Your message dated Tue, 17 Feb 2015 04:04:13 +0000
with message-id <[email protected]>
and subject line Bug#778021: fixed in ncbi-blast+ 2.2.30-2
has caused the Debian Bug report #778021,
regarding ncbi-blast+: ftbfs with GCC-5
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
778021: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778021
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:ncbi-blast+
Version: 2.2.29-3
Severity: normal
Tags: sid stretch
User: [email protected]
Usertags: ftbfs-gcc-5
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-5/g++-5, but succeeds to build with gcc-4.9/g++-4.9. The
severity of this report may be raised before the stretch release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc5-20150205/ncbi-blast+_2.2.29-3_unstable_gcc5.log
The last lines of the build log are at the end of this report.
To build with GCC 5, either set CC=gcc-5 CXX=g++-5 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t experimental install g++
Common build failures are C11 as the default C mode, new warnings
resulting in build failures with -Werror turned on, or new/dropped
symbols in Debian symbols files. For other C/C++ related build failures
see the porting guide at http://gcc.gnu.org/gcc-5/porting_to.html
[...]
Applying patch no_multiarch_rpath
patching file c++/src/build-system/configure
Hunk #1 succeeded at 6209 (offset 286 lines).
patching file c++/src/build-system/configure.ac
Hunk #1 succeeded at 1737 (offset 117 lines).
Applying patch use_pie_for_apps
patching file c++/src/build-system/Makefile.app.in
Applying patch skip_services_unit_test
patching file
c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
Applying patch fix_configure
patching file c++/configure.orig
Applying patch include_typeinfo
patching file c++/include/corelib/ncbistl.hpp
Now at patch include_typeinfo
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/ncbi-blast+-vl5_sw/ncbi-blast+-2.2.29'
cd c++ &&
LD_LIBRARY_PATH=/build/ncbi-blast+-vl5_sw/ncbi-blast+-2.2.29/c++/BUILD/lib${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}
\
CONFIG_SHELL=/bin/bash ./configure --with-dll --with-mt --without-autodep
--without-makefile-auto-update --with-flat-makefile --without-caution
--without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+
--with-build-root=BUILD --without-debug
configure: loading site script
/build/ncbi-blast+-vl5_sw/ncbi-blast+-2.2.29/c++/src/build-system/config.site
configure: creating cache config.cache
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
adjusted C compiler: /usr/bin/gcc
adjusted C++ compiler: /usr/bin/g++
configure: error: Do not know how to build MT-safe with compiler /usr/bin/g++
5.0.0
make[1]: *** [override_dh_auto_configure] Error 1
debian/rules:40: recipe for target 'override_dh_auto_configure' failed
make[1]: Leaving directory '/build/ncbi-blast+-vl5_sw/ncbi-blast+-2.2.29'
make: *** [build-arch] Error 2
debian/rules:96: recipe for target 'build-arch' failed
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--- End Message ---
--- Begin Message ---
Source: ncbi-blast+
Source-Version: 2.2.30-2
We believe that the bug you reported is fixed in the latest version of
ncbi-blast+, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <[email protected]> (supplier of updated ncbi-blast+ package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 16 Feb 2015 22:38:50 -0500
Source: ncbi-blast+
Binary: ncbi-blast+ ncbi-blast+-legacy
Architecture: source amd64 all
Version: 2.2.30-2
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Description:
ncbi-blast+ - next generation suite of BLAST sequence search tools
ncbi-blast+-legacy - NCBI Blast legacy call script
Closes: 778021
Changes:
ncbi-blast+ (2.2.30-2) experimental; urgency=medium
.
* d/patches/allow_gcc5 (new): Allow compilation with GCC 5, per upstream.
(Closes: #778021.)
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--- End Message ---
