[Debian-med-packaging] C++ help needed (Was: FYI: New Abyss 2.0 contains undistributable components)

[Shaun Jackman]

Hi, Andreas. I suspect it's specific to GCC 6 and should hopefully be
easily resolved. Can you please open a bug report at
https://github.com/bcgsc/abyss/issues

Thanks,
Shaun

-- 
http://sjackman.ca

On October 5, 2016 at 22:05:19, Andreas Tille (andreas at an3as.eu) wrote:

Hi,

On Wed, Sep 21, 2016 at 03:02:20PM -0700, Shaun Jackman wrote:
> Hi, Andreas. ABySS 2.0.1 is now GPL-3 without the non-commercial
> restriction!
>
> https://github.com/bcgsc/abyss/releases

I tried to build the latest version of ABySS. Its commited to packaging
Git[1] but does not build with the current gcc in Debian unstable:

...
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include
-I../DataLayer -I../Common -I/build/abyss-2.0.1
-isystem/usr/lib/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2
-isystem/build/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error
-fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.0.1=.
-fstack-protector-strong -Wformat -Werror=format-security -c -o
DBG/DBG_LoadAlgorithm-LoadAlgorithmTest.o `test -f
'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp
In file included from
../lib/gtest-1.7.0/include/gtest/internal/gtest-internal.h:40:0,
from ../lib/gtest-1.7.0/include/gtest/gtest.h:58,
from DBG/LoadAlgorithmTest.cpp:7:
../lib/gtest-1.7.0/include/gtest/internal/gtest-port.h:557:14: error:
'tuple' is already declared in this scope
using ::std::tuple;
^~~~~
../lib/gtest-1.7.0/include/gtest/internal/gtest-port.h:558:14: error:
'tuple_element' is already declared in this scope
using ::std::tuple_element;
^~~~~~~~~~~~~
../lib/gtest-1.7.0/include/gtest/internal/gtest-port.h:559:14: error:
'tuple_size' is already declared in this scope
using ::std::tuple_size;
^~~~~~~~~~
Makefile:1272: recipe for target
'DBG/DBG_LoadAlgorithm-LoadAlgorithmTest.o' failed
make[3]: *** [DBG/DBG_LoadAlgorithm-LoadAlgorithmTest.o] Error 1
make[3]: Leaving directory '/build/abyss-2.0.1/Unittest'


May be this is also connected to some gtest issue.

Any hint?

Kind regards

Andreas.

[1] https://anonscm.debian.org/git/debian-med/abyss.git

-- 
http://fam-tille.de
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