dev:armhf.
Preparing to unpack .../84-libnl-route-3-dev_3.7.0-0.3_armhf.deb ...
Unpacking libnl-route-3-dev:armhf (3.7.0-0.3) ...
Selecting previously unselected package libibverbs-dev:armhf.
Preparing to unpack .../85-libibverbs-dev_48.0-1.1_armhf.deb ...
Unpacking libibverbs-dev:armhf (48.0-1.1) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../86-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../87-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
Selecting previously unselected package libmunge2:armhf.
Preparing to unpack .../88-libmunge2_0.5.15-3_armhf.deb ...
Unpacking libmunge2:armhf (0.5.15-3) ...
Selecting previously unselected package libpmix2:armhf.
Preparing to unpack .../89-libpmix2_5.0.1-4_armhf.deb ...
Unpacking libpmix2:armhf (5.0.1-4) ...
Selecting previously unselected package libopenmpi3:armhf.
Preparing to unpack .../90-libopenmpi3_4.1.6-5+rpi1_armhf.deb ...
Unpacking libopenmpi3:armhf (4.1.6-5+rpi1) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../91-openmpi-common_4.1.6-5+rpi1_all.deb ...
Unpacking openmpi-common (4.1.6-5+rpi1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../92-zlib1g-dev_1%3a1.3.dfsg-3_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3) ...
Selecting previously unselected package libpmix-dev:armhf.
Preparing to unpack .../93-libpmix-dev_5.0.1-4_armhf.deb ...
Unpacking libpmix-dev:armhf (5.0.1-4) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../94-openmpi-bin_4.1.6-5+rpi1_armhf.deb ...
Unpacking openmpi-bin (4.1.6-5+rpi1) ...
Selecting previously unselected package libopenmpi-dev:armhf.
Preparing to unpack .../95-libopenmpi-dev_4.1.6-5+rpi1_armhf.deb ...
Unpacking libopenmpi-dev:armhf (4.1.6-5+rpi1) ...
Selecting previously unselected package libpstreams-dev.
Preparing to unpack .../96-libpstreams-dev_1.0.3-1_all.deb ...
Unpacking libpstreams-dev (1.0.3-1) ...
Selecting previously unselected package libterm-readkey-perl.
Preparing to unpack .../97-libterm-readkey-perl_2.38-2+b2_armhf.deb ...
Unpacking libterm-readkey-perl (2.38-2+b2) ...
Selecting previously unselected package libtext-wrapper-perl.
Preparing to unpack .../98-libtext-wrapper-perl_1.05-4_all.deb ...
Unpacking libtext-wrapper-perl (1.05-4) ...
Selecting previously unselected package sbuild-build-depends-murasaki-dummy.
Preparing to unpack .../99-sbuild-build-depends-murasaki-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-murasaki-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libpciaccess0:armhf (0.17-3) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libboost1.83-dev:armhf (1.83.0-2) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up bsdextrautils (2.39.3-6) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libcbor0.10:armhf (0.10.2-1.1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libboost-regex1.83.0:armhf (1.83.0-2) ...
Setting up libdebhelper-perl (13.13) ...
Setting up libboost-system1.83.0:armhf (1.83.0-2) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up gettext-base (0.21-14) ...
Setting up m4 (1.4.19-4) ...
Setting up libcrypto++8:armhf (8.9.0-1+rpi1) ...
Setting up file (1:5.45-2) ...
Setting up libtext-wrapper-perl (1.05-4) ...
Setting up libboost-filesystem1.83.0:armhf (1.83.0-2) ...
Setting up libboost-atomic1.83.0:armhf (1.83.0-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libmunge2:armhf (0.5.15-3) ...
Setting up libx11-data (2:1.8.7-1) ...
Setting up libboost-iostreams1.83.0:armhf (1.83.0-2) ...
Setting up libhwloc15:armhf (2.10.0-1) ...
Setting up libevent-core-2.1-7:armhf (2.1.12-stable-8) ...
Setting up libevent-2.1-7:armhf (2.1.12-stable-8) ...
Setting up autopoint (0.21-14) ...
Setting up icu-devtools (72.1-4) ...
Setting up libltdl7:armhf (2.4.7-7) ...
Setting up libgfortran5:armhf (13.2.0-9+rpi1) ...
Setting up libboost-atomic1.83-dev:armhf (1.83.0-2) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:armhf (1:1.3.dfsg-3) ...
Setting up libnuma1:armhf (2.0.16-1) ...
Setting up ocl-icd-libopencl1:armhf (2.3.2-1) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libnl-3-200:armhf (3.7.0-0.3) ...
Setting up openmpi-common (4.1.6-5+rpi1) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libboost-system1.83-dev:armhf (1.83.0-2) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libterm-readkey-perl (2.38-2+b2) ...
Setting up libfido2-1:armhf (1.14.0-1) ...
Setting up libgfortran-13-dev:armhf (13.2.0-9+rpi1) ...
Setting up libbsd0:armhf (0.11.8-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libicu-dev:armhf (72.1-4) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-8) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-8) ...
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-14) ...
Setting up libtool (2.4.7-7) ...
Setting up libedit2:armhf (3.1-20230828-1) ...
Setting up libcrypto++-dev:armhf (8.9.0-1+rpi1) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ...
Setting up libboost-filesystem1.83-dev:armhf (1.83.0-2) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnuma-dev:armhf (2.0.16-1) ...
