murasaki →
1.68.6-6+b3 →
armhf → 2016-10-07 02:09:13
sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on testwandboard
+==============================================================================+
| murasaki 1.68.6-6+b3 (armhf) Fri, 07 Oct 2016 01:19:02 +0000 |
+==============================================================================+
Package: murasaki
Version: 1.68.6-6+b3
Source Version: 1.68.6-6
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-4188a9b2-ddbf-49c2-ae8a-5b47e4b04774' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9326 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.3 MB]
Fetched 20.6 MB in 27s (752 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'murasaki' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/murasaki.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/murasaki.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 317 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main murasaki 1.68.6-6 (dsc) [2213 B]
Get:2 http://172.17.0.1/private stretch-staging/main murasaki 1.68.6-6 (tar) [308 kB]
Get:3 http://172.17.0.1/private stretch-staging/main murasaki 1.68.6-6 (diff) [6920 B]
Fetched 317 kB in 0s (1208 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/murasaki-Ac8XQR/murasaki-1.68.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/murasaki-Ac8XQR' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-oD4cLV/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-oD4cLV/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-oD4cLV/gpg/trustdb.gpg: trustdb created
gpg: key 74F692987931643C: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 74F692987931643C: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 74F692987931643C: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-oD4cLV/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-oD4cLV/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-oD4cLV/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-oD4cLV/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-oD4cLV/apt_archive ./ Packages [430 B]
Fetched 2078 B in 0s (2881 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dirmngr fuse2fs gnupg-l10n kbd libffi6 libfuse2 libgnutls30 libhogweed4
libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded.
Need to get 764 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-oD4cLV/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 764 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13385 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev
Filtered Build-Depends: debhelper (>= 9), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev
dpkg-deb: building package 'sbuild-build-depends-murasaki-dummy' in '/<<BUILDDIR>>/resolver-JesnDI/apt_archive/sbuild-build-depends-murasaki-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-murasaki-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-JesnDI/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-JesnDI/gpg/trustdb.gpg: trustdb created
gpg: key 74F692987931643C: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 74F692987931643C: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 74F692987931643C: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-JesnDI/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-JesnDI/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-JesnDI/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-JesnDI/apt_archive ./ Sources [416 B]
Get:5 copy:/<<BUILDDIR>>/resolver-JesnDI/apt_archive ./ Packages [503 B]
Fetched 2218 B in 0s (3458 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install murasaki build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dirmngr fuse2fs gnupg-l10n kbd libfuse2 libgnutls30 libhogweed4
libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev
libboost-filesystem1.61-dev libboost-filesystem1.61.0 libboost-iostreams-dev
libboost-iostreams1.61-dev libboost-iostreams1.61.0 libboost-regex-dev
libboost-regex1.61-dev libboost-regex1.61.0 libboost-system1.61-dev
libboost-system1.61.0 libboost1.61-dev libbsd0 libcroco3 libcrypto++-dev
libcrypto++6 libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0
libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1
libicu-dev libicu57 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200
libnl-route-3-200 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1
libpstreams-dev libsigsegv2 libterm-readkey-perl libtext-wrapper-perl
libtimedate-perl libtool libunistring0 libxml2 m4 man-db ocl-icd-libopencl1
openmpi-common po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libboost1.61-doc libboost-atomic1.61-dev libboost-chrono1.61-dev
libboost-context1.61-dev libboost-coroutine1.61-dev
libboost-date-time1.61-dev libboost-exception1.61-dev libboost-graph1.61-dev
libboost-graph-parallel1.61-dev libboost-locale1.61-dev libboost-log1.61-dev
libboost-math1.61-dev libboost-mpi1.61-dev libboost-mpi-python1.61-dev
libboost-program-options1.61-dev libboost-python1.61-dev
libboost-random1.61-dev libboost-serialization1.61-dev
libboost-signals1.61-dev libboost-test1.61-dev libboost-thread1.61-dev
libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev
libmpfrc++-dev libntl-dev libhwloc-contrib-plugins icu-doc libtool-doc
openmpi-doc pciutils gfortran | fortran95-compiler gcj-jdk less www-browser
opencl-icd libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
openmpi-bin xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev
libboost-filesystem1.61-dev libboost-filesystem1.61.0 libboost-iostreams-dev
libboost-iostreams1.61-dev libboost-iostreams1.61.0 libboost-regex-dev
libboost-regex1.61-dev libboost-regex1.61.0 libboost-system1.61-dev
libboost-system1.61.0 libboost1.61-dev libbsd0 libcroco3 libcrypto++-dev
libcrypto++6 libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0
libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1
libicu-dev libicu57 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200
libnl-route-3-200 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1
libpstreams-dev libsigsegv2 libterm-readkey-perl libtext-wrapper-perl
libtimedate-perl libtool libunistring0 libxml2 m4 man-db ocl-icd-libopencl1
openmpi-common po-debconf sbuild-build-depends-murasaki-dummy
0 upgraded, 65 newly installed, 0 to remove and 10 not upgraded.
