murasaki →
1.68.6-13+b5 →
armhf → 2023-01-15 20:47:12
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| murasaki 1.68.6-13+b5 (armhf) Sun, 15 Jan 2023 20:26:28 +0000 |
+==============================================================================+
Package: murasaki
Version: 1.68.6-13+b5
Source Version: 1.68.6-13
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-f0d12385-898c-4f53-9c8b-6752243655b9' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/murasaki-eczS6U/resolver-VlnbDK' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.6 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.4 MB]
Fetched 27.9 MB in 10s (2667 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-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 bookworm-staging/main murasaki 1.68.6-13 (dsc) [2792 B]
Get:2 http://172.17.4.1/private bookworm-staging/main murasaki 1.68.6-13 (tar) [3944 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main murasaki 1.68.6-13 (tar) [308 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main murasaki 1.68.6-13 (diff) [11.2 kB]
Fetched 4266 kB in 1s (7091 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/murasaki-eczS6U/murasaki-1.68.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/murasaki-eczS6U' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| 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, build-essential, fakeroot
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, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [439 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [521 B]
Fetched 1917 B in 0s (50.7 kB/s)
Reading package lists...
Reading package lists...
Install main 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
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-12 groff-base ibverbs-providers icu-devtools intltool-debian
libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.74-dev
libboost-filesystem1.74.0 libboost-iostreams-dev libboost-iostreams1.74-dev
libboost-iostreams1.74.0 libboost-regex-dev libboost-regex1.74-dev
libboost-regex1.74.0 libboost-system1.74-dev libboost-system1.74.0
libboost1.74-dev libbsd0 libcbor0.8 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-12-dev libgfortran5
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1
libicu-dev libicu72 libjs-jquery libjs-jquery-ui libltdl-dev libltdl7
libmagic-mgc libmagic1 libmd0 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-12-doc libcoarrays-dev groff
libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev
libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-graph1.74-dev libboost-graph-parallel1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-serialization1.74-dev
libboost-stacktrace1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-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-12 groff-base ibverbs-providers icu-devtools intltool-debian
libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.74-dev
libboost-filesystem1.74.0 libboost-iostreams-dev libboost-iostreams1.74-dev
libboost-iostreams1.74.0 libboost-regex-dev libboost-regex1.74-dev
libboost-regex1.74.0 libboost-system1.74-dev libboost-system1.74.0
libboost1.74-dev libbsd0 libcbor0.8 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-12-dev libgfortran5
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1
libicu-dev libicu72 libjs-jquery libjs-jquery-ui libltdl-dev libltdl7
libmagic-mgc libmagic1 libmd0 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-main-dummy zlib1g-dev
0 upgraded, 99 newly installed, 0 to remove and 50 not upgraded.
Need to get 62.3 MB of archives.
After this operation, 383 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20221030-2 [76.2 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libcbor0.8 armhf 0.8.0-2 [22.8 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libfido2-1 armhf 1.12.0-2 [67.6 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf openssh-client armhf 1:9.1p1-2 [811 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-2 [256 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.4 [942 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-10+rpi1 [238 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-12-dev armhf 12.2.0-10+rpi1 [285 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf gfortran-12 armhf 12.2.0-10+rpi1 [7508 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.7.0-0.2 [55.0 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.2 [152 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libibverbs1 armhf 42.0-1 [53.7 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf ibverbs-providers armhf 42.0-1 [28.8 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf icu-devtools armhf 72.1-3 [175 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-18.1 [9509 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libboost-filesystem1.74.0 armhf 1.74.0-18.1 [249 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libboost-system1.74.0 armhf 1.74.0-18.1 [218 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libboost-system1.74-dev armhf 1.74.0-18.1 [219 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libboost-filesystem1.74-dev armhf 1.74.0-18.1 [260 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libboost-filesystem-dev armhf 1.74.0.3+b4 [4636 B]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-18.1 [420 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libicu-dev armhf 72.1-3 [9959 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-18.1 [525 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-18.1 [235 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0-18.1 [244 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b4 [4592 B]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex-dev armhf 1.74.0.3+b4 [4876 B]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libcrypto++8 armhf 8.7.0+git220824-1+rpi1 [1011 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libcrypto++-dev armhf 8.7.0+git220824-1+rpi1 [1911 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-5+b1 [166 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-5+b1 [125 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-5+b1 [102 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-5+b1 [57.6 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-5+b1 [62.5 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-5+b1 [280 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf librdmacm1 armhf 42.0-1 [60.3 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-3 [310 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libhwloc15 armhf 2.9.0-1 [124 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.16-1 [18.4 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.16-1 [31.5 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.7-5 [390 kB]
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Get:73 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.9.0-1 [196 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.17-2 [48.8 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.3-3 [292 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.3-3 [687 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libxnvctrl0 armhf 510.108.03-1 [11.8 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.3 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.9.0-1 [16.0 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.7.0-0.2 [93.4 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.7.0-0.2 [163 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libibverbs-dev armhf 42.0-1 [188 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libmunge2 armhf 0.5.14-6 [18.6 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libpmix2 armhf 4.2.2-1 [530 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.4-3+rpi1 [1795 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf openmpi-common all 4.1.4-3+rpi1 [165 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [901 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libpmix-dev armhf 4.2.2-1 [845 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.4-3+rpi1 [192 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.4-3+rpi1 [920 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libpstreams-dev all 1.0.3-1 [134 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libterm-readkey-perl armhf 2.38-2+b1 [23.4 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libtext-wrapper-perl all 1.05-4 [10.3 kB]
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Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libevent-dev (2.1.12-stable-5+b1) ...
Setting up libpstreams-dev (1.0.3-1) ...
Setting up dh-strip-nondeterminism (1.13.0-2) ...
Setting up dwz (0.15-1) ...
Setting up libboost-regex1.74-dev:armhf (1.74.0-18.1) ...
Setting up libnl-3-dev:armhf (3.7.0-0.2) ...
Setting up groff-base (1.22.4-9) ...
Setting up libx11-6:armhf (2:1.8.3-3) ...
Setting up libhwloc-dev:armhf (2.9.0-1) ...
Setting up libboost-regex-dev:armhf (1.74.0.3+b4) ...
Setting up libibverbs1:armhf (42.0-1) ...
Setting up ibverbs-providers:armhf (42.0-1) ...
Setting up openssh-client (1:9.1p1-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up man-db (2.11.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxnvctrl0:armhf (510.108.03-1) ...
Setting up libboost-iostreams1.74-dev:armhf (1.74.0-18.1) ...
Setting up libnl-route-3-dev:armhf (3.7.0-0.2) ...
Setting up librdmacm1:armhf (42.0-1) ...
Setting up debhelper (13.11.4) ...
Setting up libboost-iostreams-dev:armhf (1.74.0.3+b4) ...
Setting up libibverbs-dev:armhf (42.0-1) ...
Setting up libhwloc-plugins:armhf (2.9.0-1) ...
Setting up libfabric1:armhf (1.11.0-3) ...
Setting up libpmix2:armhf (4.2.2-1) ...
Setting up libopenmpi3:armhf (4.1.4-3+rpi1) ...
Setting up libpmix-dev:armhf (4.2.2-1) ...
Setting up openmpi-bin (4.1.4-3+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 (4.1.4-3+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-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.36-6+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39.50.20221208-5+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-10+rpi1 gcc-12_12.2.0-10+rpi1 libc6-dev_2.36-6+rpi1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 linux-libc-dev_6.0.12-1+rpi1
Package versions: adduser_3.129 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2-2 binutils_2.39.50.20221208-5+rpi1 binutils-arm-linux-gnueabihf_2.39.50.20221208-5+rpi1 binutils-common_2.39.50.20221208-5+rpi1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.80 debhelper_13.11.4 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dirmngr_2.2.40-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-10+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-10+rpi1 gcc-12-base_12.2.0-10+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_0.21-10 gettext-base_0.21-10 gfortran-12_12.2.0-10+rpi1 gnupg_2.2.40-1 gnupg-l10n_2.2.40-1 gnupg-utils_2.2.40-1 gpg_2.2.40-1 gpg-agent_2.2.40-1 gpg-wks-client_2.2.40-1 gpg-wks-server_2.2.40-1 gpgconf_2.2.40-1 gpgsm_2.2.40-1 gpgv_2.2.40-1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1 hostname_3.23 ibverbs-providers_42.0-1 icu-devtools_72.1-3 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-1 libacl1_2.3.1-2 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libasan8_12.2.0-10+rpi1 libassuan0_2.5.5-5 libatomic1_12.2.0-10+rpi1 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39.50.20221208-5+rpi1 libblkid1_2.38.1-4 libboost-filesystem-dev_1.74.0.3+b4 libboost-filesystem1.74-dev_1.74.0-18.1 libboost-filesystem1.74.0_1.74.0-18.1 libboost-iostreams-dev_1.74.0.3+b4 libboost-iostreams1.74-dev_1.74.0-18.1 libboost-iostreams1.74.0_1.74.0-18.1 libboost-regex-dev_1.74.0.3+b4 libboost-regex1.74-dev_1.74.0-18.1 libboost-regex1.74.0_1.74.0-18.1 libboost-system1.74-dev_1.74.0-18.1 libboost-system1.74.0_1.74.0-18.1 libboost1.74-dev_1.74.0-18.1 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-6+rpi1 libc-dev-bin_2.36-6+rpi1 libc6_2.36-6+rpi1 libc6-dev_2.36-6+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcbor0.8_0.8.0-2 libcc1-0_12.2.0-10+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libcrypto++-dev_8.7.0+git220824-1+rpi1 libcrypto++8_8.7.0+git220824-1+rpi1 libctf-nobfd0_2.39.50.20221208-5+rpi1 libctf0_2.39.50.20221208-5+rpi1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.265 libdebhelper-perl_13.11.4 libdpkg-perl_1.21.9+rpi1 libedit2_3.1-20221030-2 libelf1_0.187-2+rpi2 libevent-2.1-7_2.1.12-stable-5+b1 libevent-core-2.1-7_2.1.12-stable-5+b1 libevent-dev_2.1.12-stable-5+b1 libevent-extra-2.1-7_2.1.12-stable-5+b1 libevent-openssl-2.1-7_2.1.12-stable-5+b1 libevent-pthreads-2.1-7_2.1.12-stable-5+b1 libext2fs2_1.46.6~rc1-1 libfabric1_1.11.0-3 libfakeroot_1.29-1 libffi8_3.4.4-1 libfido2-1_1.12.0-2 libfile-stripnondeterminism-perl_1.13.0-2 libgcc-12-dev_12.2.0-10+rpi1 libgcc-s1_12.2.0-10+rpi1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.2.0-10+rpi1 libgfortran5_12.2.0-10+rpi1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-4 libgomp1_12.2.0-10+rpi1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-1 libhogweed6_3.8.1-2 libhwloc-dev_2.9.0-1 libhwloc-plugins_2.9.0-1 libhwloc15_2.9.0-1 libibverbs-dev_42.0-1 libibverbs1_42.0-1 libicu-dev_72.1-3 libicu72_72.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 libksba8_1.6.2-4 libldap-2.5-0_2.5.13+dfsg-2+rpi1+b1 libltdl-dev_2.4.7-5 libltdl7_2.4.7-5 liblz4-1_1.9.4-1+rpi1 liblzma5_5.4.0-0.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-4 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libmunge2_0.5.14-6 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnl-3-200_3.7.0-0.2 libnl-3-dev_3.7.0-0.2 libnl-route-3-200_3.7.0-0.2 libnl-route-3-dev_3.7.0-0.2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnuma-dev_2.0.16-1 libnuma1_2.0.16-1 libopenmpi-dev_4.1.4-3+rpi1 libopenmpi3_4.1.4-3+rpi1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpciaccess0_0.17-2 libpcre2-8-0_10.40-3 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.36_5.36.0-6 libpipeline1_1.5.7-1 libpmix-dev_4.2.2-1 libpmix2_4.2.2-1 libpstreams-dev_1.0.3-1 librdmacm1_42.0-1 libreadline8_8.2-1.2 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-4 libsqlite3-0_3.40.0-1 libss2_1.46.6~rc1-1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.2-1+rpi1 libtasn1-6_4.19.0-2 libterm-readkey-perl_2.38-2+b1 libtext-wrapper-perl_1.05-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libubsan1_12.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_252.2-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-4 libx11-6_2:1.8.3-3 libx11-data_2:1.8.3-3 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-1.1 libxnvctrl0_510.108.03-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_6.0.12-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-2 make_4.3-4.1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-4 nano_7.1-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 ocl-icd-libopencl1_2.3.1-1 openmpi-bin_4.1.4-3+rpi1 openmpi-common_4.1.4-3+rpi1 openssh-client_1:9.1p1-2 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-6 perl-base_5.36.0-6 perl-modules-5.32_5.32.1-6 perl-modules-5.36_5.36.0-6 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.2 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-7 tar_1.34+dfsg-1 tzdata_2022f-1 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 xz-utils_5.4.0-0.1 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: murasaki
Binary: murasaki, murasaki-mpi, murasaki-common
Architecture: any all
Version: 1.68.6-13