Setting up libnl-route-3-200:armhf (3.7.0-0.3) ...
Setting up dh-autoreconf (20) ...
Setting up libltdl-dev:armhf (2.4.7-7) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up gfortran-13 (13.2.0-9+rpi1) ...
Setting up libevent-dev (2.1.12-stable-8) ...
Setting up libpstreams-dev (1.0.3-1) ...
Setting up libboost-regex1.83-dev:armhf (1.83.0-2) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up libnl-3-dev:armhf (3.7.0-0.3) ...
Setting up groff-base (1.23.0-3) ...
Setting up libx11-6:armhf (2:1.8.7-1) ...
Setting up libhwloc-dev:armhf (2.10.0-1) ...
Setting up libboost-regex-dev:armhf (1.83.0.2) ...
Setting up libboost-filesystem-dev:armhf (1.83.0.2) ...
Setting up libibverbs1:armhf (48.0-1.1) ...
Setting up ibverbs-providers:armhf (48.0-1.1) ...
Setting up libboost-iostreams1.83-dev:armhf (1.83.0-2) ...
Setting up openssh-client (1:9.6p1-3) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libboost-iostreams-dev:armhf (1.83.0.2) ...
Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxnvctrl0:armhf (525.125.06-1) ...
Setting up libnl-route-3-dev:armhf (3.7.0-0.3) ...
Setting up librdmacm1:armhf (48.0-1.1) ...
Setting up debhelper (13.13) ...
Setting up libibverbs-dev:armhf (48.0-1.1) ...
Setting up libhwloc-plugins:armhf (2.10.0-1) ...
Setting up libfabric1:armhf (1.17.0-3) ...
Setting up libpmix2:armhf (5.0.1-4) ...
Setting up libopenmpi3:armhf (4.1.6-5+rpi1) ...
Setting up libpmix-dev:armhf (5.0.1-4) ...
Setting up openmpi-bin (4.1.6-5+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 (4.1.6-5+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 sbuild-build-depends-murasaki-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-13+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.2+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 libc6-dev_2.37-13+rpi1 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 linux-libc-dev_6.5.6-1+rpi1+b1
Package versions: adduser_3.137 apt_2.7.9 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.4-3 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-9+rpi1 dash_0.5.12-6 debconf_1.5.83 debhelper_13.13 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.2+rpi1 dpkg-dev_1.22.2+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 gcc-13-base_13.2.0-9+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-14 gettext-base_0.21-14 gfortran-13_13.2.0-9+rpi1 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu2 ibverbs-providers_48.0-1.1 icu-devtools_72.1-4 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-5 libacl1_2.3.1-6 libapt-pkg6.0_2.7.9 libarchive-zip-perl_1.68-1 libasan8_13.2.0-9+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-9+rpi1 libattr1_1:2.5.1-5 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-6 libboost-atomic1.83-dev_1.83.0-2 libboost-atomic1.83.0_1.83.0-2 libboost-filesystem-dev_1.83.0.2 libboost-filesystem1.83-dev_1.83.0-2 libboost-filesystem1.83.0_1.83.0-2 libboost-iostreams-dev_1.83.0.2 libboost-iostreams1.83-dev_1.83.0-2 libboost-iostreams1.83.0_1.83.0-2 libboost-regex-dev_1.83.0.2 libboost-regex1.83-dev_1.83.0-2 libboost-regex1.83.0_1.83.0-2 libboost-system1.83-dev_1.83.0-2 libboost-system1.83.0_1.83.0-2 libboost1.83-dev_1.83.0-2 libbsd0_0.11.8-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-13+rpi1 libc-dev-bin_2.37-13+rpi1 libc6_2.37-13+rpi1 libc6-dev_2.37-13+rpi1 libcap-ng0_0.8.4-1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcbor0.10_0.10.2-1.1 libcc1-0_13.2.0-9+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcrypto++-dev_8.9.0-1+rpi1 libcrypto++8_8.9.0-1+rpi1 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.13 libdpkg-perl_1.22.2+rpi1 libedit2_3.1-20230828-1 libelf1_0.188-2.1+rpi1 libevent-2.1-7_2.1.12-stable-8 libevent-core-2.1-7_2.1.12-stable-8 libevent-dev_2.1.12-stable-8 libevent-extra-2.1-7_2.1.12-stable-8 libevent-openssl-2.1-7_2.1.12-stable-8 libevent-pthreads-2.1-7_2.1.12-stable-8 libext2fs2_1.47.0-2 libfabric1_1.17.0-3 libfakeroot_1.33-1 libffi8_3.4.4-2 libfido2-1_1.14.0-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-9+rpi1 libgcc-s1_13.2.0-9+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran-13-dev_13.2.0-9+rpi1 libgfortran5_13.2.0-9+rpi1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.3-1 libgomp1_13.2.0-9+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhwloc-dev_2.10.0-1 libhwloc-plugins_2.10.0-1 libhwloc15_2.10.0-1 libibverbs-dev_48.0-1.1 libibverbs1_48.0-1.1 libicu-dev_72.1-4 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1+b1 libltdl-dev_2.4.7-7 libltdl7_2.4.7-7 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-2 libmount1_2.39.3-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libmunge2_0.5.15-3 libncursesw6_6.4+20240113-1 libnettle8_3.9.1-2 libnl-3-200_3.7.0-0.3 libnl-3-dev_3.7.0-0.3 libnl-route-3-200_3.7.0-0.3 libnl-route-3-dev_3.7.0-0.3 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnuma-dev_2.0.16-1 libnuma1_2.0.16-1 libnumber-compare-perl_0.03-3 libopenmpi-dev_4.1.6-5+rpi1 libopenmpi3_4.1.6-5+rpi1 libp11-kit0_0.25.3-4 libpam-cap_1:2.66-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpciaccess0_0.17-3 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libpmix-dev_5.0.1-4 libpmix2_5.0.1-4 libpstreams-dev_1.0.3-1 librdmacm1_48.0-1.1 libreadline8_8.2-3 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol1_3.1-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-6 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssl1.1_1.1.1o-1 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libterm-readkey-perl_2.38-2+b2 libtext-glob-perl_0.11-3 libtext-wrapper-perl_1.05-4 libtinfo6_6.4+20240113-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-9+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-6 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.14+dfsg-1.3 libxnvctrl0_525.125.06-1 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1+b1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 mount_2.39.3-6 nano_7.2-2 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 netbase_6.4 ocl-icd-libopencl1_2.3.2-1 openmpi-bin_4.1.6-5+rpi1 openmpi-common_4.1.6-5+rpi1 openssh-client_1:9.6p1-3 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-murasaki-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.08-5 tar_1.35+dfsg-3 tzdata_2023d-1 usrmerge_38 util-linux_2.39.3-6 util-linux-extra_2.39.3-6 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Sun Aug 15 18:43:27 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./murasaki_1.68.6-13.dsc: no acceptable signature found
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.orig-debian-tests-data.tar.gz
dpkg-source: info: unpacking murasaki_1.68.6-13.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying gcc11.patch
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 disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.68.6-13+b6
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=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-90c60970-fcfb-48b6-a532-d6e9ce74a690
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package murasaki
dpkg-buildpackage: info: source version 1.68.6-13+b6
dpkg-buildpackage: info: source distribution trixie-staging
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
In file included from murasaki.h:24,
from sequence.cc:28:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from murasaki.h:24,
from murasaki.cc:37:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from murasaki.cc:29:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from murasaki.h:24,
from dinkymath.cc:27:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from dinkymath.h:24,
