[Debian-med-packaging] Bug#966876: Bug fixed, but new version needs work on autopkgtest (Was: Bug#966876: trinityrnaseq: FTBFS: sift_bam_max_cov.cpp:99:10: error: ‘string’ is not a member of =?UTF-8?Q?=E2=80=98std=E2=80=99?=)

[Andreas Tille]

Control: tags -1 pending

On Mon, Aug 03, 2020 at 10:07:38AM +0200, Lucas Nussbaum wrote:
> Relevant part (hopefully):
> > g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now sift_bam_max_cov.cpp -Wall -lhts -O2 -o bamsifter
> > sift_bam_max_cov.cpp: In function ‘int main(int, char**)’:
> > sift_bam_max_cov.cpp:99:10: error: ‘string’ is not a member of ‘std’
> >    99 |     std::string tmp_text(input_header->text, input_header->l_text);
> >       |          ^~~~~~
> > sift_bam_max_cov.cpp:16:1: note: ‘std::string’ is defined in header ‘<string>’; did you forget to ‘#include <string>’?
> >    15 | #include "htslib/bgzf.h"
> >   +++ |+#include <string>

I've fixed this bug (and I think new upstream has found another way by using
'-std=c++11' option (which would be hopefully unneeded by my patch but I did
not tested). 

Unfortunately the autopkgtest is broken by the new version which I imported
as well.  Not sure whether

   seqtk-trinity is missing and thus autopkgtest fails

is the only problem.  seqtk-trinity was provided as *binary* which needed
to be removed in Files-Excluded.  I have not checked how / whether it is
build and whether other issues might exist.

Any takers for the remaining issues?

Kind regards

       Andreas.

-- 
http://fam-tille.de