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Nilesh Patra <nilesh@debian.org>
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/murasaki
Vcs-Git: https://salsa.debian.org/med-team/murasaki.git
Testsuite: autopkgtest
Testsuite-Triggers: libboost-filesystem-dev, libboost-iostreams-dev, libboost-regex-dev, libcrypto++-dev, libopenmpi-dev, libpstreams-dev, libterm-readkey-perl, libtext-wrapper-perl
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
Package-List:
murasaki deb science optional arch=any
murasaki-common deb science optional arch=all
murasaki-mpi deb science optional arch=any
Checksums-Sha1:
039363a4ee16888adc629ebbf658ccf2805370bd 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz
398a53fe76476ec3c756754d13541dd25d98a58a 307745 murasaki_1.68.6.orig.tar.gz
9faf611f7851b6599d6242b8e05b0896988887fc 11204 murasaki_1.68.6-13.debian.tar.xz
Checksums-Sha256:
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ebb3f3df2c0b3dc9f43977685f6c5e37ea483fb4189f7d965acc634bd10aaefe 307745 murasaki_1.68.6.orig.tar.gz
3a960dbbbda6e51d8a4b98c9889c8135b85a465a29c3c33a643d0528a7492128 11204 murasaki_1.68.6-13.debian.tar.xz
Files:
f7c0e6bdc9dea8bc893e806db571d228 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz
25477c77aa21246d4a639527836e6c77 307745 murasaki_1.68.6.orig.tar.gz
445de24812178cef498ad9bd02b86b7c 11204 murasaki_1.68.6-13.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.Fr2BAlVW/trustedkeys.kbx': General error
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 signature ./murasaki_1.68.6-13.dsc
dpkg-source: info: extracting murasaki in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz
dpkg-source: info: unpacking murasaki_1.68.6.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+b5
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=f6531457acff44088f965ef4ced20cd2
JOURNAL_STREAM=8:31902
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-f0d12385-898c-4f53-9c8b-6752243655b9
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c60467
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package murasaki
dpkg-buildpackage: info: source version 1.68.6-13+b5
dpkg-buildpackage: info: source distribution bookworm-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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from dinkymath.h:24,
from dinkymath.cc:26:
/usr/include/c++/12/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;
| ^~~~
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’
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++/12/bits/stl_algobase.h:64,
from /usr/include/c++/12/bits/stl_tree.h:63:
/usr/include/c++/12/bits/stl_pair.h:185:12: note: ‘ShmVector<std::pair<long int, long int> >::val_type’ {aka ‘struct std::pair<long int, long int>’} declared here
185 | 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++/12/bits/stl_pair.h:185:12: note: ‘ShmVector<std::pair<long int, long int> >::val_type’ {aka ‘struct std::pair<long int, long int>’} declared here
185 | 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’
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++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from murasaki.cc:29:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
sequence.cc: In member function ‘std::pair<double, long int> IntervalSet::entropy() const’:
sequence.cc:3332:10: warning: variable ‘shortest’ set but not used [-Wunused-but-set-variable]
3332 | SeqPos shortest=0,shortlen=length(spaces[0]);
| ^~~~~~~~
In file included from sequence.h:44:
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++/12/bits/stl_pair.h:185:12: note: ‘struct std::pair<long int, long int>’ declared here
185 | 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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
murasaki.cc: In function ‘void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)’:
murasaki.cc:1008:8: warning: variable ‘revZero’ set but not used [-Wunused-but-set-variable]
1008 | bool revZero=false;
| ^~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc
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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from murasaki.cc:31:
/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc
In file included from /usr/include/c++/12/vector:64:
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++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1032 | _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++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32:
/usr/include/c++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
In file included from 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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from scoring.h:27,
from sequence.h:31:
/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
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++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1032 | _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
/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<HashMethod>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc
/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<HashMethod>::iterator’ changed in GCC 7.1
/usr/include/c++/12/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++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
In function ‘void std::__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++/12/bits/stl_algo.h:1901:23,
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++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/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++/12/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++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++/12/bits/stl_algo.h:1900:25,
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++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1629 | std::__make_heap(__first, __middle, __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++/12/bits/stl_vector.h:1294:21,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1639:20:
/usr/include/c++/12/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++/12/bits/stl_algo.h:4820:18,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1645:7:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __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++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1645:7:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1854 | 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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1287 | _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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1287 | _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++/12/bits/stl_algo.h:4820:18,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1672:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __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++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1672:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/map:60,