from dinkymath.cc:26:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
sequence.cc: In destructor 'Sequence::~Sequence()':
sequence.cc:377:9: 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:377:9: note: in C++11 destructors default to 'noexcept'
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 'void BitSequence::loadBinary(const SequenceBinary&)':
sequence.cc:1113:9: 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++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/bits/stl_tree.h:63:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
187 | struct pair
| ^~~~
sequence.cc:1114:9: 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]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
187 | struct pair
| ^~~~
sequence.cc: In destructor 'BitSequence::~BitSequence()':
sequence.cc:1394:9: 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:1394:9: 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]);
| ^~~~~~~~
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.cc:41:
hashing.h: In instantiation of 'SBox<T>::SBox(int) [with T = short unsigned int]':
sequence.cc:162:29: required from here
hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
56 | random_shuffle(boxes[b],boxes[b]+boxsize);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/algorithm:61,
from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
from /usr/include/boost/regex/v5/regex.hpp:29,
from /usr/include/boost/regex.hpp:34,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32:
/usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here
4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
| ^~~~~~~~~~~~~~
murasaki.cc: In function 'bool convertPattern(std::string&)':
murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<char*, __cxx11::basic_string<char> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
1287 | random_shuffle(randomStr.begin(),randomStr.end());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/algorithm:61,
from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
from /usr/include/boost/regex/v5/regex.hpp:29,
from /usr/include/boost/regex.hpp:34,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32:
/usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here
4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
| ^~~~~~~~~~~~~~
In file included from sequence.h:44:
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:1110:17: 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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair<long int, long int>' declared here
187 | struct pair
| ^~~~
In file included from msethash.cc:25:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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
In file included from options.h:28,
from options.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ecolist.h:23,
from ecohash.h:29,
from ecohash.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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 ecolist.h:23,
from ecolist.cc:20:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from murasaki.cc:31:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
ecolist.cc:467:26: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algo.h:61:
/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
254 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: 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++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void MurasakiRuntime::prep()' at murasaki.cc:378:26:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void MurasakiRuntime::prep()' at murasaki.cc:414:25:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1034 | _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
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++/13/vector:72,
from scoring.h:27,
from sequence.h:31:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'double HashMethod::fitnessCheck()' at sequence.cc:1430:17:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const HashMethod&}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {HashMethod}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' changed in GCC 7.1
In file included from murasaki.h:24,
from murasaki_mpi.cc:33:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/map:62,
from /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42,
from /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:2911,
from murasaki_mpi.cc:29:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
murasaki_mpi.cc:89:29: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
89 | struct lt_mpi_worldMemory : binary_function<int,int,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
murasaki_mpi.cc:95:29: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
95 | struct gt_mpi_worldMemory : binary_function<int,int,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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;
| ^~~~~~~~~
In file included from murasaki.h:24,
from arrayhash.cc:28:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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
/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1910:25,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_algo.h:1635:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1635 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1911:23,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_heap.h:425:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
425 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {HashMethod}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]' at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1639:20:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1645:7:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1645:7:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]',
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1662:17:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]',
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1666:17:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1672:9:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1672:9:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc
seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)':
seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations]
264 | stitchPath=stitchfile.branch_path();
| ~~~~~~~~~~~~~~~~~~~~~~^~
In file included from seqread.cc:35:
/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here
1129 | path branch_path() const { return parent_path(); }
| ^~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from scoring.h:27,
from sequence.h:31:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
murasaki_mpi.cc: In function 'void mpi_types_init()':
murasaki_mpi.cc:107:18: warning: 'msg' may be used uninitialized [-Wmaybe-uninitialized]
107 | MPI_Get_address(&msg.key,disp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1589:20: note: by argument 1 of type 'const void*' to 'int MPI_Get_address(const void*, MPI_Aint*)' declared here
1589 | OMPI_DECLSPEC int MPI_Get_address(const void *location, MPI_Aint *address);
| ^~~~~~~~~~~~~~~
murasaki_mpi.cc:102:19: note: 'msg' declared here
102 | MPI_HashMessage msg;
| ^~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void mpi_types_init()' at murasaki_mpi.cc:120:22:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from murasaki.h:24,
from scoring.cc:27:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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
In file included from ecolist.h:23,
from openhash.h:29,
