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

From: "Charles Warden" <cwarden at coh.org>
To: "Charles Warden" <cwarden at coh.org>, "Dan Tenenbaum" <dtenenba at fhcrc.org>
Cc: bioc-devel at r-project.org
Sent: Monday, January 27, 2014 11:19:46 AM
Subject: RE: [Bioc-devel] Problem running Perl script with R-devel

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)

scr <- system.file("Perl", "create_wig_files.pl", package="COHCAP")
scr

t <- tempdir()
cmd <- sprintf("perl %s %s %s", scr, file.path(t, "temp.txt"), t)
cmd

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 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:

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: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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