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  1. cpan[1]> install Bio::DB::BigWig
  2. CPAN: Storable loaded ok (v2.15)
  3. Going to read '/homes/www-potato/.cpan/Metadata'
  4.   Database was generated on Thu, 07 Oct 2010 00:30:52 GMT
  5. Running install for module 'Bio::DB::BigWig'
  6. CPAN: YAML loaded ok (v0.66)
  7. Running make for L/LD/LDS/Bio-BigFile-1.03.tar.gz
  8. CPAN: Digest::SHA loaded ok (v5.47)
  9. CPAN: Compress::Zlib loaded ok (v2.027)
  10. Checksum for /homes/www-potato/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.03.tar.gz ok
  11. Scanning cache /homes/www-potato/.cpan/build for sizes
  12. ..........................................................................--DONE
  13. DEL(1/7): /homes/www-potato/.cpan/build/XML-LibXML-1.70-4lhwKh
  14. DEL(2/7): /homes/www-potato/.cpan/build/Algorithm-Diff-1.1902-f6gAad
  15. DEL(3/7): /homes/www-potato/.cpan/build/Algorithm-Diff-1.1902-f6gAad.yml
  16. DEL(4/7): /homes/www-potato/.cpan/build/Algorithm-Diff-1.1902-mIUr3U
  17. DEL(5/7): /homes/www-potato/.cpan/build/Algorithm-Diff-1.1902-mIUr3U.yml
  18. DEL(6/7): /homes/www-potato/.cpan/build/Capture-Tiny-0.08-ws4oae
  19. DEL(7/7): /homes/www-potato/.cpan/build/Capture-Tiny-0.08-ws4oae.yml
  20. CPAN: Archive::Tar loaded ok (v1.64)
  21. Bio-BigFile-1.03/
  22. Bio-BigFile-1.03/t/
  23. Bio-BigFile-1.03/t/05.bigwig_set.t
  24. Bio-BigFile-1.03/t/04.bigbed_high.t
  25. Bio-BigFile-1.03/t/01.bigwig.t
  26. Bio-BigFile-1.03/t/03.bigwig_high.t
  27. Bio-BigFile-1.03/t/02.bigbed.t
  28. Bio-BigFile-1.03/bin/
  29. Bio-BigFile-1.03/bin/index_bigwigset.pl
  30. Bio-BigFile-1.03/bin/wigToBigWig.pl
  31. Bio-BigFile-1.03/bin/bigWigToWig.pl
  32. Bio-BigFile-1.03/lib/
  33. Bio-BigFile-1.03/lib/Bio/
  34. Bio-BigFile-1.03/lib/Bio/DB/
  35. Bio-BigFile-1.03/lib/Bio/DB/BigFile/
  36. Bio-BigFile-1.03/lib/Bio/DB/BigFile/Iterators.pm
  37. Bio-BigFile-1.03/lib/Bio/DB/BigFile/Constants.pm
  38. Bio-BigFile-1.03/lib/Bio/DB/BigBed.pm
  39. Bio-BigFile-1.03/lib/Bio/DB/BigWigSet.pm
  40. Bio-BigFile-1.03/lib/Bio/DB/BigWig.pm
  41. Bio-BigFile-1.03/lib/Bio/DB/BigFile.pm
  42. Bio-BigFile-1.03/lib/Bio/DB/BigFile.xs
  43. Bio-BigFile-1.03/DISCLAIMER
  44. Bio-BigFile-1.03/LICENSE
  45. Bio-BigFile-1.03/README
  46. Bio-BigFile-1.03/Changes
  47. Bio-BigFile-1.03/Build.PL
  48. Bio-BigFile-1.03/META.yml
  49. Bio-BigFile-1.03/typemap
  50. Bio-BigFile-1.03/MANIFEST
  51. Bio-BigFile-1.03/ExampleData/
  52. Bio-BigFile-1.03/ExampleData/refSeqTest.as
  53. Bio-BigFile-1.03/ExampleData/WS180.chrom.sizes
  54. Bio-BigFile-1.03/ExampleData/refSeqTest.flat.bed
  55. Bio-BigFile-1.03/ExampleData/refSeqTest.flat.bb
  56. Bio-BigFile-1.03/ExampleData/dpy-27-variable.bw
  57. Bio-BigFile-1.03/ExampleData/hg18.chrom.sizes
  58. Bio-BigFile-1.03/ExampleData/dpy-27-variable-trunk.wig.gz
  59. CPAN: File::Temp loaded ok (v0.22)
  60. CPAN: Time::HiRes loaded ok (v1.86)
  61.  