Need to get 48.9 MB of archives.
After this operation, 285 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-JesnDI/apt_archive ./ sbuild-build-depends-murasaki-dummy 0.invalid.0 [836 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.11 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams1.61.0 armhf 1.61.0+dfsg-2.1+b1 [48.8 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-1 [2520 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10 [823 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf icu-devtools armhf 57.1-4 [156 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libboost1.61-dev armhf 1.61.0+dfsg-2.1+b1 [6843 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libboost-system1.61.0 armhf 1.61.0+dfsg-2.1+b1 [32.1 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libboost-filesystem1.61.0 armhf 1.61.0+dfsg-2.1+b1 [57.9 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libboost-system1.61-dev armhf 1.61.0+dfsg-2.1+b1 [33.1 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libboost-filesystem1.61-dev armhf 1.61.0+dfsg-2.1+b1 [65.8 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libboost-filesystem-dev armhf 1.61.0.2 [3440 B]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libboost-regex1.61.0 armhf 1.61.0+dfsg-2.1+b1 [233 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libicu-dev armhf 57.1-4 [15.7 MB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libboost-regex1.61-dev armhf 1.61.0+dfsg-2.1+b1 [324 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams1.61-dev armhf 1.61.0+dfsg-2.1+b1 [57.9 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams-dev armhf 1.61.0.2 [3392 B]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libboost-regex-dev armhf 1.61.0.2 [3664 B]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libcrypto++6 armhf 5.6.3-8 [733 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libcrypto++-dev armhf 5.6.3-8 [1309 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.1.1-11+rpi1 [166 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libltdl7 armhf 2.4.6-2 [386 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libltdl-dev armhf 2.4.6-2 [159 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libnl-3-200 armhf 3.2.27-1 [53.4 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libnl-route-3-200 armhf 3.2.27-1 [111 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libpciaccess0 armhf 0.13.4-1 [47.4 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libpstreams-dev all 0.8.0-2 [125 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libterm-readkey-perl armhf 2.33-1+b2 [29.4 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libtext-wrapper-perl all 1.05-2 [11.0 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libhwloc5 armhf 1.11.4-1+rpi1 [82.8 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libhwloc-dev armhf 1.11.4-1+rpi1 [136 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf ocl-icd-libopencl1 armhf 2.2.9-2 [34.7 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libhwloc-plugins armhf 1.11.4-1+rpi1 [14.9 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libibverbs1 armhf 1.2.1-2 [35.4 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libibverbs-dev armhf 1.2.1-2 [104 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libopenmpi2 armhf 2.0.1-5 [1621 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf openmpi-common all 2.0.1-5 [146 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libopenmpi-dev armhf 2.0.1-5 [997 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.24-3) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.24-3 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.26.1-1 bsdmainutils_9.0.11 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-3 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.1.1-11+rpi1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.15-3 gnupg-agent_2.1.15-3 gnupg-l10n_2.1.15-3 gpgv_2.1.15-3 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-4 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3 libarchive-zip-perl_1.59-1 libasan3_6.1.1-11+rpi1 libassuan0_2.4.3-1 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1 libaudit1_1:2.6.6-1 libblkid1_2.28.2-1 libboost-filesystem-dev_1.61.0.2 libboost-filesystem1.61-dev_1.61.0+dfsg-2.1+b1 libboost-filesystem1.61.0_1.61.0+dfsg-2.1+b1 libboost-iostreams-dev_1.61.0.2 libboost-iostreams1.61-dev_1.61.0+dfsg-2.1+b1 libboost-iostreams1.61.0_1.61.0+dfsg-2.1+b1 libboost-regex-dev_1.61.0.2 libboost-regex1.61-dev_1.61.0+dfsg-2.1+b1 libboost-regex1.61.0_1.61.0+dfsg-2.1+b1 libboost-system1.61-dev_1.61.0+dfsg-2.1+b1 libboost-system1.61.0_1.61.0+dfsg-2.1+b1 libboost1.61-dev_1.61.0+dfsg-2.1+b1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-3 libc-dev-bin_2.24-3 libc6_2.24-3 libc6-dev_2.24-3 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcrypto++-dev_5.6.3-8 libcrypto++6_5.6.3-8 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.10-1 libdebconfclient0_0.217 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.3-1 libgdbm3_1.8.3-14 libgfortran3_6.1.1-11+rpi1 libglib2.0-0_2.50.0-1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.4-2 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libhogweed4_3.2-1 libhwloc-dev_1.11.4-1+rpi1 libhwloc-plugins_1.11.4-1+rpi1 libhwloc5_1.11.4-1+rpi1 libibverbs-dev_1.2.1-2 libibverbs1_1.2.1-2 libicu-dev_57.1-4 libicu57_57.1-4 libidn11_1.33-1 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libksba8_1.3.5-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.2-1 libnl-3-200_3.2.27-1 libnl-route-3-200_3.2.27-1 libnpth0_1.2-3 libopenmpi-dev_2.0.1-5 libopenmpi2_2.0.1-5 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpciaccess0_0.13.4-1 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-2 libpstreams-dev_0.8.0-2 libreadline6_6.3-8+b3 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssl1.0.2_1.0.2j-1 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_231-4 libtasn1-6_4.9-4 libterm-readkey-perl_2.33-1+b2 libtext-wrapper-perl_1.05-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.1.1-11+rpi1 libudev1_231-4 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mount_2.28.2-1 multiarch-support_2.24-3 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 netbase_5.3 ocl-icd-libopencl1_2.2.9-2 openmpi-common_2.0.1-5 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-5 po-debconf_1.0.19 procps_2:3.3.12-2 psmisc_22.21-2.1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-murasaki-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-4 systemd-sysv_231-4 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016g-1 udev_231-4 util-linux_2.28.2-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Jul 12 07:30:27 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-6.dsc
dpkg-source: info: extracting murasaki in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz
dpkg-source: info: unpacking murasaki_1.68.6-6.debian.tar.xz
