Does not build using gcc 6

[tillea]

Hi,

as you can read in the Debian bug report sga does not build when using gcc 6 due to more strict type checking:

https://bugs.debian.org/811664

It results in

g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -O3 -c -o libutil_a-VariantIndex.o test -f 'VariantIndex.cpp' || echo './'VariantIndex.cpp
ClusterReader.cpp: In member function 'bool ClusterReader::readCluster(ClusterRecord&)':
ClusterReader.cpp:70:41: error: cannot convert 'std::basic_istream' to 'bool' in initialization
bool good = getline(*m_pReader, line);
^

Makefile:722: recipe for target 'libutil_a-ClusterReader.o' failed
make[3]: *** [libutil_a-ClusterReader.o] Error 1
make[3]: *** Waiting for unfinished jobs....
StdAlnTools.cpp: In function 'std::__cxx11::string StdAlnTools::expandCigar(const string&)':
StdAlnTools.cpp:122:34: error: cannot convert 'std::basic_istream' to 'bool' in initialization
bool success = parser >> code;
^~~~

Makefile:750: recipe for target 'libutil_a-StdAlnTools.o' failed

Please note that there might be more issues later in the build sequence.

Kind regards

      Andreas.

[jts]

Thanks for the report, I will look into this.

[jts]

I don't have easy access to GCC 6 right now, is this reproducible with stricter flags on GCC 4.9.x?

[mateidavid]

Wow- so gcc6 disallows implicit conversion of std::basic_istream to bool, meaning that this becomes illegal:

std::string s;
while (std::getline(std::cin, s)) process_line(s);

I haven't read about gcc6, but this seems a bit extreme. Can this be one of those things that might get tweaked before an official release?

[tillea]

jts: is this reproducible with stricter flags on GCC 4.9.x?

I do not think so. Otherwise the bug reporter would not have given explicit hints how to use gcc-6 from Debian experimental.

[jts]

Does this error occur if you pass the -std=c++03 flag to GCC 6?

[SHuang-Broad]

This is the same error as in issue #108 . Compiling with clang has the same issue.

[mateidavid]

As explained here: #108 (comment), an easy way to add -std=c++03 is to replace make with make CXXFLAGS="-O3 -std=c++03". Please let us know if it solves the problems.

Alternatively, where can we find a docker image with gcc-6.0?

[mr-c]

@mateidavid Here's a Debian unstable + gcc 6 docker image: https://hub.docker.com/r/biocrusoe/debian-gcc6/

docker pull biocrusoe/debian-gcc6

[mateidavid]

@mr-c: Thanks for stepping in. But it doesn't work yet, I'm getting:

$ docker pull biocrusoe/docker-gcc6
Using default tag: latest
Pulling repository docker.io/biocrusoe/docker-gcc6
Tag latest not found in repository docker.io/biocrusoe/docker-gcc6

[mr-c]

@mateidavid Whoops; I forgot to tag and push. I don't do this often :-) I also renamed the image (and updated my instructions above).

Does docker pull biocrusoe/debian-gcc6 work for you?

[mateidavid]

I got it now. I needed g++ not just gcc, and the other build requirements (zlib1g-dev, etc). But I got the Dockerfile and put them in myself, thanks! I can now see the OP error.

[gerddie]

Actually, you should also be able to reproduce the error by setting -std=c++11 with any compiler that is advanced enough to support it (AFAIK that includes g++-4.9).

@mateidavid The while loop should still work, but assignment to a bool variable has to be make explicit.

[mateidavid]

PR #110 fixes this (at least it did back when I wrote it).

[gerddie]

Great, I'll try to use it to fix the Debian package.

As a side note of personal taste I'd suggest using .good() or ! ... .fail() instead of the static_cast on the stream, because it would probably look more readable ...

[tillea]

Hi,

thanks for the hint. I'll integrate the patch into the Debian
package.

Kind regards

   Andreas.

On Tue, Jul 05, 2016 at 06:32:30AM -0700, Matei David wrote:

PR #110 fixes this (at least it did back when I wrote it).

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[jts]

I've merged @mateidavid's PR (thanks)