gistfile1.txt

cpan[1]> install Bio::DB::BigWig
CPAN: Storable loaded ok (v2.25)
Going to read '/homes/dbolser/.cpan/Metadata'
  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
Running install for module 'Bio::DB::BigWig'
Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
CPAN: Digest::SHA loaded ok (v5.61)
CPAN: Compress::Zlib loaded ok (v2.03)
Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz ok
CPAN: Archive::Tar loaded ok (v1.76)
Bio-BigFile-1.05
Bio-BigFile-1.05/Changes
Bio-BigFile-1.05/LICENSE
Bio-BigFile-1.05/DISCLAIMER
Bio-BigFile-1.05/Build.PL
Bio-BigFile-1.05/typemap
Bio-BigFile-1.05/META.yml
Bio-BigFile-1.05/README
Bio-BigFile-1.05/MANIFEST
Bio-BigFile-1.05/ExampleData
Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
Bio-BigFile-1.05/ExampleData/refSeqTest.as
Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
Bio-BigFile-1.05/bin
Bio-BigFile-1.05/bin/bigWigToWig.pl
Bio-BigFile-1.05/bin/wigToBigWig.pl
Bio-BigFile-1.05/bin/index_bigwigset.pl
Bio-BigFile-1.05/lib
Bio-BigFile-1.05/lib/Bio
Bio-BigFile-1.05/lib/Bio/DB
Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
Bio-BigFile-1.05/t
Bio-BigFile-1.05/t/02.bigbed.t
Bio-BigFile-1.05/t/03.bigwig_high.t
Bio-BigFile-1.05/t/04.bigbed_high.t
Bio-BigFile-1.05/t/05.bigwig_set.t
/bin/tar: Read 9216 bytes from -
Bio-BigFile-1.05/t/01.bigwig.t
Bio-BigFile-1.05/patches
Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
CPAN: File::Temp loaded ok (v0.22)
CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
CPAN: CPAN::Meta loaded ok (v2.110580)
CPAN: Module::CoreList loaded ok (v2.46)
CPAN: Time::HiRes loaded ok (v1.9717)

  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz


This module requires the compiled jkweb.a library from Jim Kent's source tree.
If you haven't already done so, please download the source from
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
contents of the "kent/src/lib" subdirectory as directed in the README. Then
enter the location of the "kent/src" subdirectory at the prompt below. To prevent
this message from appearing in the future, set the environment variable KENT_SRC 
to point to the "kent/src" subdirectory.

Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-BigFile' version '1.05'
Building Bio-BigFile
gcc -I/homes/dbolser/build/src/kent/src/inc -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i386 -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 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -o lib/Bio/DB/BigFile.o lib/Bio/DB/BigFile.c
lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigIntervalQuery’:
lib/Bio/DB/BigFile.xs:172: warning: operation on ‘list’ may be undefined
lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigSummaryArray’:
lib/Bio/DB/BigFile.xs:193: warning: operation on ‘values’ may be undefined
lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedSummaryArray’:
lib/Bio/DB/BigFile.xs:252: warning: operation on ‘values’ may be undefined
lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigSummary’:
lib/Bio/DB/BigFile.xs:296: warning: operation on ‘summary’ may be undefined
lib/Bio/DB/BigFile.xs:302: warning: operation on ‘summaryList’ may be undefined
lib/Bio/DB/BigFile.xs:290: warning: unused variable ‘i’
lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedSummary’:
lib/Bio/DB/BigFile.xs:326: warning: operation on ‘summary’ may be undefined
lib/Bio/DB/BigFile.xs:332: warning: operation on ‘summaryList’ may be undefined
lib/Bio/DB/BigFile.xs:320: warning: unused variable ‘i’
lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended’:
lib/Bio/DB/BigFile.xs:358: warning: operation on ‘summary’ may be undefined
lib/Bio/DB/BigFile.xs:354: warning: unused variable ‘summaryList’
lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended’:
lib/Bio/DB/BigFile.xs:395: warning: operation on ‘summary’ may be undefined
lib/Bio/DB/BigFile.xs:391: warning: unused variable ‘summaryList’
lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_chromList’:
lib/Bio/DB/BigFile.xs:424: warning: operation on ‘RETVAL’ may be undefined
lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedIntervalQuery’:
lib/Bio/DB/BigFile.xs:450: warning: operation on ‘list’ may be undefined
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o /homes/dbolser/build/src/kent/src/lib/i386/jkweb.a -lz
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build -- OK
CPAN: YAML loaded ok (v0.72)
Running Build test
t/01.bigwig.t ....... Can't load '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so' for module Bio::DB::BigFile: /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so: undefined symbol: SSL_library_init at /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/01.bigwig.t line 28
Compilation failed in require at t/01.bigwig.t line 28.
BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 29/29 subtests 
t/02.bigbed.t ....... Can't load '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so' for module Bio::DB::BigFile: /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so: undefined symbol: SSL_library_init at /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at t/02.bigbed.t line 28
Compilation failed in require at t/02.bigbed.t line 28.
BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 15/15 subtests 
t/03.bigwig_high.t .. Can't load '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so' for module Bio::DB::BigFile: /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so: undefined symbol: SSL_library_init at /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWig.pm line 7
Compilation failed in require at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWig.pm line 7.
BEGIN failed--compilation aborted at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWig.pm line 7.
Compilation failed in require at t/03.bigwig_high.t line 28.
BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 32/32 subtests 
t/04.bigbed_high.t .. Can't load '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so' for module Bio::DB::BigFile: /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so: undefined symbol: SSL_library_init at /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWig.pm line 7
Compilation failed in require at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWig.pm line 7.
BEGIN failed--compilation aborted at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWig.pm line 7.
Compilation failed in require at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigBed.pm line 7.
BEGIN failed--compilation aborted at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigBed.pm line 7.
Compilation failed in require at t/04.bigbed_high.t line 28.
BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 35/35 subtests 
t/05.bigwig_set.t ... Can't load '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so' for module Bio::DB::BigFile: /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so: undefined symbol: SSL_library_init at /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
 at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWig.pm line 7
Compilation failed in require at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWig.pm line 7.
BEGIN failed--compilation aborted at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWig.pm line 7.
Compilation failed in require at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWigSet.pm line 177.
BEGIN failed--compilation aborted at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-LS5PkN/t/../lib/Bio/DB/BigWigSet.pm line 177.
Compilation failed in require at t/05.bigwig_set.t line 19.
BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
No subtests run 

Test Summary Report
-------------------
t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 29 tests but ran 0.
t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 15 tests but ran 0.
t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 32 tests but ran 0.
t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 35 tests but ran 0.
t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.02 sys +  0.95 cusr  0.13 csys =  1.14 CPU)
Result: FAIL
Failed 5/5 test programs. 0/0 subtests failed.
  LDS/Bio-BigFile-1.05.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports LDS/Bio-BigFile-1.05.tar.gz
Running Build install
  make test had returned bad status, won't install without force
Failed during this command:
 LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO