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

Warden, Charles cwarden at coh.org
Mon Jan 27 21:41:32 CET 2014

Hi Henrik,

Thanks for your feedback.

No matter what, I will implement suggestion #3 in the next version of COHCAP.  I agree that is important.


-----Original Message-----
From: henrik.bengtsson at gmail.com [mailto:henrik.bengtsson at gmail.com] On Behalf Of Henrik Bengtsson
Sent: Monday, January 27, 2014 12:38 PM
To: Warden, Charles
Cc: Dan Tenenbaum; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Problem running Perl script with R-devel

Some quick ideas:

1. Before making the full call, call res <- system2(perlbin, "-v") to
assert no errors about running Perl itself.  If an error, catch it and
given an information message ("Failed to run 'perl -v'" or something).
That will be user friendly as well for future users who run into

2. Before calling system(), you can also assert that the script and
the input files are accessible, cf. file_test("-f") and file.access().
 If not, give an informative error message.

3. Do res <- system(cmd, intern=TRUE, wait=TRUE) and report on 'res'
when there's an error.  It will show the output of your Perl session.

4. You can use x <- normalizePath(x) to create OS-consistent paths/pathnames.

My $.02


On Mon, Jan 27, 2014 at 10:56 AM, Warden, Charles <cwarden at coh.org> wrote:
> Hi Dan,
> Thanks for your prompt response. To simplify things, I'll provide the code for the truncated dataset:
> library("COHCAP")
> 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,
>                                 platform="450k-UCSC")
> 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)
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [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.
> Thanks,
> Charles
> -----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,
> Dan
>> Thanks,
>> Charles
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