See below. ----- Original Message ----- > From: "Jurat Shayidin" <juratb...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Friday, December 2, 2016 8:32:35 AM > Subject: Re: [Bioc-devel] package vignette error : external data can't be > captured when compiling package vignette
> Dear Dan : > > Really appreciated for your quick respond. Instead, I am using R CMD check > on my packages, I have an error. Here is whole session detail : > > Microsoft Windows [Version 6.3.9600] > (c) 2013 Microsoft Corporation. All rights reserved. > > C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64 > > C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL > "C:\Users\jvrat\Documents\MSPC" > * installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4' > * installing *source* package 'MSPC' ... > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ** testing if installed package can be loaded > * DONE (MSPC) > > C:\Program Files\R\R-devel\bin\x64>R CMD check > "C:\Users\jvrat\Documents\MSPC" > Warning in dir.create(pkgoutdir, mode = "0755") : > cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck', reason > 'Permission denied' > ERROR: cannot create check dir 'C:/Program > Files/R/R-devel/bin/x64/MSPC.Rcheck' You need to run R CMD check in a directory where you have write permissions. > > C:\Program Files\R\R-devel\bin\x64>R CMD build > "C:\Users\jvrat\Documents\MSPC" > * checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK > * preparing 'MSPC': > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ...Warning: running command > '"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages= -e > "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1 > ERROR > Warning in engine$weave(file, quiet = quiet, encoding = enc) : > Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to > R Markdown v1. > Quitting from lines 62-66 (vignette.Rmd) > Error: processing vignette 'vignette.Rmd' failed with diagnostics: > object 'inputData' not found > Execution halted > Line 61 of the vignette (as it is in Github; it's apparently different on yur machine based on the error message) is: total.ERs <- denoise_ERs(peakGRs = inputData, tau.w = 1.0E-04, .fileName = "noiseER", outDir = "", verbose = FALSE) As you can see, the peakGRs argument is set to inputData, but inputData is not defined anywhere. Dan > C:\Program Files\R\R-devel\bin\x64> > > > How can I fix this R CMD check error ? Instead people in stackoverflow > remind me that using devtools packages is not stable some times, so I go > for old fashion : use CMD. Plus, still my external data can't available for > vignette data, and vignette compilation is failed again. I used > system.file() to do this, but not working. Any idea please ? How can I > overcome this problem? Thanks a lot to Bioconductor project team. > > Best regards : > > Jurat > > > On Fri, Dec 2, 2016 at 5:20 PM, Dan Tenenbaum <dtene...@fredhutch.org> > wrote: > >> If your package is in github at https://github.com/julaiti/MSPC , it >> looks like there is no inst or extdata folder in that repository. >> >> Maybe it has not yet been added/committed/pushed to git? >> >> Note that everything _under_ inst gets installed when you install the >> package, but the inst directory itself goes away. >> >> If in your package source you have the following structure: >> >> inst/extdata/ >> inst/foo.txt >> >> In the installed package you end up with: >> >> extdata/ >> foo.txt >> >> HTH >> Dan >> >> >> ----- Original Message ----- >> > From: "Jurat Shayidin" <juratb...@gmail.com> >> > To: "Hervé Pagès" <hpa...@fredhutch.org>, "bioc-devel" < >> bioc-devel@r-project.org> >> > Sent: Friday, December 2, 2016 5:36:28 AM >> > Subject: Re: [Bioc-devel] package vignette error : external data can't >> be captured when compiling package vignette >> >> > Dear Hervé : >> > >> > Thanks again for your response on my issue. I've read your message very >> > carefully and did all you suggested to me, still can't fix the vignette >> > compilation error. I have developed my package on windows machine under >> > devel version of R and Bioc, all unit test works fine to me. I don't >> > understand why inst/ directory was not created when I build and install >> my >> > packages, external data can't be read during vignette compilation. >> > However, my objective is, to build my package vignette with no error in >> the >> > first place, then continue to edit the context until getting final >> version >> > of vignette file. When I install packages using devtools::install(), I >> got >> > this : >> > >> >> devtools::install() >> > Installing MSPC >> > "C:/PROGRA~1/R/R-devel/bin/x64/R" \ >> > --no-site-file --no-environ --no-save \ >> > --no-restore --quiet CMD INSTALL \ >> > "C:/Users/jvrat/Documents/MSPC" \ >> > --library="C:/Users/jvrat/Documents/R/win-library/3.4" \ >> > --install-tests >> > * installing *source* package 'MSPC' ... >> > ** R >> > ** tests >> > ** preparing package for lazy loading >> > ** help >> > *** installing help indices >> > ** building package indices >> > ** installing