generateWig errors after upgrade

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Branden Timm

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Nov 20, 2014, 3:20:25 PM11/20/14
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Greetings,
  Yesterday we updated the entire Bioconductor suite, and as of today one of my investigators is reporting errors running generateWig().  We see errors similar to the following:

Info: reading the aligned read file and processing it into bin-level files...
Number found where operator expected at run738.EDSN1552RPrep1_ATCACG_L001.sorted.f.sam line 1, near "41738	0"
	(Missing operator before 	0?)
Bareword found where operator expected at run738.EDSN1552RPrep1_ATCACG_L001.sorted.f.sam line 1, near "0	MG1655"
	(Missing operator before MG1655?)
Number found where operator expected at run738.EDSN1552RPrep1_ATCACG_L001.sorted.f.sam line 1, near "MG1655	12"
	(Do you need to predeclare MG1655?)
Number found where operator expected at run738.EDSN1552RPrep1_ATCACG_L001.sorted.f.sam line 1, near "12	37"
	(Missing operator before 	37?)
Number found where operator expected at run738.EDSN1552RPrep1_ATCACG_L001.sorted.f.sam line 1, near "37	31"
	(Missing operator before 	31?)
Bareword found where operator expected at run738.EDSN1552RPrep1_ATCACG_L001.sorted.f.sam line 1, near "31M"
	(Missing operator before M?)

Some cursory investigation makes me believe that these are actually coming from Perl's regexp engine.  I see that Perl is listed as a prerequisite on the Bioconductor page for Mosaics, but it doesn't specify any specific version.

Platform: CentOS 6.6 x86_64
R  version: 3.1.1
Perl version: 5.10.1
Bioconductor version: 3.0

Any help would be greatly appreciated.  Thanks!

-Branden

Branden Timm

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Nov 24, 2014, 4:42:07 PM11/24/14
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Just FYI, I tracked down the root of this problem. First of all, the root cause was that the perl command was not being built up properly.  The end of the mosaics output would note:

Warning message:
running command 'perl  <sanitized input filename> ./ sam 200 1 200 0 N N -   ' had status 2 

As you can probably tell, it was missing the name of the perl script, and therefore perl tried to run the sam file as code.  I tracked down the error to the following line, present in both generateWig.R and constructBins.R:

Fn.Path <- system.file( file.path("Perl",script), package="mosaics2")

The problem was the package name "mosaics2".  I don't know if the author did this in preparation for renaming the package to mosaics2, but changing it to just "mosaics" and reinstalling the package from source solved our problem.

I found what appears to be the mosaics page on GitHub (https://github.com/dongjunchung/mosaics), but it appears to be abandoned since version 1.5.7?  Is mosaics no longer kept in a public source control repository?  I'd like to submit my fixes, if possible.

-Branden

Dongjun Chung

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Nov 25, 2014, 3:02:56 PM11/25/14
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Hi Branden,

Thank you very much for reporting the bug and your great effort to identify the source of the problem.

With the help of your analysis, I fixed the bug in the newer version of mosaics package and updated the mosaics package in bioconductor 3.0, i.e., mosaics version 2.0.1. This new version will be available in bioconductor soon. mosaics package version 2.0.1 will be available in the GitHub package accordingly soon as well.

Thank you again!

Best,
Dongjun

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Jin-Rui Xu

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Apr 1, 2017, 11:35:32 AM4/1/17
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Hi Dongjun,

This problem is back again at least since 6/2015. There are quite a few posts about this same problem. Could you please fix it? 
Thanks.

Jinrui
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