read_fastq: "Error. You have specified 'C' as an Inline programming language."

[GoogleCodeExporter]

Dear All

I've installed biopieces with all dependencies but vmatch. I use the latest 
bash installer for both: Ruby and Biopieces. When I run:

read_fastq 

I get the following error

Error. You have specified 'C' as an Inline programming language.

I currently only know about the following languages:
    Foo, foo

If you have installed a support module for this language, try deleting the
config-x86_64-linux-gnu-thread-multi-5.014002 file from the following Inline 
DIRECTORY, and run again:

    /home/rivasas2/tools/biopieces/tmp

(And if that works, please file a bug report.)

 at /home/rivasas2/tools/biopieces/code_perl/Maasha/Common.pm line 47.
BEGIN failed--compilation aborted at 
/home/rivasas2/tools/biopieces/code_perl/Maasha/Common.pm line 145.
Compilation failed in require at 
/home/rivasas2/tools/biopieces/code_perl/Maasha/Match.pm line 35.
BEGIN failed--compilation aborted at 
/home/rivasas2/tools/biopieces/code_perl/Maasha/Match.pm line 35.
Compilation failed in require at 
/home/rivasas2/tools/biopieces/code_perl/Maasha/Biopieces.pm line 34.
BEGIN failed--compilation aborted at 
/home/rivasas2/tools/biopieces/code_perl/Maasha/Biopieces.pm line 34.
Compilation failed in require at 
/home/rivasas2/tools/biopieces/bp_bin/print_wiki line 32.
BEGIN failed--compilation aborted at 
/home/rivasas2/tools/biopieces/bp_bin/print_wiki line 32.
/home/rivasas2/tools/biopieces/code_ruby/lib/maasha/biopieces.rb:441:in 
`print_usage_and_exit': Failed printing wiki: 
/home/rivasas2/tools/biopieces/bp_usage/read_fasta.wiki (RuntimeError)
    from /home/rivasas2/tools/biopieces/code_ruby/lib/maasha/biopieces.rb:391:in `options_parse'
    from /home/rivasas2/tools/biopieces/code_ruby/lib/maasha/biopieces.rb:75:in `options_parse'
    from ./read_fasta:38:in `<main>'

Thanks in advance for your suggestions.

Original issue reported on code.google.com by marcelor...@gmail.com on 1 Aug 2014 at 9:34

[GoogleCodeExporter]

I believe this error message comes from the Perl module Inline.pm. Did you run 
bp_test - and does that tell us something useful?  

Original comment by martinah...@gmail.com on 3 Aug 2014 at 5:43

[GoogleCodeExporter]

For Perl, bp_test says:

Testing Perl version ... OK
Testing required Perl module - "Inline": OK
Testing required Perl module - "JSON::XS": OK
Testing required Perl module - "SVG": OK
Testing required Perl module - "Bit::Vector": OK
Testing required Perl module - "Time::HiRes": OK

In case of been informative, I'm attaching the whole output.

Thanks

Original comment by marcelor...@gmail.com on 3 Aug 2014 at 6:55

Attachments:

• bp_test_output

[GoogleCodeExporter]

The problem was solved after installing Perl's module Inline::C

To install this module:

cpan -f -i Inline::C

Original comment by marcelor...@gmail.com on 3 Aug 2014 at 8:53

[GoogleCodeExporter]

Let me get this right: when you ran bp_test it stopped and let you know you 
were missing the Inline::C module. After you installed the module, all was OK?

Original comment by martinah...@gmail.com on 8 Aug 2014 at 7:21

[GoogleCodeExporter]

When I ran bp_test, it said OK (Testing required Perl module - "Inline": OK) 
but read_fastq wasn't working. Only after I install the Inline::C module 
read_fastq was all OK. 

Original comment by marcelor...@gmail.com on 8 Aug 2014 at 8:00

[GoogleCodeExporter]

Right, I am probably only checking for the Inline.pm and not also on Inline::C. 
Thanks,

Martin

Original comment by martinah...@gmail.com on 18 Aug 2014 at 1:42