R devel - May 2016 - vignette/knitr help

I need some help understanding a problem running the tests on the 
'digest' package. Initially, I got the message that the 'knitr'
package
was needed to run vignettes:

Running vignettes for package ?digest?
Error in loadVignetteBuilder(vigns$pkgdir) :
   vignette builder 'knitr' not found

So I installed the knitr package and all its dependents (?mime?, 
?stringi?, ?magrittr?, ?evaluate?, ?formatR?, ?highr?, ?markdown?, 
?stringr?, ?yaml?) . Now I get some different warnings:

Running vignettes for package ?digest?
   Running ?sha1.Rmd?
Warning messages:
1: In readLines(if (is.character(input2)) { :
   cannot open file 'sha1.Rmd': No such file or directory
2: In engine$weave(file, quiet = TRUE, encoding = enc) :
   The vignette engine knitr::rmarkdown is not available, because the 
rmarkdown package is not installed. Please install it.
3: In readLines(con) :
   cannot open file 'sha1.Rmd': No such file or directory

So why is sha1.Rmd missing? And why is it complaining about rmarkdown? 
Or more precisely why did it not install it as a dependent? It installed 
plain markdown.

Mick Jordan

Dear Mick,

Note that both knitr and rmarkdown are listed under Suggests: both are
required to compile the vignette. Installing rmarkdown should solve
the problem. If not, please provide more information. OS, R version,
digest version, ...

Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey


2016-05-03 20:10 GMT+02:00 Mick Jordan <mick.jordan at
oracle.com>:
> I need some help understanding a problem running the tests on the
'digest'
> package. Initially, I got the message that the 'knitr' package was
needed to
> run vignettes:
>
> Running vignettes for package ?digest?
> Error in loadVignetteBuilder(vigns$pkgdir) :
>   vignette builder 'knitr' not found
>
> So I installed the knitr package and all its dependents (?mime?, ?stringi?,
> ?magrittr?, ?evaluate?, ?formatR?, ?highr?, ?markdown?, ?stringr?, ?yaml?)
.
> Now I get some different warnings:
>
> Running vignettes for package ?digest?
>   Running ?sha1.Rmd?
> Warning messages:
> 1: In readLines(if (is.character(input2)) { :
>   cannot open file 'sha1.Rmd': No such file or directory
> 2: In engine$weave(file, quiet = TRUE, encoding = enc) :
>   The vignette engine knitr::rmarkdown is not available, because the
> rmarkdown package is not installed. Please install it.
> 3: In readLines(con) :
>   cannot open file 'sha1.Rmd': No such file or directory
>
> So why is sha1.Rmd missing? And why is it complaining about rmarkdown? Or
> more precisely why did it not install it as a dependent? It installed plain
> markdown.
>
> Mick Jordan
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

On 5/3/16 11:29 AM, Thierry Onkelinx wrote:
> Dear Mick,
>
> Note that both knitr and rmarkdown are listed under Suggests: both are
> required to compile the vignette. Installing rmarkdown should solve
> the problem. If not, please provide more information. OS, R version,
> digest version, ...
>
>
This is occurring in the context of an automated testing environment 
that compares the output of GnuR and FastR. I'm using 
tools::testInstalledPackage with the default values for 'types'. I guess
the problem is that there is no connection between this step and the 
previous package install step (that did use --install-tests) but didn't 
install the "Suggests" dependencies because in general these are not 
needed. But I still am not clear why knitr doesn't list rmarkdown as a 
dependency when it clearly will try to use it. To me that is is not  
"Suggests" dependency.

Mick