From thierry.onkelinx at inbo.be  Tue May  3 21:19:35 2016
From: thierry.onkelinx at inbo.be (Thierry Onkelinx)
Date: Tue, 3 May 2016 21:19:35 +0200
Subject: [Rd] vignette/knitr help
In-Reply-To: <5728F662.7090903@oracle.com>
References: <5728E988.9010207@oracle.com>
	<CAJuCY5znayA7AGATc6hz3oy-OpfQvxHV+jethpP-UwyHV+3vwg@mail.gmail.com>
	<5728F662.7090903@oracle.com>
Message-ID: <CAJuCY5yp7PGVi_EuGT6=ThuLsbwYCo0mTd4JL-1wPZTjhJKnDQ@mail.gmail.com>

Dear Mick,

knitr doesn't depends on rmarkdown. It's the vignette that depends on
both knitr (for handle the R chunks) and rmarkdown (for the output
format rmarkdown::html_vignette).

https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies
states: "The ?Suggests? field ...snip...  lists packages that are not
necessarily needed. This includes packages used only in examples,
tests or vignettes  ...snip...   Then it is not necessary to have bar
use foo unless one wants to execute all the examples/tests/vignettes"

So packages in Suggests might be required to compile vignettes.

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 21:05 GMT+02:00 Mick Jordan <mick.jordan at oracle.com>:
> 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
>



[Rd] vignette/knitr help
Thierry Onkelinx