From wewol@ki @ending from gm@il@com  Fri Jul 13 08:32:01 2018
From: wewol@ki @ending from gm@il@com (Witold E Wolski)
Date: Fri, 13 Jul 2018 08:32:01 +0200
Subject: [Rd] 
 RMarkdown Vignettest in R packages with child is failing in
 package build
In-Reply-To: <b3c7e9b2-f9a6-855c-9029-e6af1dc0ca60@gmail.com>
References: <CAAjnpdj7FFxJhj0b=AbX6dvXY5ErqDrEtpRfvohPFF40ra0c_Q@mail.gmail.com>
 <b3c7e9b2-f9a6-855c-9029-e6af1dc0ca60@gmail.com>
Message-ID: <CAAjnpdiZN9QFnAgrko_x-MqNXRMh9DPJTEnm813u7-eQ7g=eUQ@mail.gmail.com>

Dear Duncan,

Thank you, got it working with your advice.

I did placed the child markdown documents into inst/ParametrizedReportsChild

And this is the code in the main vignette by which I include them:

child_docs <- "Grp2Analysis_MissingInOneCondtion.Rmd_t"

if(!sum(NAinfo$nrProteins > 0) > 0){
  child_docs <- "Grp2Analysis_Empty.Rmd_t"
}

child_docs <- system.file(file.path("ParametrizedReportsChild",child_docs),package
= "SRMService")


However, according to writing package vignettes
[https://cran.r-project.org/doc/manuals/R-exts.html#Writing-package-vignettes]
:
"All other files needed to re-make the vignettes (such as LaTeX style
files, BibTeX input files and files for any figures not created by
running the code in the vignette) _must_ be in the vignette source
directory."

So why placing those files i.e.
Grp2Analysis_MissingInOneCondtion.Rmd_t and Grp2Analysis_Empty.Rmd_t
in the vignettes folder and including them by:

child_docs <- "Grp2Analysis_MissingInOneCondtion.Rmd_t"

if(!sum(NAinfo$nrProteins > 0) > 0){
  child_docs <- "Grp2Analysis_Empty.Rmd_t"
}

, did not work?

Have a great day,
best regards
Witek


On 10 July 2018 at 19:52, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> On 10/07/2018 11:44 AM, Witold E Wolski wrote:
>>
>> Dear List,
>>
>> I am working on moving some Rmarkdown reports into the vignettes
>> folder of a package. While I was able to solve to problem of
>> parametrized reports in vignettes folder thanks to your invaluable
>> help (Thank you), I am now struggling with the following problem.
>>
>>
>> One of the reports which I am moving to vignettes includes the following
>> code :
>>
>>
>> ```{r}
>> child_docs <- "Grp2Analysis_MissingInOneCondtion.Rmd_t"
>> if(TRUE){
>>    child_docs <- "Grp2Analysis_Empty.Rmd_t"
>> }
>>
>> ```
>>
>> ```{r includeMissingInOne, child = child_docs}
>> ```
>>     # this is line 351 from the error message
>>
>> which depending on a test outcome includes one or the other Rmarkdown
>> document into the main document.
>>
>>
>> While this report renders executing rmarkdown::render or
>> devtools::build_vignettes, it fails when building the package with
>> devtools::build or R CMD build
>> given the following error:
>>
>>
>> Error in eval(x, envir = envir) : object 'child_docs' not found
>> Warning in readLines(if (is.character(input2)) { :
>>    cannot open file './child_docs': No such file or directory
>> Quitting from lines 351-351 (./child_docs)
>> Error in readLines(if (is.character(input2)) { :
>>    cannot open the connection
>> ERROR: installing vignettes failed
>> * removing
>> 'C:/Users/wolski/AppData/Local/Temp/RtmpIti891/Rinst2cec49ca2170/SRMService'
>> In R CMD INSTALL
>>
>
>
> Since you didn't give a path to that file, it will use the current working
> directory, which might be a temporary directory used during the package
> installation.  Since you want this to work as a vignette, you need to
> include the child docs in your package.  One way to do that is to put them
> in a new directory called "inst/children", which will be installed to
> "children" when your package is installed.  Then the vignette can find the
> file as
>
>     system.file(file.path("children", child_docs), package = "yourpackage")
>
> You could also put them in the "vignettes" directory, but there are special
> rules for how files there are installed or not, so I'd recommend against it.
>
> Duncan Murdoch



-- 
Witold Eryk Wolski



[Rd] RMarkdown Vignettest in R packages with child is failing in package build
Witold E Wolski