from openhash.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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:158:9: 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++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/string:51,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/istream:40,
from /usr/include/c++/13/fstream:40,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/13/bits/stl_pair.h:187:12: 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
187 | struct pair
| ^~~~
binseq.cc:160:9: 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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_pair.h:187:12: 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
187 | struct pair
| ^~~~
binseq.cc:162:9: 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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_pair.h:187:12: 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
187 | 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
cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::sampleHighLow(double, double)':
cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
339 | delete alt;
| ^~~
cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)'
330 | pix *alt=new pix[size];
| ^
cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::sampleHighLow(int, int)':
cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
354 | delete alt;
| ^~~
cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)'
345 | pix *alt=new pix[size];
| ^
cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::findNiceRange()':
cgr.cc:395:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
395 | delete alt;
| ^~~
cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)'
376 | pix *alt=new pix[size];
| ^
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: 'width' may be used uninitialized [-Wmaybe-uninitialized]
557 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:493:7: note: 'width' was declared here
493 | int width,height;
| ^~~~~
cgr.cc:557:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized]
557 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:493:13: note: 'height' was declared here
493 | int width,height;
| ^~~~~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized]
485 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:426:7: note: 'width' was declared here
426 | int width,height;
| ^~~~~
cgr.cc:485:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized]
485 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:426:13: note: 'height' was declared here
426 | int width,height;
| ^~~~~~
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;
| ^~~~~~~~~~
In file included from ecolist.h:23,
from testeco.cc:20:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:41: 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 alignments.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-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
In file included from align-best.cc:33:
In function 'std::ostream& Itree::operator<<(std::ostream&, const Interval<_IntType>&) [with _IntType = long int]',
inlined from 'int main(int, char**)' at align-best.cc:173:35:
itree.h:79:27: warning: array subscript -1 is outside array bounds of 'Itree::Interval<long int> [268435455]' [-Warray-bounds=]
79 | return os << "[" << i.start << "~" << i.stop << "]";
| ~~^~~~~
itree.h:79:45: warning: array subscript -1 is outside array bounds of 'Itree::Interval<long int> [268435455]' [-Warray-bounds=]
79 | return os << "[" << i.start << "~" << i.stop << "]";
| ~~^~~~
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;
| ^~~~~~~~
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
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 ../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 ../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 ../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 ../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 ../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
In file included from murasaki.h:24,
from dinkymath.cc:27:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from dinkymath.h:24,
from dinkymath.cc:26:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from murasaki.h:24,
from sequence.cc:28:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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;
| ^~~~
In file included from murasaki.h:24,
from murasaki.cc:37:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from murasaki.cc:29:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)':
sequence.cc:1113:9: 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++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/bits/stl_tree.h:63:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
187 | struct pair
| ^~~~
sequence.cc:1114:9: 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]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
187 | struct pair
| ^~~~
sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
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;
| ^~~~~~~
murasaki.cc: In function 'bool convertPattern(std::string&)':
murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<char*, __cxx11::basic_string<char> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
1287 | random_shuffle(randomStr.begin(),randomStr.end());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/algorithm:61,
from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
from /usr/include/boost/regex/v5/regex.hpp:29,
from /usr/include/boost/regex.hpp:34,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32:
/usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here
4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
| ^~~~~~~~~~~~~~
In file included from sequence.cc:41:
hashing.h: In instantiation of 'SBox<T>::SBox(int) [with T = short unsigned int]':
sequence.cc:162:29: required from here
hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
56 | random_shuffle(boxes[b],boxes[b]+boxsize);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/algorithm:61,
from /usr/include/boost/regex/v5/regex_workaround.hpp:23,
from /usr/include/boost/regex/v5/regex.hpp:29,
from /usr/include/boost/regex.hpp:34,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32:
/usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here
4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
| ^~~~~~~~~~~~~~
In file included from sequence.h:44:
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:1110:17: 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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair<long int, long int>' declared here
187 | struct pair
| ^~~~
In file included from msethash.cc:25:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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
In file included from options.h:28,
from options.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ecolist.h:23,
from ecohash.h:29,
from ecohash.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecolist.cc
In file included from ecolist.h:23,
from ecolist.cc:20:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ecolist.cc:467:26: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algo.h:61:
/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
254 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c seqread.cc
In file included from /usr/include/c++/13/vector:72,
from scoring.h:27,
from sequence.h:31:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
529 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'double HashMethod::fitnessCheck()' at sequence.cc:1430:17:
