exist prior to running the code? I tried running your code snippet on
a directory that didn't exist and got an error (not the same error
as you).
It could be some other issue related to the output directory (perhaps
you don't have permission to write to it).
What if you set project.folder to tempdir() and run the code again,
does it work?
Dan
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
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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