code stopped working

[yaximik]

Hi,

I have not used BioPieces for quite a while and my cleaning scripts that used to work fine stopped working with new data. I run bp_update and get the latest version, yet still the same result. Error output runs off top, but here are some of the lower portion of the output:

Can't find 'boot_Maasha__Common_b495' symbol in /home/yaximik/tmp/lib/auto/Maasha/Common_b495/Common_b495.so
 at /usr/lib/perl5/site_perl/5.8.8/Inline.pm line 535


 at /home/yaximik/Bioinformatics/biopieces/code_perl/Maasha/Common.pm line 47
BEGIN failed--compilation aborted at /home/yaximik/Bioinformatics/biopieces/code_perl/Maasha/Common.pm line 145.
Compilation failed in require at /home/yaximik/Bioinformatics/biopieces/code_perl/Maasha/Match.pm line 35.
BEGIN failed--compilation aborted at /home/yaximik/Bioinformatics/biopieces/code_perl/Maasha/Match.pm line 35.
Compilation failed in require at /home/yaximik/Bioinformatics/biopieces/code_perl/Maasha/Biopieces.pm line 34.
BEGIN failed--compilation aborted at /home/yaximik/Bioinformatics/biopieces/code_perl/Maasha/Biopieces.pm line 34.
Compilation failed in require at /home/yaximik/Bioinformatics/biopieces/bp_bin/grab line 32.
BEGIN failed--compilation aborted at /home/yaximik/Bioinformatics/biopieces/bp_bin/grab line 32.
/home/yaximik/Bioinformatics/biopieces/code_ruby/lib/maasha/biopieces.rb:118:in `write': Broken pipe - <STDOUT> (Errno::EPIPE)
        from /home/yaximik/Bioinformatics/biopieces/code_ruby/lib/maasha/biopieces.rb:118:in `<<'
        from /home/yaximik/Bioinformatics/biopieces/code_ruby/lib/maasha/biopieces.rb:118:in `puts'
        from /home/yaximik/Bioinformatics/biopieces/bp_bin/read_fastq:126:in `block (4 levels) in <main>'
        from /home/yaximik/Bioinformatics/biopieces/code_ruby/lib/maasha/filesys.rb:104:in `each'
        from /home/yaximik/Bioinformatics/biopieces/bp_bin/read_fastq:108:in `block (3 levels) in <main>'
        from /home/yaximik/Bioinformatics/biopieces/code_ruby/lib/maasha/filesys.rb:76:in `open'
        from /home/yaximik/Bioinformatics/biopieces/bp_bin/read_fastq:107:in `block (2 levels) in <main>'
        from /home/yaximik/Bioinformatics/biopieces/bp_bin/read_fastq:106:in `each'
        from /home/yaximik/Bioinformatics/biopieces/bp_bin/read_fastq:106:in `block in <main>'
        from /home/yaximik/Bioinformatics/biopieces/code_ruby/lib/maasha/biopieces.rb:89:in `open'
        from /home/yaximik/Bioinformatics/biopieces/bp_bin/read_fastq:51:in `<main>'
Had problems bootstrapping Inline module 'Maasha::Common_b495'

Can't find 'boot_Maasha__Common_b495' symbol in /home/yaximik/tmp/lib/auto/Maasha/Common_b495/Common_b495.so
 at /usr/lib/perl5/site_perl/5.8.8/Inline.pm line 535


 at /home/yaximik/Bioinformatics/biopieces/code_perl/Maasha/Common.pm line 47
BEGIN failed--compilation aborted at /home/yaximik/Bioinformatics/biopieces/code_perl/Maasha/Common.pm line 145.

What may be the problem? Like I said, the scripts worked without flaws earlier.

Vladimir

[Martin Asser Hansen]

Obviously you should be using Biopieces daily! ;o)

But seriously, this looks like an issue with the inline C code. If you upgraded Perl version or if perhaps I upgrade some inline C code (I can't remember if I did this for a long time) then that code should be compiled automatically to a static library, however, this fails sometimes. I think the solution is to find the directories where the inline C code is compiled and wipe those ($BP_TMP/build and $BP_TMP/lib). They will be rebuild automatically next time you run bp_test.

Cheers,

Martin

 

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