Question: Error installing package_bedtools_2_24
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gravatar for Guy Reeves
23 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

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

error install bedtools • 467 views
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