/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1034 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const HashMethod&}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {HashMethod}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<HashMethod>::iterator' changed in GCC 7.1
In file included from murasaki.h:24,
from arrayhash.cc:28:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)':
seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations]
264 | stitchPath=stitchfile.branch_path();
| ~~~~~~~~~~~~~~~~~~~~~~^~
In file included from seqread.cc:35:
/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here
1129 | path branch_path() const { return parent_path(); }
| ^~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.cc
/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1910:25,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_algo.h:1635:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1635 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1911:23,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_heap.h:425:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
425 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {HashMethod}; _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]' at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1639:20:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1645:7:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1645:7:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]',
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1662:17:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = HashMethod; _Alloc = std::allocator<HashMethod>]',
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1666:17:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1672:9:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18,
inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1672:9:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c openhash.cc
In file included from murasaki.h:24,
from scoring.cc:27:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c genopts.cc
In file included from ecolist.h:23,
from openhash.h:29,
from openhash.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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
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;
| ^~~~~~~~~
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:158:9: 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++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/string:51,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/istream:40,
from /usr/include/c++/13/fstream:40,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/13/bits/stl_pair.h:187:12: 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
187 | struct pair
| ^~~~
binseq.cc:160:9: 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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_pair.h:187:12: 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
187 | struct pair
| ^~~~
binseq.cc:162:9: 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));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_pair.h:187:12: 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
187 | struct pair
| ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-compare.cc
cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::sampleHighLow(double, double)':
cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
339 | delete alt;
| ^~~
cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)'
330 | pix *alt=new pix[size];
| ^
cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::sampleHighLow(int, int)':
cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
354 | delete alt;
| ^~~
cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)'
345 | pix *alt=new pix[size];
| ^
cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> Cgr::findNiceRange()':
cgr.cc:395:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
395 | delete alt;
| ^~~
cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)'
376 | pix *alt=new pix[size];
| ^
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: 'width' may be used uninitialized [-Wmaybe-uninitialized]
557 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:493:7: note: 'width' was declared here
493 | int width,height;
| ^~~~~
cgr.cc:557:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized]
557 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:493:13: note: 'height' was declared here
493 | int width,height;
| ^~~~~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)':
cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized]
485 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:426:7: note: 'width' was declared here
426 | int width,height;
| ^~~~~
cgr.cc:485:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized]
485 | if(data.size()<(uint)(height*width))
| ~~~~~~~^~~~~~~
cgr.cc:426:13: note: 'height' was declared here
426 | int width,height;
| ^~~~~~
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
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;
| ^~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c alignments.cc
In file included from ecolist.h:23,
from testeco.cc:20:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_tree.h:65,
from /usr/include/c++/13/set:62,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:41: 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 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
In file included from align-best.cc:33:
In function 'std::ostream& Itree::operator<<(std::ostream&, const Interval<_IntType>&) [with _IntType = long int]',
inlined from 'int main(int, char**)' at align-best.cc:173:35:
itree.h:79:27: warning: array subscript -1 is outside array bounds of 'Itree::Interval<long int> [268435455]' [-Warray-bounds=]
79 | return os << "[" << i.start << "~" << i.stop << "]";
| ~~^~~~~
itree.h:79:45: warning: array subscript -1 is outside array bounds of 'Itree::Interval<long int> [268435455]' [-Warray-bounds=]
79 | return os << "[" << i.start << "~" << i.stop << "]";
| ~~^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.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 -c mbfa.cc
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 ../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 ../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 ../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_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-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-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/bin/mbfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/mbfa-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-best contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-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/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/bin/murasaki contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/geneparse-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-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-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-and contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-or contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-image contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/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/align-coverage-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-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/align-compare-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' in '../murasaki_1.68.6-13+b6_armhf.deb'.
dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-13+b6_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-13+b6_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-13+b6_armhf.deb'.
