[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
troubles.
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
/Henrik
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 [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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