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

Fri Dec 2 17:20:39 CET 2016

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
> 
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> 
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