dpkg-genbuildinfo --build=any -O../murasaki_1.68.6-13+b6_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../murasaki_1.68.6-13+b6_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 2024-02-07T22:57:08Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
murasaki_1.68.6-13+b6_armhf.changes:
------------------------------------
Format: 1.8
Date: Mon, 16 Aug 2021 00:06:48 +0530
Source: murasaki (1.68.6-13)
Binary: murasaki murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 1.68.6-13+b6
Distribution: trixie-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
murasaki - homology detection tool across multiple large genomes
murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio
Changes:
murasaki (1.68.6-13+b6) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
562f08febd63578569dd3e4bc4e1c0058c2f3623 13789708 murasaki-dbgsym_1.68.6-13+b6_armhf.deb
2d820bc84d5d25bab40b7c1576baf790c82616a3 14433484 murasaki-mpi-dbgsym_1.68.6-13+b6_armhf.deb
debddecbf0874780c87f3866bc90d365650216c2 468028 murasaki-mpi_1.68.6-13+b6_armhf.deb
7480a55a03849ff3a55bae10b5a51bbca83f0adc 8474 murasaki_1.68.6-13+b6_armhf.buildinfo
418bdb9a0dace5f6efcf5bee1f5e187f5f91f680 433164 murasaki_1.68.6-13+b6_armhf.deb
Checksums-Sha256:
dbab0555fd606cc5ce365bc0cf098a776971895d1cb7ef24dc5c03ffb8e09722 13789708 murasaki-dbgsym_1.68.6-13+b6_armhf.deb
4f6c17293fa82e406b8f7859861417c8e6d567591edcfb19339ed74433922a53 14433484 murasaki-mpi-dbgsym_1.68.6-13+b6_armhf.deb
fd4f60f98265077553c4a327a1c57c4992e8937f0d070f3d238ad31dde94e14d 468028 murasaki-mpi_1.68.6-13+b6_armhf.deb
8809d6644815fdc9e6fa7de015e43f6d7fc10f18453e544c15f8b7b09b6d7b8f 8474 murasaki_1.68.6-13+b6_armhf.buildinfo
51101b1d6acc882f6461362dfa1995ab54a17367cea89edd28f3aa05271ff651 433164 murasaki_1.68.6-13+b6_armhf.deb
Files:
275914dd1dbdc308f630158e0b64060b 13789708 debug optional murasaki-dbgsym_1.68.6-13+b6_armhf.deb
fcda83acea4b61c21d5cbd0b7e875c13 14433484 debug optional murasaki-mpi-dbgsym_1.68.6-13+b6_armhf.deb
e677f43cbdc055795f8af65e2c71402c 468028 science optional murasaki-mpi_1.68.6-13+b6_armhf.deb
d764cd47cdec7d14ab016ac980b7845d 8474 science optional murasaki_1.68.6-13+b6_armhf.buildinfo
7367f3ab6882f68aa1f8e89a5b024e8d 433164 science optional murasaki_1.68.6-13+b6_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
murasaki-dbgsym_1.68.6-13+b6_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 13789708 bytes: control archive=1192 bytes.
890 bytes, 12 lines control
1466 bytes, 14 lines md5sums
Package: murasaki-dbgsym
Source: murasaki (1.68.6-13)
Version: 1.68.6-13+b6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 14830
Depends: murasaki (= 1.68.6-13+b6)
Section: debug
Priority: optional
Description: debug symbols for murasaki
Build-Ids: 00f520b14a92b22bb87c56e3065c8cd10666745b 0268664b68527175198a795bd3bd10772697ef4b 74bfbd03c5e910e0ac4512ce1dc6edb12bd9a7f8 7822f9d8cf527be9fd38fb28f2c445ae23b4c1fb 7a0a516835a7d57488e174fb53720f37fe071d02 8e25cdb57bcd0ff68d42679e6b4fc47c9ce0c83e b4c45ae836387970906ebee8f74bf399afcce737 c7373fc15e34dfb8564a87b8c9e06d87bf42efb4 c9417fe08478419542050072ba1fd63db117e1ea df0d99b0a95f54f77ba382215a06d287cc499417 e4c8572445c890dff1f32421c48a3f399752cc94 ef42db7f26113b19b195ad7efb33da8f9f9d749b fdec87e147d1127a31ea93e1f7b91769de785f06
drwxr-xr-x root/root 0 2021-08-15 18:36 ./
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/00/
-rw-r--r-- root/root 955020 2021-08-15 18:36 ./usr/lib/debug/.build-id/00/f520b14a92b22bb87c56e3065c8cd10666745b.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/02/
-rw-r--r-- root/root 1139240 2021-08-15 18:36 ./usr/lib/debug/.build-id/02/68664b68527175198a795bd3bd10772697ef4b.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/74/
-rw-r--r-- root/root 3451464 2021-08-15 18:36 ./usr/lib/debug/.build-id/74/bfbd03c5e910e0ac4512ce1dc6edb12bd9a7f8.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/78/
-rw-r--r-- root/root 1108680 2021-08-15 18:36 ./usr/lib/debug/.build-id/78/22f9d8cf527be9fd38fb28f2c445ae23b4c1fb.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/7a/
-rw-r--r-- root/root 1680752 2021-08-15 18:36 ./usr/lib/debug/.build-id/7a/0a516835a7d57488e174fb53720f37fe071d02.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/8e/
-rw-r--r-- root/root 913944 2021-08-15 18:36 ./usr/lib/debug/.build-id/8e/25cdb57bcd0ff68d42679e6b4fc47c9ce0c83e.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/b4/
-rw-r--r-- root/root 331448 2021-08-15 18:36 ./usr/lib/debug/.build-id/b4/c45ae836387970906ebee8f74bf399afcce737.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/c7/
-rw-r--r-- root/root 846916 2021-08-15 18:36 ./usr/lib/debug/.build-id/c7/373fc15e34dfb8564a87b8c9e06d87bf42efb4.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/c9/
-rw-r--r-- root/root 295788 2021-08-15 18:36 ./usr/lib/debug/.build-id/c9/417fe08478419542050072ba1fd63db117e1ea.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/df/
-rw-r--r-- root/root 1479788 2021-08-15 18:36 ./usr/lib/debug/.build-id/df/0d99b0a95f54f77ba382215a06d287cc499417.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/e4/
-rw-r--r-- root/root 169656 2021-08-15 18:36 ./usr/lib/debug/.build-id/e4/c8572445c890dff1f32421c48a3f399752cc94.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/ef/
-rw-r--r-- root/root 830080 2021-08-15 18:36 ./usr/lib/debug/.build-id/ef/42db7f26113b19b195ad7efb33da8f9f9d749b.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/fd/
-rw-r--r-- root/root 1104060 2021-08-15 18:36 ./usr/lib/debug/.build-id/fd/ec87e147d1127a31ea93e1f7b91769de785f06.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 847596 2021-08-15 18:36 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/murasaki.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-08-15 18:36 ./usr/share/doc/murasaki-dbgsym -> murasaki
murasaki-mpi-dbgsym_1.68.6-13+b6_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 14433484 bytes: control archive=1200 bytes.
