[Debian-med-packaging] Bug#853568: nanopolish: ftbfs with GCC-7

[Matthias Klose]

Package: src:nanopolish
Version: 0.5.0-1
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-7

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-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/nanopolish_0.5.0-1_unstable_gcc7.log
The last lines of the build log are at the end of this report.

To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are 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-7/porting_to.html

[...]
 extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;
            ^~~
In file included from /usr/include/c++/7/cstdlib:77:0,
                 from /usr/include/c++/7/stdlib.h:36,
                 from src/nanopolish_call_variants.cpp:9:
/usr/include/c++/7/bits/std_abs.h:56:3: note: candidate: long int std::abs(long int)
   abs(long __i) { return __builtin_labs(__i); }
   ^~~
/usr/include/c++/7/bits/std_abs.h:61:3: note: candidate: long long int std::abs(long long int)
   abs(long long __x) { return __builtin_llabs (__x); }
   ^~~
/usr/include/c++/7/bits/std_abs.h:70:3: note: candidate: constexpr double std::abs(double)
   abs(double __x)
   ^~~
/usr/include/c++/7/bits/std_abs.h:74:3: note: candidate: constexpr float std::abs(float)
   abs(float __x)
   ^~~
/usr/include/c++/7/bits/std_abs.h:78:3: note: candidate: constexpr long double std::abs(long double)
   abs(long double __x)
   ^~~
src/nanopolish_call_variants.cpp:599:209: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat=]
                    fprintf(stderr, "SUM_VAR\t%zu\t%d\t%d\t%d\t%d\t%.5lf\t%.2lf\n", ref_hp_start, hp_length, var_sequence_length, call_window, variant_offset_end - variant_offset_start, sum_duration, log_gamma);
                                                                                                                                                                                                                 ^
src/nanopolish_call_variants.cpp:599:209: warning: format '%d' expects argument of type 'int', but argument 7 has type 'size_t {aka long unsigned int}' [-Wformat=]
Makefile:98: recipe for target 'src/hmm/nanopolish_profile_hmm.o' failed
make[1]: *** [src/hmm/nanopolish_profile_hmm.o] Error 1
make[1]: *** Waiting for unfinished jobs....
src/alignment/nanopolish_eventalign.cpp: In function 'void emit_sam_header(samFile*, const bam_hdr_t*)':
src/alignment/nanopolish_eventalign.cpp:225:18: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
     sam_hdr_write(fp, hdr);
     ~~~~~~~~~~~~~^~~~~~~~~
src/alignment/nanopolish_eventalign.cpp: In function 'void emit_event_alignment_sam(htsFile*, const SquiggleRead&, const bam_hdr_t*, const bam1_t*, const std::vector<EventAlignment>&)':
src/alignment/nanopolish_eventalign.cpp:364:15: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
     sam_write1(fp, base_hdr, event_record);
     ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
Makefile:98: recipe for target 'src/common/nanopolish_variant.o' failed
make[1]: *** [src/common/nanopolish_variant.o] Error 1
Makefile:98: recipe for target 'src/alignment/nanopolish_eventalign.o' failed
make[1]: *** [src/alignment/nanopolish_eventalign.o] Error 1
Makefile:98: recipe for target 'src/nanopolish_scorereads.o' failed
make[1]: *** [src/nanopolish_scorereads.o] Error 1
Makefile:98: recipe for target 'src/nanopolish_consensus.o' failed
make[1]: *** [src/nanopolish_consensus.o] Error 1
Makefile:98: recipe for target 'src/nanopolish_call_variants.o' failed
make[1]: *** [src/nanopolish_call_variants.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: make -j64 returned exit code 2
debian/rules:11: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2