Dear Dan : I forgot to commit vignette file, now I pushed new changes, so now error could be something else. People in stackoverflow suggest me to put all my external data (a.k.a, bed files) into vignette folder, try to run R CMD check and see what happen, I did this solution, but it doesn't work. Plus, I checked file permission of my package parent directory, seems fine to me. How I check file permission of my package ? How can I fix this write permission on my machine ? This is not intuitive to me, Any hint please ?
Herve suggest me don't create inst/extdata directory manually, but I still can't let external data available for vignette code. FYI, my objective in vignette file : let external data available for package use, compile trivial version of vignette with no error, then continue to make it perfect. Here is updated session of R CMD check : 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' 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 60-64 (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: subscript out of bounds Execution halted C:\Program Files\R\R-devel\bin\x64> How I fix R CMD check error above ? system.file() still can't detect external data. Any idea please ? Thanks a lot Best regards : Jurat On Fri, Dec 2, 2016 at 5:43 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > 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 > -- 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