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[R-pkg-devel] Error in loadNamespace(x) : there is no package called 'formatR'

12 messages · Joseph Park, Henrik Bengtsson, Gábor Csárdi +2 more

Original
Joseph Park
# 
Dear r-package-devel,

The rEDM package is failing the automated check, as noted here:

https://win-builder.r-project.org/incoming_pretest/rEDM_1.7.0_20201113_131811/Windows/00check.log

When running rhub::check_for_cran(), disk file errors were reported.

The automated check seems to be failing with:

Error in loadNamespace(x) : there is no package called 'formatR'

This package does not explicitly use formatR:

Imports: methods, Rcpp (>= 1.0.1)
LinkingTo: Rcpp, RcppThread
Suggests: knitr, rmarkdown
VignetteBuilder: knitr

Could it be these errors (disk full, no formatR) are related?? If not, 
does formatR need to be listed as a dependency?

If the former (R server config/resource build errors), do I need to 
resubmit the package?

Thank you.

J Park
Gábor Csárdi
# 
I think you need to Suggest the formatR package, because your
vignettes use it. From 'Writing R extensions':

"Many packages using knitr also need the package formatR which it
suggests and so the user package needs to do so too and include this
in ?VignetteBuilder?."

Gabor
On Fri, Nov 13, 2020 at 1:49 PM Joseph Park <JosephPark at ieee.org> wrote:
Joseph Park
# 
Ah, yes... I see it now in Writing R Extensions.? Apologies for the 
oversight.

Regarding rmarkdown, is it redundant to include rmarkdown in 
VignetteBuilder if it is in Suggests, or is perhaps needed in the build 
config as a separate entity?

e.g:

Suggests: knitr, rmarkdown
VignetteBuilder: knitr, formatR

or

Suggests: knitr, rmarkdown
VignetteBuilder: knitr, rmarkdown, formatR

Thank you.

J Park
On 11/13/20 8:58 AM, G?bor Cs?rdi wrote:
Gábor Csárdi
# 
"Note that if, for example, a vignette has engine ?knitr::rmarkdown?,
then knitr provides the engine but both knitr and rmarkdown are needed
for using it, so both these packages need to be in the
?VignetteBuilder? field and at least suggested (as rmarkdown is only
suggested by knitr, and hence not available automatically along with
it). Many packages using knitr also need the package formatR which it
suggests and so the user package needs to do so too and include this
in ?VignetteBuilder?."

So I think you need

Suggests: knitr, rmarkdown, formatR
VignetteBuilder: knitr, rmarkdown, formatR
On Fri, Nov 13, 2020 at 3:23 PM Joseph Park <JosephPark at ieee.org> wrote:
Joseph Park
# 
Thank you.
On 11/13/20 10:31 AM, G?bor Cs?rdi wrote:
Henrik Bengtsson
# 
I'm quite sure you want to use the following:

Suggests: knitr, rmarkdown, formatR
VignetteBuilder: knitr

Here are the details.  For the 'VignetteBuilder' field, you want to
put all packages that provide the **vignette engines** you are using.
For example, if your package vignettes use either of

%\VignetteEngine{knitr::knitr}
%\VignetteEngine{knitr::rmarkdown}

your package is using a vignette engine from the 'knitr' package, so
you need to specify:

VignetteBuilder: knitr

Next, with 'knitr' listed in 'VignetteBuilder', you need to make sure
'knitr' is listed in either 'Depends' or 'Suggests' (or possibly
'Imports' - not sure).  If 'knitr' is only used for your vignettes, it
is sufficient to specify it under 'Suggests', which is also the most
common way to use it, i.e.

Suggests: knitr

The above settles the **vignette-engine package**.  Then your vignette
engine might depend on additional packages.  Your package needs to
depend on those too, typically also listed under 'Suggests'.  For
example, when you use %\VignetteEngine{knitr::rmarkdown}, that
vignette engine requires the 'rmarkdown' package (can be guessed from
them name but reading the docs is the only way to be sure - I think
there's work in 'tools' to improve on this).    So, this means you
need to use:

Suggests: knitr, rmarkdown

Finally, if your vignettes make use of additional, optional features
from other packages, you need to make sure your package depends on
those too.  Since you make use of 'formatR' features, you need to add
that to Suggests as well;

Suggests: knitr, rmarkdown, formatR

/Henrik

PS. Vignettes are a bit of special creatures. Their dependencies are
only needed during 'R CMD build' and 'R CMD check', which most
end-users never perform. I think it could be favorable if we could
declare vignette dependencies separate from install/run-time
dependencies, e.g.

VignetteBuilder: knitr
VignetteDepends: rmarkdown, formatR

It should make the above process a bit clearer.  It would also make it
clear to those who are only interested in viewing vignettes, but have
no interest in rebuilding vignettes, what packages they need to
install in order to access all of the package's functions.  Just an
idea.
On Fri, Nov 13, 2020 at 7:55 AM Joseph Park <JosephPark at ieee.org> wrote:
Joseph Park
# 
Thank you for the clarification.