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:2887,
from murasaki_mpi.cc:29:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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++/12/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++/12/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;
| ^~~~~~~~~
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
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
In file included from /usr/include/c++/12/vector:70,
from scoring.h:27,
from sequence.h:31:
/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
523 | 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:1565:20: note: by argument 1 of type ‘const void*’ to ‘int MPI_Get_address(const void*, MPI_Aint*)’ declared here
1565 | 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++/12/vector:64:
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++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1032 | _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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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 genopts.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc
binseq.cc: In member function ‘bool SequenceBinary::save(std::string)’:
binseq.cc:70:28: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=]
70 | }catch(ofstream::failure e){
| ^
binseq.cc: In member function ‘void SequenceBinary::fillCopyVectors()’:
binseq.cc:158:9: 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++/12/bits/stl_algobase.h:64,
from /usr/include/c++/12/string:50,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/12/bits/stl_pair.h:185:12: 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
185 | 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++/12/bits/stl_pair.h:185:12: 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
185 | 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++/12/bits/stl_pair.h:185:12: 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
185 | 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];
| ^
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 ‘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];
| ^
cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::string)’:
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: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;
| ^~~~~
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
cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’:
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;
| ^~~~~~
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;
| ^~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc
cgr-sample.cc: In function ‘int main(int, char**)’:
cgr-sample.cc:54:8: warning: variable ‘repeatmask’ set but not used [-Wunused-but-set-variable]
54 | bool repeatmask=false,save=false;
| ^~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc
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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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 align-or.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc
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
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 -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
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 ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \
mv ${bin} ${bin}-mpi ; \
done
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf *.o *~ .*~ core
make -C src clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -- USE_MPI=NO
make -j4 "INSTALL=install --strip-program=true" USE_MPI=NO
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C src all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c timing.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c dinkymath.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c sequence.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c msethash.cc
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++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from dinkymath.h:24,
from dinkymath.cc:26:
/usr/include/c++/12/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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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;
| ^~~~
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++/12/bits/stl_algobase.h:64,
from /usr/include/c++/12/bits/stl_tree.h:63:
/usr/include/c++/12/bits/stl_pair.h:185:12: note: ‘ShmVector<std::pair<long int, long int> >::val_type’ {aka ‘struct std::pair<long int, long int>’} declared here
185 | 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++/12/bits/stl_pair.h:185:12: note: ‘ShmVector<std::pair<long int, long int> >::val_type’ {aka ‘struct std::pair<long int, long int>’} declared here
185 | struct pair
| ^~~~
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++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from murasaki.cc:29:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
sequence.cc: In member function ‘std::pair<double, long int> IntervalSet::entropy() const’:
sequence.cc:3332:10: warning: variable ‘shortest’ set but not used [-Wunused-but-set-variable]
3332 | SeqPos shortest=0,shortlen=length(spaces[0]);
| ^~~~~~~~
In file included from sequence.h:44:
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++/12/bits/stl_pair.h:185:12: note: ‘struct std::pair<long int, long int>’ declared here
185 | struct pair
| ^~~~
murasaki.cc: In function ‘void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)’:
murasaki.cc:1008:8: warning: variable ‘revZero’ set but not used [-Wunused-but-set-variable]
1008 | bool revZero=false;
| ^~~~~~~
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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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 /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from /usr/include/boost/regex/v4/regex_workaround.hpp:33,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from seqread.h:33,
from binseq.hh:31,
from sequence.h:32:
/usr/include/c++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
In file included from 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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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++/12/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 murasaki_mpi.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc
In file included from /usr/include/c++/12/vector:70,
from scoring.h:27,
from sequence.h:31:
/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
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++/12/vector:64:
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++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<HashMethod>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.cc