902 bytes, 12 lines control
1470 bytes, 14 lines md5sums
Package: murasaki-mpi-dbgsym
Source: murasaki (1.68.6-13)
Version: 1.68.6-13+b6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 15457
Depends: murasaki-mpi (= 1.68.6-13+b6)
Section: debug
Priority: optional
Description: debug symbols for murasaki-mpi
Build-Ids: 00f520b14a92b22bb87c56e3065c8cd10666745b 1b36a739eab16f28b57747bb2ffbdbe70db30560 5403a9f29e3cc31c69bba2dc1f88c3325b67dca7 8865522050d9645e4c6a21ef8633a2437308751f ab97746607736f142d472742a76653cde5413124 b8a6cd5f0db54bdc6bdbf785d57e8876393adc06 c29e5bc64fbb6b55b061d39bb66bf0a60cd09bed e048a6bd04e87b330367bc379355c21ef2be2049 e14d451421f85d090e870c253b6e2e53fceb8109 e1739219c5c5eebf4f009077bb41be3af350c74f e81534c274ec2fd22f509d6cbaef26fbc75c16a2 ef0aabcc9df960d7483d02ea8b44fad244923ca6 fdec87e147d1127a31ea93e1f7b91769de785f06
drwxr-xr-x root/root 0 2021-08-15 18:36 ./
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/00/
-rw-r--r-- root/root 955060 2021-08-15 18:36 ./usr/lib/debug/.build-id/00/f520b14a92b22bb87c56e3065c8cd10666745b.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/1b/
-rw-r--r-- root/root 1680972 2021-08-15 18:36 ./usr/lib/debug/.build-id/1b/36a739eab16f28b57747bb2ffbdbe70db30560.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/54/
-rw-r--r-- root/root 4089968 2021-08-15 18:36 ./usr/lib/debug/.build-id/54/03a9f29e3cc31c69bba2dc1f88c3325b67dca7.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/88/
-rw-r--r-- root/root 295772 2021-08-15 18:36 ./usr/lib/debug/.build-id/88/65522050d9645e4c6a21ef8633a2437308751f.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/ab/
-rw-r--r-- root/root 830184 2021-08-15 18:36 ./usr/lib/debug/.build-id/ab/97746607736f142d472742a76653cde5413124.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/b8/
-rw-r--r-- root/root 846972 2021-08-15 18:36 ./usr/lib/debug/.build-id/b8/a6cd5f0db54bdc6bdbf785d57e8876393adc06.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/c2/
-rw-r--r-- root/root 914060 2021-08-15 18:36 ./usr/lib/debug/.build-id/c2/9e5bc64fbb6b55b061d39bb66bf0a60cd09bed.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/e0/
-rw-r--r-- root/root 331532 2021-08-15 18:36 ./usr/lib/debug/.build-id/e0/48a6bd04e87b330367bc379355c21ef2be2049.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/e1/
-rw-r--r-- root/root 169860 2021-08-15 18:36 ./usr/lib/debug/.build-id/e1/4d451421f85d090e870c253b6e2e53fceb8109.debug
-rw-r--r-- root/root 1480240 2021-08-15 18:36 ./usr/lib/debug/.build-id/e1/739219c5c5eebf4f009077bb41be3af350c74f.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/e8/
-rw-r--r-- root/root 1139464 2021-08-15 18:36 ./usr/lib/debug/.build-id/e8/1534c274ec2fd22f509d6cbaef26fbc75c16a2.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/ef/
-rw-r--r-- root/root 1109088 2021-08-15 18:36 ./usr/lib/debug/.build-id/ef/0aabcc9df960d7483d02ea8b44fad244923ca6.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.build-id/fd/
-rw-r--r-- root/root 1104172 2021-08-15 18:36 ./usr/lib/debug/.build-id/fd/ec87e147d1127a31ea93e1f7b91769de785f06.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 850220 2021-08-15 18:36 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/murasaki-mpi.debug
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-08-15 18:36 ./usr/share/doc/murasaki-mpi-dbgsym -> murasaki-mpi
murasaki-mpi_1.68.6-13+b6_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 468028 bytes: control archive=1628 bytes.