J Park
On 11/13/20 1:09 PM, Henrik Bengtsson wrote:
Gábor Csárdi
# 
On Fri, Nov 13, 2020 at 6:10 PM Henrik Bengtsson
<henrik.bengtsson at gmail.com> wrote:
So this means that WRE is wrong? It says:

"Note that if, for example, a vignette has engine ?knitr::rmarkdown?,
then knitr provides the engine but both knitr and rmarkdown are needed
for using it, so both these packages need to be in the
?VignetteBuilder? field and at least suggested (as rmarkdown is only
suggested by knitr, and hence not available automatically along with
it). Many packages using knitr also need the package formatR which it
suggests and so the user package needs to do so too and include this
in ?VignetteBuilder?."

My understanding is that R CMD build (and possibly other
commands/functions as well) checks for the packages in
'VignetteBulider`, this is why you need to include rmarkdown and
formatR as well. See the source code in build.R and e.g.
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15775 etc.

G.

[...]
Duncan Murdoch
#
On 13/11/2020 1:48 p.m., G?bor Cs?rdi wrote:
> "Note that if, for example, a vignette has engine ?knitr::rmarkdown?,
 > then knitr provides the engine but both knitr and rmarkdown are needed
 > for using it, so both these packages need to be in the
 > ?VignetteBuilder? field and at least suggested (as rmarkdown is only
 > suggested by knitr, and hence not available automatically along with
 > it). Many packages using knitr also need the package formatR which it
 > suggests and so the user package needs to do so too and include this
 > in ?VignetteBuilder?."

Things may have changed since Henrik and I wrote the code, but his 
description matches my understanding as well (and I think he's 
contributed more recently than I have).

The way non-Sweave vignettes work is that some packages register 
themselves to recognize vignette files in the vignettes directory.  The 
default one recognizes .Rnw files as vignettes (and a few other 
extensions too); the knitr::rmarkdown one recognizes .Rmd files and some 
others.  The only way for a package's registration code to be called is 
for it to be listed as a VignetteBuilder.  See ?tools::vignetteEngine 
for details of the engine.

The rmarkdown package doesn't register any vignette engines, so it 
doesn't need to be in VignetteBuilder.  Same for formatR.

It's fairly common to have a package only used in the vignette, so you 
list it in Suggests.  But that wouldn't apply only to rmarkdown and 
formatR, there are lots of other examples.  However, I'd guess it's 
pretty common to forget to include rmarkdown and formatR, since they may 
not be explicitly used.  Then putting them in the VignetteBuilder field 
will trigger an error if they are not also in Suggests.

Duncan Murdoch
Gábor Csárdi
#
On Fri, Nov 13, 2020 at 9:02 PM Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
[...]
Can one of you please fix WRE then? The part that says

"...then knitr provides the engine but both knitr and rmarkdown are
needed for using it, so both these packages need to be in the
?VignetteBuilder? field..."

Thanks a lot!

Gabor

[...]
Duncan Murdoch
#
On 13/11/2020 4:32 p.m., G?bor Cs?rdi wrote:
No, neither of us are members of R Core.  Only R Core can edit the manuals.

Duncan Murdoch
4 days later
Martin Maechler
# 

        
> On 13/11/2020 4:32 p.m., G?bor Cs?rdi wrote:

        
>> On Fri, Nov 13, 2020 at 9:02 PM Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

        
>> [...]
    >>> Things may have changed since Henrik and I wrote the code, but his
    >>> description matches my understanding as well (and I think he's
    >>> contributed more recently than I have).
    >>> 
    >>> The way non-Sweave vignettes work is that some packages register
    >>> themselves to recognize vignette files in the vignettes directory.  The
    >>> default one recognizes .Rnw files as vignettes (and a few other
    >>> extensions too); the knitr::rmarkdown one recognizes .Rmd files and some
    >>> others.  The only way for a package's registration code to be called is
    >>> for it to be listed as a VignetteBuilder.  See ?tools::vignetteEngine
    >>> for details of the engine.
    >> 
    >> Can one of you please fix WRE then? The part that says
    >> 
    >> "...then knitr provides the engine but both knitr and rmarkdown are
    >> needed for using it, so both these packages need to be in the
    >> ?VignetteBuilder? field..."
    >> 

    > No, neither of us are members of R Core.  Only R Core can edit the manuals.

    > Duncan Murdoch

I've (finaly) followed this thread to here  ((too many e-mails, too many ...)).

I think I have understood what you wrote and why R Core should
change WRE in this part.

Notably as I have not written it, there needs to be consultation
--> Forwarding to R-core  ((i.e., a very rare cross-post !))

Thank you, very much for the discussion, G?bor, Henrik and Duncan!
Martin

--
Martin Maechler
ETH Zurich  and  R Core team