[Bioc-devel] Problem running Perl script with R-devel
Dan Tenenbaum
dtenenba at fhcrc.org
Mon Jan 27 21:40:53 CET 2014
----- 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
> >
> >
> >
> > ---------------------------------------------------------------------
> > *SECURITY/CONFIDENTIALITY WARNING:
> > This message and any attachments are intended solely for the
> > individual or entity to which they are addressed. This
> > communication
> > may contain information that is privileged, confidential, or exempt
> > from disclosure under applicable law (e.g., personal health
> > information, research data, financial information). Because this
> > e-mail has been sent without encryption, individuals other than the
> > intended recipient may be able to view the information, forward it
> > to others or tamper with the information without the knowledge or
> > consent of the sender. If you are not the intended recipient, or
> > the
> > employee or person responsible for delivering the message to the
> > intended recipient, any dissemination, distribution or copying of
> > the communication is strictly prohibited. If you received the
> > communication in error, please notify the sender immediately by
> > replying to this message and deleting the message and any
> > accompanying files from your system. If, due to the security risks,
> > you do not wi!
> > sh to receive further communications via e-mail, please reply to
> > this message and inform the sender that you do not wish to receive
> > further e-mail from the sender. (fpc5p)
> > ---------------------------------------------------------------------
> >
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
More information about the Bioc-devel
mailing list