/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: 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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/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++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
In function ‘void std::__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++/12/bits/stl_algo.h:1901:23,
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++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/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++/12/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++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++/12/bits/stl_algo.h:1900:25,
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++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1629 | std::__make_heap(__first, __middle, __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++/12/bits/stl_vector.h:1294:21,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1639:20:
/usr/include/c++/12/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++/12/bits/stl_algo.h:4820:18,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1645:7:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __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++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1645:7:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1854 | 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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1287 | _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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1287 | _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++/12/bits/stl_algo.h:4820:18,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1672:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __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++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void BitSequence::compileHashFunc()’ at sequence.cc:1672:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >’ changed in GCC 7.1
1854 | 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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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 cgr-image.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr.cc
binseq.cc: In member function ‘bool SequenceBinary::save(std::string)’:
binseq.cc:70:28: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=]
70 | }catch(ofstream::failure e){
| ^
binseq.cc: In member function ‘void SequenceBinary::fillCopyVectors()’:
binseq.cc:158:9: 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++/12/bits/stl_algobase.h:64,
from /usr/include/c++/12/string:50,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from seqread.h:30,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/c++/12/bits/stl_pair.h:185:12: 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
185 | 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++/12/bits/stl_pair.h:185:12: 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
185 | 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++/12/bits/stl_pair.h:185:12: 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
185 | struct pair
| ^~~~
cgr.cc: In member function ‘void Cgr::merge(Cgr&)’:
cgr.cc:140:7: warning: variable ‘redist’ set but not used [-Wunused-but-set-variable]
140 | int redist=(unsigned long)(rez*rez)<=seedcount;
| ^~~~~~
cgr.cc: In member function ‘bool Cgr::savePNG(std::string)’:
cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable]
288 | int res;
| ^~~
cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’:
cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable]
435 | int wordwidth=1;
| ^~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-compare.cc
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];
| ^
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 ‘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];
| ^
cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::string)’:
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: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: In member function ‘int PgmBuffer::loadPGM(std::string)’:
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;
| ^~~~~~
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;
| ^~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-sample.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c alignments.cc
cgr-sample.cc: In function ‘int main(int, char**)’:
cgr-sample.cc:54:8: warning: variable ‘repeatmask’ set but not used [-Wunused-but-set-variable]
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++/12/bits/stl_tree.h:65,
from /usr/include/c++/12/set:60,
from cmultiset.h:33,
from sequence.h:30:
/usr/include/c++/12/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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.cc
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
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;
| ^~~~~~~~
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 ../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
getsegments.cc: In function ‘size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, std::string)’:
getsegments.cc:153:29: warning: catching polymorphic type ‘class boost::bad_lexical_cast’ by value [-Wcatch-value=]
153 | }catch(bad_lexical_cast e){
| ^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../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 ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../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/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/align-or-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-image contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/mbfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/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/lib/murasaki/cgr-image-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-and contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-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/cgr-random contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-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/lib/murasaki/align-or contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-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-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/murasaki contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-random-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/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/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-mpi/usr/lib/murasaki/align-best-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/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-best contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/testeco contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/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-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
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-dbgsym' in '../murasaki-dbgsym_1.68.6-13+b5_armhf.deb'.
dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-13+b5_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-13+b5_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-13+b5_armhf.deb'.
dpkg-genbuildinfo --build=any -O../murasaki_1.68.6-13+b5_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../murasaki_1.68.6-13+b5_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 2023-01-15T20:47:02Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
murasaki_1.68.6-13+b5_armhf.changes:
------------------------------------
Format: 1.8
Date: Sun, 15 Jan 2023 20:38:50 +0000
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+b5
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Raspbian pi4 based autobuilder <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+b5) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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Files:
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7016e8ee1c6087ffd5092fdb19fea27f 8299 science optional murasaki_1.68.6-13+b5_armhf.buildinfo
c4092c47f3443f8a4fb1e3b8aa19e89d 358124 science optional murasaki_1.68.6-13+b5_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: murasaki (1.68.6-13)
Binary: murasaki murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym
Architecture: armhf
Version: 1.68.6-13+b5
Binary-Only-Changes:
murasaki (1.68.6-13+b5) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi4 based autobuilder <root@raspbian.org> Sun, 15 Jan 2023 20:38:50 +0000
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sun, 15 Jan 2023 20:47:01 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
adduser (= 3.129),
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-10),
autotools-dev (= 20220109.1),
base-files (= 12.3+rpi1),
base-passwd (= 3.6.1),
bash (= 5.2-2),
binutils (= 2.39.50.20221208-5+rpi1),
binutils-arm-linux-gnueabihf (= 2.39.50.20221208-5+rpi1),
binutils-common (= 2.39.50.20221208-5+rpi1),
bsdextrautils (= 2.38.1-4),
bsdutils (= 1:2.38.1-4),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:12.2.0-1+rpi1),
cpp-12 (= 12.2.0-10+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-9),
debconf (= 1.5.80),
debhelper (= 13.11.4),
debianutils (= 5.7-0.4),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.0-2),
diffutils (= 1:3.8-1),
dpkg (= 1.21.9+rpi1),
dpkg-dev (= 1.21.9+rpi1),
dwz (= 0.15-1),
file (= 1:5.41-4),
findutils (= 4.9.0-3),
g++ (= 4:12.2.0-1+rpi1),
g++-12 (= 12.2.0-10+rpi1),
gcc (= 4:12.2.0-1+rpi1),
gcc-12 (= 12.2.0-10+rpi1),
gcc-12-base (= 12.2.0-10+rpi1),
gettext (= 0.21-10),
gettext-base (= 0.21-10),
gfortran-12 (= 12.2.0-10+rpi1),
grep (= 3.8-3),
groff-base (= 1.22.4-9),
gzip (= 1.12-1),
hostname (= 3.23),
ibverbs-providers (= 42.0-1),
icu-devtools (= 72.1-3),
init-system-helpers (= 1.64),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-2),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 12.2.0-10+rpi1),
libatomic1 (= 12.2.0-10+rpi1),
libattr1 (= 1:2.5.1-3),
libaudit-common (= 1:3.0.7-1.1),
libaudit1 (= 1:3.0.7-1.1),
libbinutils (= 2.39.50.20221208-5+rpi1),
libblkid1 (= 2.38.1-4),
libboost-filesystem-dev (= 1.74.0.3+b4),
libboost-filesystem1.74-dev (= 1.74.0-18.1),
libboost-filesystem1.74.0 (= 1.74.0-18.1),
libboost-iostreams-dev (= 1.74.0.3+b4),
libboost-iostreams1.74-dev (= 1.74.0-18.1),
libboost-iostreams1.74.0 (= 1.74.0-18.1),
libboost-regex-dev (= 1.74.0.3+b4),
libboost-regex1.74-dev (= 1.74.0-18.1),
libboost-regex1.74.0 (= 1.74.0-18.1),
libboost-system1.74-dev (= 1.74.0-18.1),
libboost-system1.74.0 (= 1.74.0-18.1),
libboost1.74-dev (= 1.74.0-18.1),
libbsd0 (= 0.11.7-1),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.36-6+rpi1),