dpkg-source: info: applying use_proper_libboost_names.patch
dpkg-source: info: applying include_libpstream.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying man_syntax.patch
dpkg-source: info: applying freebsd.patch
dpkg-source: info: applying gcc-6.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.68.6-6+b3
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-4188a9b2-ddbf-49c2-ae8a-5b47e4b04774
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package murasaki
dpkg-buildpackage: info: source version 1.68.6-6+b3
dpkg-buildpackage: info: source distribution stretch-staging
dpkg-source --before-build murasaki-1.68.6
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf *.o *~ .*~ core
make -C src clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- USE_MPI=YES
make -j1 USE_MPI=YES
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C src all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from murasaki.cc:37:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from murasaki.cc:37:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from murasaki.cc:37:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
bool revZero=false;
^~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c timing.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from dinkymath.cc:27:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from dinkymath.cc:27:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from dinkymath.cc:27:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
dinkymath.cc: In function 'std::__cxx11::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
dinkymath.cc: In function 'std::__cxx11::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
sequence.cc: In destructor 'Sequence::~Sequence()':
sequence.cc:377:123: warning: throw will always call terminate() [-Wterminate]
throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno));
^
sequence.cc:377:123: note: in C++11 destructors default to noexcept
sequence.cc: In destructor 'BitSequence::~BitSequence()':
sequence.cc:1394:133: warning: throw will always call terminate() [-Wterminate]
throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno));
^
sequence.cc:1394:133: note: in C++11 destructors default to noexcept
sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
SeqPos shortest=0,shortlen=length(spaces[0]);
^~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c msethash.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from msethash.cc:25:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from msethash.cc:25:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from msethash.cc:25:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c options.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from options.h:28,
from options.cc:26:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from options.h:28,
from options.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from options.h:28,
from options.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecohash.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecohash.h:29,
from ecohash.cc:26:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecohash.h:29,
from ecohash.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecohash.h:29,
from ecohash.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecolist.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecolist.cc:20:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecolist.cc:20:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecolist.cc:20:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from murasaki_mpi.cc:33:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
murasaki_mpi.cc: In function 'void mpi_types_init()':
murasaki_mpi.cc:107:3: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.key,disp);
^~~~~~~~~~~
In file included from murasaki_mpi.cc:29:0:
/usr/lib/openmpi/include/mpi.h:1200:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:107:28: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.key,disp);
^
In file included from murasaki_mpi.cc:29:0:
/usr/lib/openmpi/include/mpi.h:1200:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:108:3: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.seqno,disp+1);
^~~~~~~~~~~
In file included from murasaki_mpi.cc:29:0:
/usr/lib/openmpi/include/mpi.h:1200:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:108:32: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.seqno,disp+1);
^
In file included from murasaki_mpi.cc:29:0:
/usr/lib/openmpi/include/mpi.h:1200:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:109:3: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.pos,disp+1);
^~~~~~~~~~~
In file included from murasaki_mpi.cc:29:0:
/usr/lib/openmpi/include/mpi.h:1200:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:109:30: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
MPI_Address(&msg.pos,disp+1);
^
In file included from murasaki_mpi.cc:29:0:
/usr/lib/openmpi/include/mpi.h:1200:20: note: declared here
OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address)
^~~~~~~~~~~
murasaki_mpi.cc:112:3: warning: 'int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations]
MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type);
^~~~~~~~~~~~~~~
In file included from murasaki_mpi.cc:29:0:
/usr/lib/openmpi/include/mpi.h:1817:20: note: declared here
OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[],
^~~~~~~~~~~~~~~
murasaki_mpi.cc:112:61: warning: 'int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations]
MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type);
^
In file included from murasaki_mpi.cc:29:0:
/usr/lib/openmpi/include/mpi.h:1817:20: note: declared here
OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[],
^~~~~~~~~~~~~~~
murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)':
murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable]
int send_done;
^~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c arrayhash.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from arrayhash.cc:28:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from arrayhash.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from arrayhash.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c seqread.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from seqread.cc:28:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from seqread.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from seqread.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c scoring.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from scoring.cc:27:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from scoring.cc:27:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from scoring.cc:27:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c openhash.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from openhash.h:29,