1370 bytes, 28 lines control
1413 bytes, 21 lines md5sums
Package: murasaki-mpi
Source: murasaki (1.68.6-13)
Version: 1.68.6-13+b6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3174
Depends: murasaki-common, libboost-filesystem1.83.0 (>= 1.83.0), libboost-iostreams1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.5), libopenmpi3 (>= 4.1.6), libstdc++6 (>= 13.1)
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 2021-08-15 18:36 ./
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/bin/
-rwxr-xr-x root/root 252336 2021-08-15 18:36 ./usr/bin/geneparse-mpi
-rwxr-xr-x root/root 280948 2021-08-15 18:36 ./usr/bin/mbfa-mpi
-rwxr-xr-x root/root 663036 2021-08-15 18:36 ./usr/bin/murasaki-mpi
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/murasaki/
-rwxr-xr-x root/root 219472 2021-08-15 18:36 ./usr/lib/murasaki/align-and-mpi
-rwxr-xr-x root/root 223584 2021-08-15 18:36 ./usr/lib/murasaki/align-best-mpi
-rwxr-xr-x root/root 256376 2021-08-15 18:36 ./usr/lib/murasaki/align-compare-mpi
-rwxr-xr-x root/root 321904 2021-08-15 18:36 ./usr/lib/murasaki/align-coverage-mpi
-rwxr-xr-x root/root 215360 2021-08-15 18:36 ./usr/lib/murasaki/align-or-mpi
-rwxr-xr-x root/root 67284 2021-08-15 18:36 ./usr/lib/murasaki/cgr-compare-mpi
-rwxr-xr-x root/root 293292 2021-08-15 18:36 ./usr/lib/murasaki/cgr-image-mpi
-rwxr-xr-x root/root 7138 2010-08-24 14:18 ./usr/lib/murasaki/cgr-image.pl-mpi
-rwxr-xr-x root/root 75496 2021-08-15 18:36 ./usr/lib/murasaki/cgr-random-mpi
-rwxr-xr-x root/root 285076 2021-08-15 18:36 ./usr/lib/murasaki/cgr-sample-mpi
-rwxr-xr-x root/root 46744 2021-08-15 18:36 ./usr/lib/murasaki/testeco-mpi
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/murasaki-mpi/
-rw-r--r-- root/root 249 2021-03-19 18:45 ./usr/share/doc/murasaki-mpi/README.test
-rw-r--r-- root/root 222 2021-08-15 18:36 ./usr/share/doc/murasaki-mpi/changelog.Debian.armhf.gz
-rw-r--r-- root/root 798 2021-08-15 18:36 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz
-rw-r--r-- root/root 2225 2021-03-19 18:45 ./usr/share/doc/murasaki-mpi/copyright
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/man1/
-rw-r--r-- root/root 2518 2021-08-15 18:36 ./usr/share/man/man1/geneparse-mpi.1.gz
-rw-r--r-- root/root 2721 2021-08-15 18:36 ./usr/share/man/man1/mbfa-mpi.1.gz
-rw-r--r-- root/root 10888 2021-08-15 18:36 ./usr/share/man/man1/murasaki-mpi.1.gz
murasaki_1.68.6-13+b6_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 433164 bytes: control archive=1480 bytes.
1158 bytes, 24 lines control
1265 bytes, 20 lines md5sums
Package: murasaki
Source: murasaki (1.68.6-13)
Version: 1.68.6-13+b6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3075
Depends: murasaki-common, libboost-filesystem1.83.0 (>= 1.83.0), libboost-iostreams1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.5), libstdc++6 (>= 13.1)
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 2021-08-15 18:36 ./
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/bin/
-rwxr-xr-x root/root 252332 2021-08-15 18:36 ./usr/bin/geneparse
-rwxr-xr-x root/root 280944 2021-08-15 18:36 ./usr/bin/mbfa
-rwxr-xr-x root/root 568808 2021-08-15 18:36 ./usr/bin/murasaki
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/murasaki/
-rwxr-xr-x root/root 219468 2021-08-15 18:36 ./usr/lib/murasaki/align-and
-rwxr-xr-x root/root 223580 2021-08-15 18:36 ./usr/lib/murasaki/align-best
-rwxr-xr-x root/root 256372 2021-08-15 18:36 ./usr/lib/murasaki/align-compare
-rwxr-xr-x root/root 321900 2021-08-15 18:36 ./usr/lib/murasaki/align-coverage
-rwxr-xr-x root/root 215356 2021-08-15 18:36 ./usr/lib/murasaki/align-or
-rwxr-xr-x root/root 67280 2021-08-15 18:36 ./usr/lib/murasaki/cgr-compare
-rwxr-xr-x root/root 293288 2021-08-15 18:36 ./usr/lib/murasaki/cgr-image
-rwxr-xr-x root/root 75492 2021-08-15 18:36 ./usr/lib/murasaki/cgr-random
-rwxr-xr-x root/root 285072 2021-08-15 18:36 ./usr/lib/murasaki/cgr-sample
-rwxr-xr-x root/root 46740 2021-08-15 18:36 ./usr/lib/murasaki/testeco
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/murasaki/
-rw-r--r-- root/root 249 2021-03-19 18:45 ./usr/share/doc/murasaki/README.test
-rw-r--r-- root/root 222 2021-08-15 18:36 ./usr/share/doc/murasaki/changelog.Debian.armhf.gz
-rw-r--r-- root/root 796 2021-08-15 18:36 ./usr/share/doc/murasaki/changelog.Debian.gz
-rw-r--r-- root/root 2225 2021-03-19 18:45 ./usr/share/doc/murasaki/copyright
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/
drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/man1/
-rw-r--r-- root/root 2518 2021-08-15 18:36 ./usr/share/man/man1/geneparse.1.gz
-rw-r--r-- root/root 2721 2021-08-15 18:36 ./usr/share/man/man1/mbfa.1.gz
-rw-r--r-- root/root 10888 2021-08-15 18:36 ./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: 244064
Build-Time: 330
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 481
Job: murasaki_1.68.6-13
Machine Architecture: armhf
Package: murasaki
Package-Time: 832
Source-Version: 1.68.6-13
Space: 244064
Status: successful
Version: 1.68.6-13+b6
--------------------------------------------------------------------------------
Finished at 2024-02-07T22:57:08Z
Build needed 00:13:52, 244064k disk space