libc-dev-bin (= 2.36-6+rpi1),
libc6 (= 2.36-6+rpi1),
libc6-dev (= 2.36-6+rpi1),
libcap-ng0 (= 0.8.3-1),
libcap2 (= 1:2.44-1),
libcbor0.8 (= 0.8.0-2),
libcc1-0 (= 12.2.0-10+rpi1),
libcom-err2 (= 1.46.6~rc1-1),
libcrypt-dev (= 1:4.4.33-1),
libcrypt1 (= 1:4.4.33-1),
libcrypto++-dev (= 8.7.0+git220824-1+rpi1),
libcrypto++8 (= 8.7.0+git220824-1+rpi1),
libctf-nobfd0 (= 2.39.50.20221208-5+rpi1),
libctf0 (= 2.39.50.20221208-5+rpi1),
libdb5.3 (= 5.3.28+dfsg1-0.10),
libdebconfclient0 (= 0.265),
libdebhelper-perl (= 13.11.4),
libdpkg-perl (= 1.21.9+rpi1),
libedit2 (= 3.1-20221030-2),
libelf1 (= 0.187-2+rpi2),
libevent-2.1-7 (= 2.1.12-stable-5+b1),
libevent-core-2.1-7 (= 2.1.12-stable-5+b1),
libevent-dev (= 2.1.12-stable-5+b1),
libevent-extra-2.1-7 (= 2.1.12-stable-5+b1),
libevent-openssl-2.1-7 (= 2.1.12-stable-5+b1),
libevent-pthreads-2.1-7 (= 2.1.12-stable-5+b1),
libfabric1 (= 1.11.0-3),
libfido2-1 (= 1.12.0-2),
libfile-stripnondeterminism-perl (= 1.13.0-2),
libgcc-12-dev (= 12.2.0-10+rpi1),
libgcc-s1 (= 12.2.0-10+rpi1),
libgcrypt20 (= 1.10.1-3),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgfortran-12-dev (= 12.2.0-10+rpi1),
libgfortran5 (= 12.2.0-10+rpi1),
libgmp10 (= 2:6.2.1+dfsg1-1.1),
libgomp1 (= 12.2.0-10+rpi1),
libgpg-error0 (= 1.46-1),
libgssapi-krb5-2 (= 1.20.1-1),
libhwloc-dev (= 2.9.0-1),
libhwloc-plugins (= 2.9.0-1),
libhwloc15 (= 2.9.0-1),
libibverbs-dev (= 42.0-1),
libibverbs1 (= 42.0-1),
libicu-dev (= 72.1-3),
libicu72 (= 72.1-3),
libisl23 (= 0.25-1),
libjansson4 (= 2.14-2),
libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
libjs-jquery-ui (= 1.13.2+dfsg-1),
libk5crypto3 (= 1.20.1-1),
libkeyutils1 (= 1.6.3-1),
libkrb5-3 (= 1.20.1-1),
libkrb5support0 (= 1.20.1-1),
libltdl-dev (= 2.4.7-5),
libltdl7 (= 2.4.7-5),
liblz4-1 (= 1.9.4-1+rpi1),
liblzma5 (= 5.4.0-0.1),
libmagic-mgc (= 1:5.41-4),
libmagic1 (= 1:5.41-4),
libmd0 (= 1.0.4-2),
libmount1 (= 2.38.1-4),
libmpc3 (= 1.2.1-2),
libmpfr6 (= 4.1.0-3),
libmunge2 (= 0.5.14-6),
libnl-3-200 (= 3.7.0-0.2),
libnl-3-dev (= 3.7.0-0.2),
libnl-route-3-200 (= 3.7.0-0.2),
libnl-route-3-dev (= 3.7.0-0.2),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libnuma-dev (= 2.0.16-1),
libnuma1 (= 2.0.16-1),
libopenmpi-dev (= 4.1.4-3+rpi1),
libopenmpi3 (= 4.1.4-3+rpi1),
libpam-modules (= 1.5.2-5),
libpam-modules-bin (= 1.5.2-5),
libpam-runtime (= 1.5.2-5),
libpam0g (= 1.5.2-5),
libpciaccess0 (= 0.17-2),
libpcre2-8-0 (= 10.40-3),
libperl5.36 (= 5.36.0-6),
libpipeline1 (= 1.5.7-1),
libpmix-dev (= 4.2.2-1),
libpmix2 (= 4.2.2-1),
libpstreams-dev (= 1.0.3-1),
librdmacm1 (= 42.0-1),
libseccomp2 (= 2.5.4-1+rpi1),
libselinux1 (= 3.4-1),
libsemanage-common (= 3.4-1),
libsemanage2 (= 3.4-1),
libsepol2 (= 3.4-2),
libsmartcols1 (= 2.38.1-4),
libssl3 (= 3.0.7-1),
libstdc++-12-dev (= 12.2.0-10+rpi1),
libstdc++6 (= 12.2.0-10+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 252.2-1+rpi1),
libterm-readkey-perl (= 2.38-2+b1),
libtext-wrapper-perl (= 1.05-4),
libtinfo6 (= 6.3+20220423-2),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-5),
libubsan1 (= 12.2.0-10+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 252.2-1+rpi1),
libunistring2 (= 1.0-2),
libuuid1 (= 2.38.1-4),
libx11-6 (= 2:1.8.3-3),
libx11-data (= 2:1.8.3-3),
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-1.1),
libxnvctrl0 (= 510.108.03-1),
libzstd1 (= 1.5.2+dfsg-1),
linux-libc-dev (= 6.0.12-1+rpi1),
login (= 1:4.13+dfsg1-1),
m4 (= 1.4.19-2),
make (= 4.3-4.1),
man-db (= 2.11.1-1),
mawk (= 1.3.4.20200120-3.1),
ncurses-base (= 6.3+20220423-2),
ncurses-bin (= 6.3+20220423-2),