from openhash.cc:26:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from openhash.h:29,
from openhash.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from openhash.h:29,
from openhash.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c genopts.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c binseq.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-image.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-image.cc:33:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-image.cc:33:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-image.cc:33:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr.cc
cgr.cc: In member function 'void Cgr::merge(Cgr&)':
cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
int redist=(unsigned long)(rez*rez)<=seedcount;
^~~~~~
cgr.cc: In member function 'bool Cgr::savePNG(std::__cxx11::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
int res;
^~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
int wordwidth=1;
^~~~~~~~~
cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::__cxx11::string)':
cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
~~~~~~~^~~~~~~
cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
~~~~~~~^~~~~~~
cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-sample.cc:35:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-sample.cc:35:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-sample.cc:35:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
cgr-sample.cc: In function 'int main(int, char**)':
cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
bool repeatmask=false,save=false;
^~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c testeco.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from testeco.cc:20:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from testeco.cc:20:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from testeco.cc:20:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:43: warning: left shift count >= width of type [-Wshift-count-overflow]
return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
^~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-compare.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c alignments.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-or.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c geneparse.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from geneparse.cc:30:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from geneparse.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from geneparse.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-and.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-best.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from align-coverage.cc:35:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from align-coverage.cc:35:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from align-coverage.cc:35:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
align-coverage.cc: In function 'int main(int, char**)':
align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
bool seqStats=true;
^~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c getsegments.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from getsegments.cc:30:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from getsegments.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from getsegments.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c mbfa.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from mbfa.cc:30:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from mbfa.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from mbfa.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \
mv ${bin} ${bin}-mpi ; \
done
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf *.o *~ .*~ core
make -C src clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -- USE_MPI=NO
make -j1 USE_MPI=NO
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C src all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from murasaki.cc:37:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from murasaki.cc:37:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from murasaki.cc:37:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
bool revZero=false;
^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c timing.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from dinkymath.cc:27:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from dinkymath.cc:27:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from dinkymath.cc:27:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
dinkymath.cc: In function 'std::__cxx11::string littleEndianStr(unsigned int, int)':
dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
dinkymath.cc: In function 'std::__cxx11::string littleEndianPat(unsigned int, int)':
dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int last=0;
^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
sequence.cc: In member function 'std::pair<double, long int> IntervalSet::entropy() const':
sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable]
SeqPos shortest=0,shortlen=length(spaces[0]);
^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c msethash.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from msethash.cc:25:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from msethash.cc:25:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from msethash.cc:25:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c options.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from options.h:28,
from options.cc:26:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from options.h:28,
from options.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from options.h:28,
from options.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecohash.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecohash.h:29,
from ecohash.cc:26:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecohash.h:29,
from ecohash.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecohash.h:29,
from ecohash.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecolist.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecolist.cc:20:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecolist.cc:20:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from ecolist.cc:20:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c arrayhash.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from arrayhash.cc:28:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from arrayhash.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from arrayhash.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c seqread.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from seqread.cc:28:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from seqread.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from seqread.cc:28:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c scoring.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from scoring.cc:27:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from scoring.cc:27:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from murasaki.h:24,