  62.   CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.03.tar.gz
  63.  
  64. Creating new 'MYMETA.yml' with configuration results
  65. Creating new 'Build' script for 'Bio-BigFile' version '1.03'
  66. CPAN: Module::Build loaded ok (v0.3607)
  67. Building Bio-BigFile
  68. gcc -I/homes/www-potato/build/src/kent/src/inc -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -DXS_VERSION="1.03" -DVERSION="1.03" -fPIC -Wformat=0 -DMACHTYPE_x86_64 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o lib/Bio/DB/BigFile.o lib/Bio/DB/BigFile.c
  69. lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigIntervalQuery’:
  70. lib/Bio/DB/BigFile.xs:172: warning: operation on ‘list’ may be undefined
  71. lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigSummaryArray’:
  72. lib/Bio/DB/BigFile.xs:193: warning: comparison is always false due to limited range of data type
  73. lib/Bio/DB/BigFile.xs:193: warning: operation on ‘values’ may be undefined
  74. lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedSummaryArray’:
  75. lib/Bio/DB/BigFile.xs:252: warning: comparison is always false due to limited range of data type
  76. lib/Bio/DB/BigFile.xs:252: warning: operation on ‘values’ may be undefined
  77. lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigSummary’:
  78. lib/Bio/DB/BigFile.xs:296: warning: comparison is always false due to limited range of data type
  79. lib/Bio/DB/BigFile.xs:296: warning: operation on ‘summary’ may be undefined
  80. lib/Bio/DB/BigFile.xs:302: warning: operation on ‘summaryList’ may be undefined
  81. lib/Bio/DB/BigFile.xs:290: warning: unused variable ‘i’
  82. lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedSummary’:
  83. lib/Bio/DB/BigFile.xs:326: warning: comparison is always false due to limited range of data type
  84. lib/Bio/DB/BigFile.xs:326: warning: operation on ‘summary’ may be undefined
  85. lib/Bio/DB/BigFile.xs:332: warning: operation on ‘summaryList’ may be undefined
  86. lib/Bio/DB/BigFile.xs:320: warning: unused variable ‘i’
  87. lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended’:
  88. lib/Bio/DB/BigFile.xs:358: warning: comparison is always false due to limited range of data type
  89. lib/Bio/DB/BigFile.xs:358: warning: operation on ‘summary’ may be undefined
  90. lib/Bio/DB/BigFile.xs:354: warning: unused variable ‘summaryList’
  91. lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended’:
  92. lib/Bio/DB/BigFile.xs:395: warning: comparison is always false due to limited range of data type
  93. lib/Bio/DB/BigFile.xs:395: warning: operation on ‘summary’ may be undefined
  94. lib/Bio/DB/BigFile.xs:391: warning: unused variable ‘summaryList’
  95. lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_chromList’:
  96. lib/Bio/DB/BigFile.xs:424: warning: operation on ‘RETVAL’ may be undefined
  97. lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedIntervalQuery’:
  98. lib/Bio/DB/BigFile.xs:450: warning: operation on ‘list’ may be undefined
  99. ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
  100. gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o /homes/www-potato/build/src/kent/src/lib/x86_64/jkweb.a -lz
  101. /usr/bin/ld: /homes/www-potato/build/src/kent/src/lib/x86_64/jkweb.a(bbiRead.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC
  102. /homes/www-potato/build/src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
  103. collect2: ld returned 1 exit status
  104. error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from lib/Bio/DB/BigFile.o at /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
  105.   LDS/Bio-BigFile-1.03.tar.gz
  106.   ./Build -- NOT OK
  107. Running Build test
  108.   Can't test without successful make
  109. Running Build install
  110.   Make had returned bad status, install seems impossible
  111. Failed during this command:
  112.  LDS/Bio-BigFile-1.03.tar.gz                  : make NO
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