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! Best, Charles -----Original Message----- From: Dan Tenenbaum [mailto:dtene...@fhcrc.org] Sent: Monday, January 27, 2014 12:41 PM 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) > 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@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 > > > > > > > > --------------------------------------------------------------------- > > *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). 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