HI
I have successfully installing quite a few tools on my galaxy instance. However I have a problem with 'bedtools' to install correctly from the main tool shed (Revision:f8b7dc21b4ee). The samtool dependencies install without reported error. However package_bedtools_2_24 has an error. I have uninstalled and reinstalled this component but the error persists. Any suggestions? Thanks Guy
This is the error info I get from the admin interface
Name Version Type Status Error
bedtools 2.24 package Error make[1]: Warning: File ../../../obj//FileRecordMergeMgr.o' has modification time 2.9 s in the future
make[1]: warning: Clock skew detected. Your build may be incomplete.
make[1]: Warning: File../../../../obj//RecordMgr.o' has modification time 1.7 s in the future
make[1]: warning: Clock skew detected. Your build may be incomplete.
ParseTools.cpp: In function ‘int str2chrPos(const char, size_t)’:
ParseTools.cpp:31: warning: unused variable ‘hasExponent’
src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
src/api/internal/index/BamStandardIndex_p.cpp:958: warning: comparison between signed and unsigned integer expressions
src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendRequest(size_t)’:
src/api/internal/io/BamHttp_p.cpp:396: warning: comparison between signed and unsigned integer expressions
src/api/internal/io/TcpSocket_p.cpp: In member function ‘std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)’:
src/api/internal/io/TcpSocket_p.cpp:336: warning: comparison between signed and unsigned integer expressions
slopBed.cpp: In member function ‘void BedSlop::AddSlop(BED&)’:
slopBed.cpp:86: warning: comparison between signed and unsigned integer expressions
slopBed.cpp:100: warning: comparison between signed and unsigned integer expressions
splitBed.cpp: In member function ‘FILE BedSplit::saveFileChunk(std::string&, size_t)’:
splitBed.cpp:151: warning: format ‘%05d’ expects type ‘int’, but argument 3 has type ‘size_t’
obj/gzstream.o: In function gzstreambuf::open(char const*, int)':
gzstream.C:(.text+0x2a2): undefined reference togzopen64'
collect2: ld returned 1 exit status
make: * [all] Error 1