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.
Best,
Charles
-----Original Message-----
From: Warden, Charles
Sent: Monday, January 27, 2014 10:57 AM
To: 'Dan Tenenbaum'
Cc: bioc-devel@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:
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
[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.
Thanks,
Charles
-----Original Message-----
From: Dan Tenenbaum [mailto:dtene...@fhcrc.org]
Sent: Monday, January 27, 2014 10:51 AM
To: Warden, Charles
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Problem running Perl script with R-devel
Hi Charles,
----- Original Message -----
> From: "Charles Warden" <cwar...@coh.org>
> To: bioc-devel@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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