from scoring.cc:27:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c openhash.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from openhash.h:29,
from openhash.cc:26:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from openhash.h:29,
from openhash.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from openhash.h:29,
from openhash.cc:26:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c genopts.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c binseq.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from binseq.cc:21:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-image.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-image.cc:33:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-image.cc:33:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-image.cc:33:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr.cc
cgr.cc: In member function 'void Cgr::merge(Cgr&)':
cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable]
int redist=(unsigned long)(rez*rez)<=seedcount;
^~~~~~
cgr.cc: In member function 'bool Cgr::savePNG(std::__cxx11::string)':
cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable]
int res;
^~~
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable]
int wordwidth=1;
^~~~~~~~~
cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::__cxx11::string)':
cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
~~~~~~~^~~~~~~
cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)':
cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(data.size()<(uint)(height*width))
~~~~~~~^~~~~~~
cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-sample.cc:35:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-sample.cc:35:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from cgr-sample.cc:35:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
cgr-sample.cc: In function 'int main(int, char**)':
cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable]
bool repeatmask=false,save=false;
^~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c testeco.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from testeco.cc:20:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from testeco.cc:20:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from binseq.hh:31,
from sequence.h:32,
from ecolist.h:23,
from testeco.cc:20:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:43: warning: left shift count >= width of type [-Wshift-count-overflow]
return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
^~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-compare.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c alignments.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-or.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c geneparse.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from geneparse.cc:30:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from geneparse.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from geneparse.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-and.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-best.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from align-coverage.cc:35:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from align-coverage.cc:35:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from align-coverage.cc:35:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
align-coverage.cc: In function 'int main(int, char**)':
align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable]
bool seqStats=true;
^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c getsegments.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from getsegments.cc:30:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from getsegments.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from getsegments.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c mbfa.cc
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from mbfa.cc:30:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from mbfa.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/include/boost/iostreams/detail/push.hpp:24,
from /usr/include/boost/iostreams/chain.hpp:29,
from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
from seqread.h:34,
from mbfa.cc:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install -a
# using wildcards in install files is practical but it duplicates some files
find debian/murasaki/usr -name "*-mpi" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
debian/rules override_dh_link
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_link
mkdir -p debian/murasaki-mpi/usr/share/man/man1
for man in debian/murasaki/usr/share/man/man1/* ; do \
ln -s `basename ${man}`.gz debian/murasaki-mpi/usr/share/man/man1/`basename ${man} .1`-mpi.1.gz ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/murasaki contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/geneparse contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/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-and contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/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/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/cgr-random contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-or contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/testeco contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/mbfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-best contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/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-mpi/usr/lib/murasaki/align-best-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-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/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-mpi/usr/bin/mbfa-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-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-mpi/usr/lib/murasaki/align-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/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/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/cgr-random-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi debian/murasaki-mpi/usr/bin/mbfa-mpi debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi debian/murasaki-mpi/usr/bin/murasaki-mpi debian/murasaki-mpi/usr/bin/geneparse-mpi debian/murasaki-mpi/usr/lib/murasaki/cgr-random-mpi debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi were not linked against libmpi_cxx.so.20 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package murasaki-mpi: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package murasaki-mpi: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-6+b3_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-6+b3_armhf.deb'.
dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-6+b3_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-6+b3_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../murasaki_1.68.6-6+b3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build murasaki-1.68.6
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-10-07T02:08:58Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
murasaki_1.68.6-6+b3_armhf.changes:
-----------------------------------
Format: 1.8
Date: Thu, 30 Jun 2016 09:15:01 +0000
Source: murasaki (1.68.6-6)
Binary: murasaki murasaki-mpi murasaki-common
Binary-Only: yes
Architecture: armhf
Version: 1.68.6-6+b3
Distribution: stretch-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
murasaki - homology detection tool across multiple large genomes
murasaki-common - homology detection tool across multiple large genomes (common fil
murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio
Changes:
murasaki (1.68.6-6+b3) stretch-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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41272a4a660a2113475a24b9e82eb560 380700 science optional murasaki-mpi_1.68.6-6+b3_armhf.deb
58ec859199a80b97110903b6476761f6 364224 science optional murasaki_1.68.6-6+b3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
murasaki-dbgsym_1.68.6-6+b3_armhf.deb
-------------------------------------
new debian package, version 2.0.
size 11058766 bytes: control archive=1153 bytes.
935 bytes, 13 lines control
1378 bytes, 13 lines md5sums
Package: murasaki-dbgsym
Source: murasaki (1.68.6-6)
Version: 1.68.6-6+b3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 11903
Depends: murasaki (= 1.68.6-6+b3)
Section: debug
Priority: extra
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Description: Debug symbols for murasaki
Auto-Built-Package: debug-symbols
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lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/doc/murasaki-dbgsym -> murasaki
murasaki-mpi-dbgsym_1.68.6-6+b3_armhf.deb
-----------------------------------------
new debian package, version 2.0.
size 11881828 bytes: control archive=1156 bytes.
947 bytes, 13 lines control
1378 bytes, 13 lines md5sums
Package: murasaki-mpi-dbgsym
Source: murasaki (1.68.6-6)
Version: 1.68.6-6+b3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 12721
Depends: murasaki-mpi (= 1.68.6-6+b3)
Section: debug
Priority: extra
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Description: Debug symbols for murasaki-mpi
Auto-Built-Package: debug-symbols
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drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi-dbgsym -> murasaki-mpi
murasaki-mpi_1.68.6-6+b3_armhf.deb
----------------------------------
new debian package, version 2.0.
size 380700 bytes: control archive=1499 bytes.
1390 bytes, 28 lines control
1203 bytes, 18 lines md5sums
Package: murasaki-mpi
Source: murasaki (1.68.6-6)
Version: 1.68.6-6+b3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2458
Depends: murasaki-common, libboost-filesystem1.61.0, libboost-iostreams1.61.0, libboost-regex1.61.0, libboost-system1.61.0, libc6 (>= 2.4), libcrypto++6, libgcc1 (>= 1:3.5), libopenmpi2, libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Description: homology detection tool across multiple large genomes (MPI-version)
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
scale multiple genome global alignments. Supports unlimited length
gapped-seed patterns and unique TF-IDF based filtering.
.
Murasaki is an anchor alignment software, which is
* exteremely fast (17 CPU hours for whole Human x Mouse genome (with
40 nodes: 52 wall minutes))
* scalable (Arbitrarily parallelizable across multiple nodes using MPI.
Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
* unlimited pattern length
* repeat tolerant
* intelligent noise reduction
.