vignettes >> > ** testing if installed package can be loaded >> > * DONE (MSPC) >> > Reloading installed MSPC >> > >> > >> > I believe doing this is right in vignette file after I follow your >> advise : >> > >> > ```{r} >> > library(MSPC) >> > inputBed <- list.files(system.file("extdata", package = "MSPC"), >> full.names >> > = TRUE) >> > inputData <- readPeakFile(peakFolder = inputBed) >> > >> > inputData >> > ``` >> > >> > >> > However, I should not add inst/extdata manually , without this I can't >> > allow to load external data for package use, and vignette compilation >> keep >> > failed. To be honest, this is my very first time building R packages, I >> > don't know how to fix this error. Just out of curiosity, during package >> > installation, everything is under the inst/ , but I don't have this >> folder. >> > Why is that ? Is that possible to get further help from Bioconductor >> > project team to review the package source in github ? >> > >> > I am stuck with this problem, I searched all possible answer from all >> over >> > the place, cannot fix my issues. I am very sorry if my question is naive >> to >> > ask here. Could you point me out how to possibly solve this problem? >> Thanks >> > again for your great favor. >> > >> > Best regards : >> > >> > Jurat >> > >> > >> > >> > On Fri, Dec 2, 2016 at 2:04 AM, Hervé Pagès <hpa...@fredhutch.org> >> wrote: >> > >> >> Hi, >> >> >> >> Make sure you understand the difference between the *package source >> >> tree*, which you control and where you must create the inst/ folder, >> >> and the *package installation folder*, which gets created and >> >> populated by 'R CMD INSTALL'. The exact location of the *package >> >> installation folder* doesn't really matter but if you are curious >> >> you can use the .libPaths() command to see it. The *package installation >> >> folder* is the subfolder of .libPaths() that has the name of the >> >> package. You can also see it with find.package("mypackage"). >> >> >> >> During installation, everything that is under the inst/ folder will >> >> get installed *directly* under the *package installation folder*. >> >> So if you created the extdata/ folder under inst/ (as it should be), >> >> extdata/ will end up being installed at .libPaths()/mypackage/extdata/ >> >> The code in your examples can get the path to the *installed* extdata/ >> >> folder with >> >> >> >> system.file(package="mypackage", "extdata") >> >> >> >> or get the path to any file under extdata/ with e.g. >> >> >> >> system.file(package="mypackage", "extdata", "data1.bed") >> >> >> >> Don't do >> >> >> >> system.file(package="mypackage", "extdata/data1.bed") >> >> >> >> even if it works for you because it's not portable (the use of / as >> >> a separator is a platform-dependent thing). >> >> >> >> Finally note that you should never try to modify anything that is under >> >> .libPaths() by hand. Furthermore, and that's a mistake we see sometimes >> >> with contributed packages, the code in your package should always >> >> treat the *package installation folder* as a read-only folder. >> >> >> >> Hope this helps, >> >> >> >> H. >> >> >> >> >> >> On 12/01/2016 04:34 PM, Jurat Shayidin wrote: >> >> >> >>> Hi BiocDevel : >> >>> >> >>> I am getting vignette error when I building my packages, and external >> data >> >>> can't be captured by system.file() . I did unit test all function of my >> >>> packages, it works fine. When I am going to compile package vignette, >> test >> >>> input bed file can't be detected. However, I used >> >>> devtools::install()command >> >>> to install my packages, but installation directory inst/ was not >> created >> >>> automatically. By R package convention, all external data must be >> located >> >>> in inst/, so I manually created this folder inst/extdata and paste my >> >>> data, but vignette compilation still failed. According to convention >> of R >> >>> package, my package structure will be: >> >>> >> >>> myPackage >> >>> `- inst >> >>> `- extdata >> >>> `- data1.bed >> >>> `- data2.bed >> >>> `- R >> >>> `- ... >> >>> `- NAMESPACE >> >>> `- DESCRIPTION >> >>> >> >>> >> >> -- >> >> Hervé Pagès >> >> >> >> Program in Computational Biology >> >> Division of Public Health Sciences >> >> Fred Hutchinson Cancer Research Center >> >> 1100 Fairview Ave. N, M1-B514 >> >> P.O. Box 19024 >> >> Seattle, WA 98109-1024 >> >> >> >> E-mail: hpa...@fredhutch.org >> >> Phone: (206) 667-5791 >> >> Fax: (206) 667-1319 >> >> >> > >> > >> > >> > -- >> > Jurat Shahidin >> > >> > Dipartimento di Elettronica, Informazione e Bioingegneria >> > Politecnico di Milano >> > Piazza Leonardo da Vinci 32 - 20133 Milano, Italy >> > Mobile : +39 3279366608 >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioc-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > > -- > Jurat Shahidin > > Dipartimento di Elettronica, Informazione e Bioingegneria > Politecnico di Milano > Piazza Leonardo da Vinci 32 - 20133 Milano, Italy > Mobile : +39 3279366608 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel