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

[Hervé Pagès]

On 12/02/2016 09:11 AM, Jurat Shayidin 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,

I didn't say that. Please re-read carefully what I wrote and make sure
you understand it.

H.

> 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
>>
>
>
>

-- 
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