[Debian-med-packaging] Bug#938472: Autoconf detection of libsparsehash-dev fails in sga (Was: Bug#938472: sga: Python2 removal in sid/bullseye)

[Andreas Tille]

Hi again (after long delay),

On Fri, Sep 13, 2019 at 06:55:05PM +0300, Yavor Doganov wrote:
> Andreas Tille wrote:
> > The configure faulure is rather:
> > 
> > checking google/sparse_hash_set usability... no
> > checking google/sparse_hash_set presence... yes
> > configure: WARNING: google/sparse_hash_set: present but cannot be compiled
> 
> > +export DEB_CXXFLAGS_MAINT_APPEND=-std=c++98
> 
> The problem is exactly the opposite -- configure.ac is enforcing c++98
> while these headers assume a newer standard.  The configure check
> should pass if you remove this line in configure.ac:
> 
> | AC_SUBST(CXXFLAGS, "-std=c++98 -O3")
> 
> However, you may encounter compilation errors if the software is not
> yet ready for GCC's default C++ standard.

I implemented this and the configure step succeeded.  Thanks a lot for that hint.

However, as expected, I'm running into a C++ error:

...
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 -g -O2 -fdebug-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-MultiAlignment.o `test -f 'MultiAlignment.cpp' || echo './'`MultiAlignment.cpp
ClusterReader.cpp: In member function 'bool ClusterReader::readCluster(ClusterRecord&)':
ClusterReader.cpp:70:24: error: cannot convert 'std::basic_istream<char>' to 'bool' in initialization
   70 |     bool good = getline(*m_pReader, line);
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~
      |                        |
      |                        std::basic_istream<char>
make[3]: *** [Makefile:754: libutil_a-ClusterReader.o] Error 1


The error is in

   https://salsa.debian.org/med-team/sga/blob/debian/unstable/src/Util/ClusterReader.cpp#L70


Any quick hint how to fix this?

Kind regards

     Andreas.


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