This package provides the MPI-enabled binary for murasaki. While this
will speed up operation on multi-processor machines it will slow down
on a single processor.
drwxr-xr-x root/root 0 2016-06-30 09:15 ./
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/bin/
-rwxr-xr-x root/root 186048 2016-06-30 09:15 ./usr/bin/geneparse-mpi
-rwxr-xr-x root/root 222848 2016-06-30 09:15 ./usr/bin/mbfa-mpi
-rwxr-xr-x root/root 576272 2016-06-30 09:15 ./usr/bin/murasaki-mpi
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-rwxr-xr-x root/root 7138 2010-08-24 14:18 ./usr/lib/murasaki/cgr-image.pl-mpi
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-rwxr-xr-x root/root 50692 2016-06-30 09:15 ./usr/lib/murasaki/testeco-mpi
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/
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drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/
-rw-r--r-- root/root 249 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/README.test
-rw-r--r-- root/root 222 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/changelog.Debian.armhf.gz
-rw-r--r-- root/root 708 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz
-rw-r--r-- root/root 2221 2016-06-30 09:15 ./usr/share/doc/murasaki-mpi/copyright
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/man/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/man/man1/geneparse-mpi.1.gz -> geneparse.1.gz
lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/man/man1/mbfa-mpi.1.gz -> mbfa.1.gz
lrwxrwxrwx root/root 0 2016-06-30 09:15 ./usr/share/man/man1/murasaki-mpi.1.gz -> murasaki.1.gz
murasaki_1.68.6-6+b3_armhf.deb
------------------------------
new debian package, version 2.0.
size 364224 bytes: control archive=1439 bytes.
1189 bytes, 24 lines control
1265 bytes, 20 lines md5sums
Package: murasaki
Source: murasaki (1.68.6-6)
Version: 1.68.6-6+b3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2385
Depends: murasaki-common, libboost-filesystem1.61.0, libboost-iostreams1.61.0, libboost-regex1.61.0, libboost-system1.61.0, libc6 (>= 2.4), libcrypto++6, libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Description: homology detection tool across multiple large genomes
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
scale multiple genome global alignments. Supports unlimited length
gapped-seed patterns and unique TF-IDF based filtering.
.
Murasaki is an anchor alignment software, which is
* exteremely fast (17 CPU hours for whole Human x Mouse genome (with
40 nodes: 52 wall minutes))
* scalable (Arbitrarily parallelizable across multiple nodes using MPI.
Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
* unlimited pattern length
* repeat tolerant
* intelligent noise reduction
drwxr-xr-x root/root 0 2016-06-30 09:15 ./
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/bin/
-rwxr-xr-x root/root 186048 2016-06-30 09:15 ./usr/bin/geneparse
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-rwxr-xr-x root/root 494336 2016-06-30 09:15 ./usr/bin/murasaki
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-rwxr-xr-x root/root 50692 2016-06-30 09:15 ./usr/lib/murasaki/testeco
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/doc/murasaki/
-rw-r--r-- root/root 249 2016-06-30 09:15 ./usr/share/doc/murasaki/README.test
-rw-r--r-- root/root 222 2016-06-30 09:15 ./usr/share/doc/murasaki/changelog.Debian.armhf.gz
-rw-r--r-- root/root 708 2016-06-30 09:15 ./usr/share/doc/murasaki/changelog.Debian.gz
-rw-r--r-- root/root 2221 2016-06-30 09:15 ./usr/share/doc/murasaki/copyright
drwxr-xr-x root/root 0 2016-06-30 09:15 ./usr/share/man/
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-rw-r--r-- root/root 2518 2016-06-30 09:15 ./usr/share/man/man1/geneparse.1.gz
-rw-r--r-- root/root 2721 2016-06-30 09:15 ./usr/share/man/man1/mbfa.1.gz
-rw-r--r-- root/root 10888 2016-06-30 09:15 ./usr/share/man/man1/murasaki.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 162904
Build-Time: 2585
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 355
Job: murasaki_1.68.6-6
Machine Architecture: armhf
Package: murasaki
Package-Time: 2996
Source-Version: 1.68.6-6
Space: 162904
Status: successful
Version: 1.68.6-6+b3
--------------------------------------------------------------------------------
Finished at 2016-10-07T02:08:58Z
Build needed 00:49:56, 162904k disc space