[Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Leonardo Collado Torres]

Dear Jurat,

Maybe it'll be helpful to you if you see how other packages have their
data. For example, take a look at one of my packages:
https://github.com/lcolladotor/derfinder

You'll see that I have two directories inside /inst/extdata with some
files that I use in my vignette code. See
https://github.com/lcolladotor/derfinder/tree/master/inst/extdata for
the files and search system.file() inside
https://github.com/lcolladotor/derfinder/blob/master/vignettes/derfinder-quickstart.Rmd
to see how I use it in the vignette.

Regarding your permissions issue, I don't recall right now how to get
this to work with Windows. But basically you can see that error at:

Warning in dir.create(pkgoutdir, mode = "0755") :
  cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
reason 'Permission denied'


Is your user in your windows machine part of the "administrators"
group? If not, that could be why. You could otherwise run R CMD build
and upload your tar ball (a .tar.gz file) to
https://builder.r-hub.io/.

Finally, you might want to search the manual of how to create R
extensions for other details.
https://cran.r-project.org/doc/manuals/r-release/R-exts.html


Best,
Leo

On Fri, Dec 2, 2016 at 12:11 PM, Jurat Shayidin <juratbupt at gmail.com> wrote:
> 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 <dtenenba at fredhutch.org>
> wrote:
>
>> See below.
>>
>> ----- Original Message -----
>> > From: "Jurat Shayidin" <juratbupt at gmail.com>
>> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <
>> bioc-devel at 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 <dtenenba at 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" <juratbupt at gmail.com>
>> >> > To: "Hervé Pagès" <hpages at fredhutch.org>, "bioc-devel" <
>> >> bioc-devel at 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 <hpages at 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: hpages at 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 at 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 at r-project.org mailing list
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