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

Sun Dec 4 14:12:50 CET 2016

Dear Dan :

Thanks again for your kind help. I did clean up my package git working
tree, make every commit readable, tractable. I've read about R writing
extension manual and that helped a lot. Many thanks to Herve' insightful
answer to overcome file permission issue, R CMD check working perfectly
now. Through the long list of R CMD check report, CMD check alarmed me
several possible issues on my packages, and I am working on it.  Plus, R
CMD check complained about some hidden file such as .gitignore,
.Rproj.user, .git . Therefore I did strip away these files following this
way :

C:\Windows\system32>cd C:\Program Files\R\R-devel\bin\x64

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 ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory 'MSPC/tests/testthat'
* building 'MSPC_0.99.0.tar.gz'

C:\Program Files\R\R-devel\bin\x64>R CMD check "MSPC_0.99.0.tar.gz"
* using log directory 'C:/Program Files/R/R-devel/bin/x64/MSPC.Rcheck'
* using R Under development (unstable) (2016-11-09 r71642)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'MSPC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSPC' version '0.99.0'
* checking package namespace information ... OK

Now inst/ directory is created in MSPC_0.99.0.tar.gz, I could add my
external data in extdata (I think I need manually create extdata folder)
and make available these data for vignette code. But How can I commit these
changes to git automatically ? Because MSPC_0.99.0.tar.gz was not in my
package directory, I cannot push these changes to git. Could you give me
possible idea please ? Many thanks to Bioconductor Project team.

Best regards :
Jurat

On Fri, Dec 2, 2016 at 7:05 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

> I tried building your package, there are a number of issues with it.
>
> I recommend that you 1) always be aware of what is and is not in github,
> by using the 'git status' command. Bear in mind that if files are not
> committed to git then we will not be able to see them and not be able to
> help you. Specifically, the inst folder and everything under it does not
> exist in the github repository. Therefore I get an error in the chunk at
> lines 45-50, I don't get as far as you (error in lines 60-64).
>
> As Herve suggests, please run R CMD check from a directory that you have
> write permission in, such as your home directory.
>
> R CMD check will alert you about various problems, including referring to
> packages in NAMESPACE but not DESCRIPTION, relying on BiocStyle but not
> mentioning it in DESCRIPTION, etc.
>
> Dan
>
>
>
> ----- 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 9:11:29 AM
> > Subject: Re: [Bioc-devel] package vignette error : external data can't
> be captured when compiling package vignette
>
> > 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
>

-- 
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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