Cannot compile mosaik-2.2.3 nor current checkout

Hi,
  I am trying to compile it on Gentoo Linux but it fails.
  Second, the make process does not exit upon and error but silently continues.

Building MOSAIK for the following platform: linux
=========================================================
- Building in fann-2.1.0
  * compiling floatfann.c
In file included from floatfann.c:25:
fann.c: In function 'fann_print_connections':
fann.c:890: warning: format '%3d' expects type 'int', but argument 2 has type 
'long int'
fann.c:890: warning: format '%4d' expects type 'int', but argument 3 has type 
'long int'
fann.c: In function 'fann_print_parameters':
fann.c:991: warning: format '%4d' expects type 'int', but argument 2 has type 
'long int'
fann.c:996: warning: format '%4d' expects type 'int', but argument 2 has type 
'long int'
In file included from floatfann.c:26:
fann_io.c: In function 'fann_save_internal_fd':
fann_io.c:177: warning: format '%u' expects type 'unsigned int', but argument 3 
has type 'long int'
In file included from floatfann.c:26:
fann_io.c:239: warning: format '%u' expects type 'unsigned int', but argument 3 
has type 'long int'
fann_io.c:321: warning: format '%u' expects type 'unsigned int', but argument 3 
has type 'long int'
fann_io.c:326: warning: format '%u' expects type 'unsigned int', but argument 3 
has type 'long int'

- Building in CommonSource
- Building in DataStructures
  * compiling AbstractDnaHash.cpp
  * compiling AlignedReadCache.cpp
  * compiling DnaHash.cpp
  * compiling HashRegionTree.cpp
  * compiling JumpDnaHash.cpp
  * compiling MosaikString.cpp
  * compiling MultiDnaHash.cpp
  * compiling NaiveAlignmentSet.cpp
  * compiling UbiqDnaHash.cpp

- Building in ExternalReadFormats
  * compiling Fasta.cpp
Fasta.cpp: In member function 'void CFasta::Open(const std::string&)':
Fasta.cpp:259: error: conditional expression between distinct pointer types 
'gzFile_s*' and 'FILE*' lacks a cast
Fasta.cpp:261: error: conditional expression between distinct pointer types 
'gzFile_s*' and 'FILE*' lacks a cast
Fasta.cpp:267: error: conditional expression between distinct pointer types 
'gzFile_s*' and 'FILE*' lacks a cast
Fasta.cpp:269: error: conditional expression between distinct pointer types 
'gzFile_s*' and 'FILE*' lacks a cast
Makefile:24: recipe for target '../../../obj/Fasta.o' failed
make[2]: *** [../../../obj/Fasta.o] Error 1

- Building in MosaikReadFormat
  * compiling AlignmentReader.cpp
  * compiling AlignmentWriter.cpp
  * compiling ReadReader.cpp
  * compiling ReadWriter.cpp
  * compiling ReferenceSequenceReader.cpp

- Building in PairwiseAlignment
  * compiling SmithWatermanGotoh.cpp
  * compiling BandedSmithWaterman.cpp

- Building in Utilities
  * compiling ArchiveMerge.cpp
  * compiling ArchiveSort.cpp
  * compiling Benchmark.cpp
  * compiling BestNSecondBestSelection.cpp
  * compiling CigarTager.cpp
  * compiling ColorspaceUtilities.cpp
  * compiling ConsoleUtilities.cpp
  * compiling Entropy.cpp
  * compiling FastLZIO.cpp
  * compiling FileUtilities.cpp
  * compiling MdTager.cpp
  * compiling MemoryUtilities.cpp
  * compiling Options.cpp
  * compiling PairwiseUtilities.cpp
  * compiling QualityNeuralNetwork.cpp
  * compiling RegexUtilities.cpp
  * compiling SequenceUtilities.cpp
  * compiling SHA1.cpp
  * compiling SortNMergeUtilities.cpp
  * compiling SortThread.cpp
  * compiling StatisticsMaps.cpp
  * compiling TimeSupport.cpp
  * compiling ZaTager.cpp
  * compiling fastlz.c
  * compiling md5.c

- Building in MosaikBuild
  * compiling BuildMain.cpp
  * compiling MosaikBuild.cpp
make[2]: Nothing to be done for 'all'.
  * compiling Fasta.cpp
Fasta.cpp: In member function 'void CFasta::Open(const std::string&)':
Fasta.cpp:259: error: conditional expression between distinct pointer types 
'gzFile_s*' and 'FILE*' lacks a cast
Fasta.cpp:261: error: conditional expression between distinct pointer types 
'gzFile_s*' and 'FILE*' lacks a cast
Fasta.cpp:267: error: conditional expression between distinct pointer types 
'gzFile_s*' and 'FILE*' lacks a cast
Fasta.cpp:269: error: conditional expression between distinct pointer types 
'gzFile_s*' and 'FILE*' lacks a cast
Makefile:24: recipe for target '../../../obj/Fasta.o' failed
make[2]: *** [../../../obj/Fasta.o] Error 1
Makefile:36: recipe for target '../../obj/Fasta.o' failed
make[1]: *** [../../obj/Fasta.o] Error 2

- Building in MosaikAligner
  * compiling AlignerMain.cpp
  * compiling AlignmentThread.cpp
  * compiling MosaikAligner.cpp
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
  * linking MosaikAligner
g++: ../../obj/BamWriter.o: No such file or directory
Makefile:67: recipe for target 'MosaikAligner' failed
make[1]: *** [MosaikAligner] Error 1

- Building in MosaikJump
  * compiling JumpMain.cpp
  * compiling JumpCreator.cpp
  * linking MosaikJump

- Building in MosaikText
  * compiling TextMain.cpp
  * compiling MosaikText.cpp
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
  * linking MosaikText
g++: ../../obj/BamWriter.o: No such file or directory
Makefile:28: recipe for target 'MosaikText' failed
make[1]: *** [MosaikText] Error 1

>>> Source compiled.
>>> Test phase [not enabled]: sci-biology/mosaik-9999

The Makefile should really return "exit 255" or whatever if one of the targets 
failed.
Original issue reported on code.google.com by mmokr...@gmail.com on 15 Jan 2015 at 9:52
duncanca / mosaik-aligner

Cannot compile mosaik-2.2.3 nor current checkout #135
