[Bioc-devel] Problem running Perl script with R-devel

Warden, Charles cwarden at coh.org
Mon Jan 27 20:19:46 CET 2014

Hi Dan,

Here is the trackback output:

> traceback()
2: read.table(sample.file, header = F, sep = "\t")
1: COHCAP.site(sample.file, beta.table, project.name, project.folder, 
       ref = "parental")
> help(traceback)

I have no problem running Perl via command line (and it works with the non-devel version of R).

This is the command being run within COHCAP (with the specific values filled in):

cmd <- 'perl C:/Program Files/R/R-devel/library/COHCAP/Perl/create_wig_files.pl T:\BIC\cwarden\Methylation_Package\Protocol_Exchange\minfi_example/CpG_Site/450k_avg_by_island_test_wig/temp.txt T:\BIC\cwarden\Methylation_Package\Protocol_Exchange\minfi_example/CpG_Site/450k_avg_by_island_test_wig'

system(cmd, intern=TRUE, wait=TRUE)

Please let me know if you need anything else.


-----Original Message-----
From: Warden, Charles 
Sent: Monday, January 27, 2014 10:57 AM
To: 'Dan Tenenbaum'
Cc: bioc-devel at r-project.org
Subject: RE: [Bioc-devel] Problem running Perl script with R-devel

Hi Dan,

Thanks for your prompt response. To simplify things, I'll provide the code for the truncated dataset:


dir <- system.file("extdata", package="COHCAP")
beta.file <- file.path(dir,"GSE42308_truncated.txt")
sample.file <- file.path(dir,"sample_GSE42308.txt")
project.folder <- "T:\\BIC\\cwarden\\Methylation_Package\\Protocol_Exchange\\minfi_example"
project.name <- "450k_avg_by_island_test"
beta.table <- COHCAP.annotate(beta.file, project.name, project.folder,

filtered.sites <- COHCAP.site(sample.file, beta.table, project.name,
				project.folder, ref="parental")

And here is the sessionInfo() and warning() outputs:

Warning message:
running command 'perl C:/Program Files/R/R-devel/library/COHCAP/Perl/create_wig_files.pl T:\BIC\cwarden\Methylation_Package\Protocol_Exchange\minfi_example/CpG_Site/450k_avg_by_island_test_wig/temp.txt T:\BIC\cwarden\Methylation_Package\Protocol_Exchange\minfi_example/CpG_Site/450k_avg_by_island_test_wig' had status 2 

> sessionInfo()
R Under development (unstable) (2014-01-20 r64849)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] COHCAP_0.99.5     COHCAPanno_0.99.2 WriteXLS_3.3.1   

loaded via a namespace (and not attached):
[1] tools_3.1.0

Please let me know if you need anything else.


-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] 
Sent: Monday, January 27, 2014 10:51 AM
To: Warden, Charles
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Problem running Perl script with R-devel

Hi Charles,

----- Original Message -----
> From: "Charles Warden" <cwarden at coh.org>
> To: bioc-devel at r-project.org
> Sent: Monday, January 27, 2014 10:45:42 AM
> Subject: [Bioc-devel] Problem running Perl script with R-devel
> Hi,
> I am testing out my newly released COHCAP package:
> http://bioconductor.org/packages/devel/bioc/html/COHCAP.html
> I didn't see any warnings when I created the package, and there
> weren't any warnings when Bioconductor tests the package (on any of
> the operating systems).
> However, I have been testing the package using R-devel (since the
> package is a currently only available as a devel package, it looks
> like I can only use lazy loading with R-devel), and I've noticed
> that the Perl command (creating the .wig files within the function
> COHCAP.site()) doesn't work properly for either the truncated demo
> dataset that is included with the package or the entire dataset that
> I am trying to use to test the package.
> To be clear, I can download COHCAP and COHCAPanno and use R CMD
> INSTALL to run the package in the normal version of R (v.3.0.2), and
> the package runs just fine with both the truncated and full
> datasets.
> I am trying to provide users with instructions on how to use the
> package while it is only available as a devel version.  I'm trying
> to make the instructions as simple as possible, so I was hoping to
> use the lazy loading via biocLite("COHCAP").
> I am running R-devel on Windows (v.3.1.0 pre-release) and the
> system() command script is existing with status 2.
> Does anyone know what is causing this error to specifically occur
> with R-devel?

Can you provide the exact commands you entered which caused the error? As well as the output of sessionInfo()?

> Thanks,
> Charles
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