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' 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 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel