[Debian-med-packaging] Bug#811615: FTBFS with GCC 6: cannot convert x to y

[Martin Michlmayr]

Package: rsem
Version: 1.2.23+dfsg-1
Severity: important
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-6 gcc-6-cannot-convert

This package fails to build with GCC 6.  GCC 6 has not been released
yet, but it's expected that GCC 6 will become the default compiler for
stretch.

Note that only the first error is reported; there might be more.  You
can find a snapshot of GCC 6 in experimental.  To build with GCC 6,
you can set CC=gcc-6 CXX=g++-6 explicitly.

> sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux
...
> g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o rsem-scan-for-paired-end-reads
> buildReadIndex.cpp: In function 'void buildIndex(char*, int, bool)':
> buildReadIndex.cpp:38:32: error: cannot convert 'std::basic_istream<char>' to 'bool' in assignment
>    success = (getline(fin, line));
>                                 ^
> 
> buildReadIndex.cpp:40:32: error: cannot convert 'std::basic_istream<char>' to 'bool' in assignment
>    success = (getline(fin, line));
>                                 ^
> 
> buildReadIndex.cpp:44:33: error: cannot convert 'std::basic_istream<char>' to 'bool' in assignment
>     success = (getline(fin, line));
>                                  ^
> 
> buildReadIndex.cpp:46:33: error: cannot convert 'std::basic_istream<char>' to 'bool' in assignment
>     success = (getline(fin, line));
>                                  ^
> 
> Makefile:59: recipe for target 'rsem-build-read-index' failed
> make[2]: *** [rsem-build-read-index] Error 1
> make[2]: *** Waiting for unfinished jobs....
> In file included from getUnique.cpp:12:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
>  static bool verbose = true; // show detail intermediate outputs
>              ^~~~~~~
> 
> In file included from wiggle.cpp:10:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
>  static bool verbose = true; // show detail intermediate outputs
>              ^~~~~~~
> 
> In file included from samValidator.cpp:12:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
>  static bool verbose = true; // show detail intermediate outputs
>              ^~~~~~~
> 
> In file included from parseIt.cpp:22:0:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>   return (in>>sid>>pos);
>                       ^
> 
> In file included from parseIt.cpp:23:0:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>      return (in>>sid>>pos>>insertL);
>                                   ^
> 
> In file included from scanForPairedEndReads.cpp:13:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
>  static bool verbose = true; // show detail intermediate outputs
>              ^~~~~~~
> 
> Makefile:55: recipe for target 'parseIt.o' failed
> make[2]: *** [parseIt.o] Error 1
> In file included from tbam2gbam.cpp:5:0:
> utils.h:26:13: warning: 'verbose' defined but not used [-Wunused-variable]
>  static bool verbose = true; // show detail intermediate outputs
>              ^~~~~~~
> 
> In file included from EM.cpp:24:0:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>   return (in>>sid>>pos);
>                       ^
> 
> In file included from EM.cpp:25:0:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>      return (in>>sid>>pos>>insertL);
>                                   ^
> 
> In file included from SingleModel.h:26:0,
>                  from simulation.cpp:22:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>   return (in>>sid>>pos);
>                       ^
> 
> In file included from PairedEndModel.h:27:0,
>                  from simulation.cpp:24:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>      return (in>>sid>>pos>>insertL);
>                                   ^
> 
> In file included from SingleModel.h:26:0,
>                  from Gibbs.cpp:15:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>   return (in>>sid>>pos);
>                       ^
> 
> In file included from SingleModel.h:26:0,
>                  from calcCI.cpp:16:
> SingleHit.h: In member function 'bool SingleHit::read(std::istream&)':
> SingleHit.h:46:22: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>   return (in>>sid>>pos);
>                       ^
> 
> In file included from PairedEndModel.h:27:0,
>                  from Gibbs.cpp:17:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>      return (in>>sid>>pos>>insertL);
>                                   ^
> 
> In file included from PairedEndModel.h:27:0,
>                  from calcCI.cpp:18:
> PairedEndHit.h: In member function 'bool PairedEndHit::read(std::istream&)':
> PairedEndHit.h:29:34: error: cannot convert 'std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}' to 'bool' in return
>      return (in>>sid>>pos>>insertL);
>                                   ^
> 
> Makefile:104: recipe for target 'simulation.o' failed
> make[2]: *** [simulation.o] Error 1
> Makefile:111: recipe for target 'Gibbs.o' failed
> make[2]: *** [Gibbs.o] Error 1
> Makefile:120: recipe for target 'calcCI.o' failed
> make[2]: *** [calcCI.o] Error 1
> Makefile:84: recipe for target 'EM.o' failed
> make[2]: *** [EM.o] Error 1

-- 
Martin Michlmayr
Linux for HPE Helion, Hewlett Packard Enterprise