[Bioc-devel] Problem running Perl script with R-devel
Warden, Charles
cwarden at coh.org
Mon Jan 27 21:12:00 CET 2014
Hi Dan,
Here is the output from the requested command:
C:\\Perl64\\site\\bin;C:\\Perl64\\bin;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files\\MATLAB\\R2011b\\runtime\\win64;C:\\Program Files\\MATLAB\\R2011b\\bin;C:\\Program Files\\MATLAB\\R2010b\\runtime\\win64;C:\\Program Files\\MATLAB\\R2010b\\bin;C:\\Program Files (x86)\\Common Files\\Roxio Shared\\DLLShared\\;C:\\Program Files (x86)\\QuickTime\\QTSystem\\;c:\\Program Files (x86)\\Microsoft SQL Server\\100\\Tools\\Binn\\VSShell\\Common7\\IDE\\;c:\\Program Files (x86)\\Microsoft SQL Server\\100\\Tools\\Binn\\;c:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Binn\\;c:\\Program Files (x86)\\Microsoft SQL Server\\100\\DTS\\Binn\\;C:\\Program Files\\Java\\jdk1.7.0_05\\bin;C:\\Program Files (x86)\\Subversion\\bin;C:\\Rtools\\bin;C:\\Rtools\\gcc-4.6.3\\bin;C:\\Program Files\\MiKTeX 2.9\\miktex\\bin\\x64\\;C:\\Program Files\\R\\R-3.0.2\\bin\\x64\\;C:\\Program Files\\gs\\gs9.10\\bin"
"C:\\Perl64\\site\\bin" contains perl.exe and perl5.12.4.exe. Also, this command works with the following output:
> cmd2 <- "perl -v"
> system(cmd2)
This is perl 5, version 12, subversion 4 (v5.12.4) built for MSWin32-x64-multi-thread
(with 9 registered patches, see perl -V for more detail)
Copyright 1987-2010, Larry Wall
Binary build 1205 [294981] provided by ActiveState http://www.ActiveState.com
Built Jun 20 2011 18:11:54
Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.
Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.
So, I assume the problem occurs after the perl command is run (and, for whatever reason, the problem only occurs with R-devel).
Thanks,
Charles
-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
Sent: Monday, January 27, 2014 11:54 AM
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: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: bioc-devel at 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:dtenenba at fhcrc.org]
> Sent: Monday, January 27, 2014 11:27 AM
> 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)
> >
> > 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 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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