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
Original issue reported on code.google.com by
mmokr...@gmail.com
on 15 Jan 2015 at 9:52