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

Fri Dec 2 17:32:35 CET 2016

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 :

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 <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

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