[Bioc-devel] Problem running Perl script with R-devel
Dan Tenenbaum
dtenenba at fhcrc.org
Tue Jan 28 23:14:03 CET 2014
Hi Charles,
----- Original Message -----
> From: "Charles Warden" <cwarden at coh.org>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: bioc-devel at r-project.org
> Sent: Tuesday, January 28, 2014 2:12:09 PM
> Subject: RE: [Bioc-devel] Problem running Perl script with R-devel
>
> Hi,
>
> For those interested in this thread, it appears that the problem is
> caused by the library location.
>
> Normally, R uses "C:\Users\cwarden\Documents\R\win-library", but
> R-devel uses "C:/Program Files/R/R-devel/library".
>
> The problem is that the file paths are not provided to Perl in
> quotes. Thus, the more specific error is "Can't open perl script
> "C:/Program": No such file or directory". So, I should now be able
> to fix the problem.
>
> Thanks for all of your help!
>
I'm glad you figured it out. The location where R is installed doesn't change between release and devel versions, it's just an option you can set when installing R.
Dan
> Best,
> Charles
>
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
> Sent: Monday, January 27, 2014 12:41 PM
> To: Warden, Charles
> Cc: bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] Problem running Perl script with R-devel
>
>
>
> ----- Original Message -----
> > 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)
> >
>
> What happens if you just run the command above in isolation?
>
> Is T: a networked drive?
> what does tempdir() display? Is it also a directory on drive T:?
> If so, try using a directory on a physical (local) drive as your
> output directory.
>
> I'm not sure if the error code 2 that you are seeing is from perl or
> from R, but the googles (http://www.perlmonks.org/?node_id=274896)
> suggests that error 2 is "no such file or directory" so it could be
> a problem with one of the parameters you're passing to perl.
>
> BTW, I tried the following (forgive the bad line wrapping, that's
> what happens when I paste from windows into my mac):
>
> > scr <- system.file("Perl", "create_wig_files.pl", package="COHCAP")
> > scr
> [1]
> "E:/biocbld/bbs-2.14-bioc/R/library/COHCAP/Perl/create_wig_files.pl"
> > t <- tempdir()
> > cmd <- sprintf("perl %s %s %s", scr, file.path(t, "temp.txt"), t)
> > cmd
> [1] "perl
> E:/biocbld/bbs-2.14-bioc/R/library/COHCAP/Perl/create_wig_files.pl
> C:\\Users\\BI
> OCBU~1\\AppData\\Local\\Temp\\2\\Rtmp4KS893/temp.txt
> C:\\Users\\BIOCBU~1\\AppData\\Local\\
> Temp\\2\\Rtmp4KS893"
> > system(cmd, intern=TRUE, wait=TRUE)
> Uncaught exception from user code:
> Could not open
> C:\Users\BIOCBU~1\AppData\Local\Temp\2\Rtmp4KS893/temp.txt!
> at E:/b
> iocbld/bbs-2.14-bioc/R/library/COHCAP/Perl/create_wig_files.pl line
> 35.
> at
> E:/biocbld/bbs-2.14-bioc/R/library/COHCAP/Perl/create_wig_files.pl
> line 35
> character(0)
> attr(,"status")
> [1] 2
> Warning message:
> running command 'perl
> E:/biocbld/bbs-2.14-bioc/R/library/COHCAP/Perl/create_wig_files.pl C
> :\Users\BIOCBU~1\AppData\Local\Temp\2\Rtmp4KS893/temp.txt
> C:\Users\BIOCBU~1\AppData\Local\
> Temp\2\Rtmp4KS893' had status 2
> >
>
> So this is complaining because the temp.txt file does not exist.
>
> Henrik's suggestions are good too.
>
> Dan
>
>
>
>
>
> > 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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