ocl-icd-libopencl1 (= 2.3.1-1),
openmpi-bin (= 4.1.4-3+rpi1),
openmpi-common (= 4.1.4-3+rpi1),
openssh-client (= 1:9.1p1-2),
passwd (= 1:4.13+dfsg1-1),
patch (= 2.7.6-7),
perl (= 5.36.0-6),
perl-base (= 5.36.0-6),
perl-modules-5.36 (= 5.36.0-6),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sysvinit-utils (= 3.05-7),
tar (= 1.34+dfsg-1),
util-linux (= 2.38.1-4),
util-linux-extra (= 2.38.1-4),
xz-utils (= 5.4.0-0.1),
zlib1g (= 1:1.2.13.dfsg-1),
zlib1g-dev (= 1:1.2.13.dfsg-1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1673815130"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
murasaki-dbgsym_1.68.6-13+b5_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 9999580 bytes: control archive=1196 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+b5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10829
Depends: murasaki (= 1.68.6-13+b5)
Section: debug
Priority: optional
Description: debug symbols for murasaki
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lrwxrwxrwx root/root 0 2023-01-15 20:38 ./usr/share/doc/murasaki-dbgsym -> murasaki
murasaki-mpi-dbgsym_1.68.6-13+b5_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 10653784 bytes: control archive=1208 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+b5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 11485
Depends: murasaki-mpi (= 1.68.6-13+b5)
Section: debug
Priority: optional
Description: debug symbols for murasaki-mpi
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lrwxrwxrwx root/root 0 2023-01-15 20:38 ./usr/share/doc/murasaki-mpi-dbgsym -> murasaki-mpi
murasaki-mpi_1.68.6-13+b5_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 395624 bytes: control archive=1640 bytes.
1396 bytes, 28 lines control
1413 bytes, 21 lines md5sums
Package: murasaki-mpi
Source: murasaki (1.68.6-13)
Version: 1.68.6-13+b5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2692
Depends: murasaki-common, libboost-filesystem1.74.0 (>= 1.74.0), libboost-iostreams1.74.0 (>= 1.74.0), libboost-regex1.74.0-icu72, libc6 (>= 2.34), libgcc-s1 (>= 3.5), libopenmpi3 (>= 4.1.4), libstdc++6 (>= 11)
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 2023-01-15 20:38 ./
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-rw-r--r-- root/root 798 2023-01-15 20:38 ./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
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-rw-r--r-- root/root 10888 2023-01-15 20:38 ./usr/share/man/man1/murasaki-mpi.1.gz
murasaki_1.68.6-13+b5_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 358124 bytes: control archive=1492 bytes.
1184 bytes, 24 lines control
1265 bytes, 20 lines md5sums
Package: murasaki
Source: murasaki (1.68.6-13)
Version: 1.68.6-13+b5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2621
Depends: murasaki-common, libboost-filesystem1.74.0 (>= 1.74.0), libboost-iostreams1.74.0 (>= 1.74.0), libboost-regex1.74.0-icu72, libc6 (>= 2.34), libgcc-s1 (>= 3.5), libstdc++6 (>= 11)
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 2023-01-15 20:38 ./
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-rw-r--r-- root/root 10888 2023-01-15 20:38 ./usr/share/man/man1/murasaki.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 189400
Build-Time: 491
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 710
Job: murasaki_1.68.6-13
Machine Architecture: armhf
Package: murasaki
Package-Time: 1234
Source-Version: 1.68.6-13
Space: 189400
Status: successful
Version: 1.68.6-13+b5
--------------------------------------------------------------------------------
Finished at 2023-01-15T20:47:02Z
Build needed 00:20:34, 189400k disk space