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

[Dan Tenenbaum]

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