----- Original Message -----
> From: "Charles Warden" <cwar...@coh.org>
> To: "Dan Tenenbaum" <dtene...@fhcrc.org>
> Cc: bioc-devel@r-project.org
> Sent: Monday, January 27, 2014 11:38:10 AM
> Subject: RE: [Bioc-devel] Problem running Perl script with R-devel
>
> Hi Dan,
>
> 1) When I first ran the code, the folder didn't exist (it is created
> from the COHCAP function). When I run the same set of code in my
> non-devel version of R (with COHCAP installed via R CMD INSTALL,
> instead of biocLite), all the files are created properly (in the
> exact same location)
>
What do you see if you run
Sys.getenv("PATH")
?
Does it include the directory that contains perl.exe?
If not, then perl is not in your PATH. Note that running
echo %PATH%
in the command shell and running Sys.getenv("PATH") in R can give different
results because R modifies the path.
Dan
> 2)If I set project.folder to tempdir(), then I encounter the same
> problem.
>
> 3) Yes, I wish that the slashes and backslashes were consistent. I
> am not actually specifying them directly. Instead, I am using
> system.path to add the subfolders within project.folder. In other
> words, this is the actual code (I was just trying to show you what
> the text of the command looks like in this specific case):
>
> temp.stat.file <- file.path(wig.folder, "temp.txt")
> Perl.Path <- file.path(path.package("COHCAP"), "Perl")
> perl.script <- file.path(Perl.Path , "create_wig_files.pl")
> write.table(stat.table, temp.stat.file, quote=F, row.names=F,
> sep="\t")
> cmd <- paste("perl",perl.script, temp.stat.file, wig.folder, sep="
> ")
> system(cmd, intern=TRUE, wait=TRUE)
>
> I hope this clarifies things. Please let me know if you still have
> any questions.
>
> Thanks,
> Charles
>
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtene...@fhcrc.org]
> Sent: Monday, January 27, 2014 11:27 AM
> To: Warden, Charles
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Problem running Perl script with R-devel
>
>
>
> ----- Original Message -----
> > From: "Charles Warden" <cwar...@coh.org>
> > To: "Charles Warden" <cwar...@coh.org>, "Dan Tenenbaum"
> > <dtene...@fhcrc.org>
> > Cc: bioc-devel@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)
> >
> > Please let me know if you need anything else.
> >
>
> Does the directory
> T:\BIC\cwarden\Methylation_Package\Protocol_Exchange\minfi_example/CpG_Site/4
> 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@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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