[R-pkg-devel] Data docs

2019-10-26 Thread Luis-Miguel Rodríguez Rojas 
Dear all,

I maintain a package that has data fields, and didn't have any problems
with this before. However, in my latest update, I'm getting the following
error message from the CRAN tests:

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: for code/documentation mismatches, Result: WARNING
  Variables with usage in documentation object 'growth.curves' but not in
code:
'growth.curves'

  Variables with usage in documentation object 'phyla.counts' but not in
code:
'phyla.counts'

The variables are indeed NOT in the code, because they're only to be used
in the examples. In this version I moved my documentation from the old (now
defunct) inlinedocs to ROxygen2. In the previous form, I had to define a
structure in the code including both the function and the example, so
technically the code was using the variables. In the new form, I simply
define the examples with the @examples tag (that ends up in the .rd file
within an \examples{} block).

Does anyone have any idea on how I should define data in the code to avoid
this issue? I could simply add the example lines after the return (so
they're never reached), but that sounds like a horrible hack.

Just in case it's useful:
GitHub repository (inside the enveomics.R folder):
https://github.com/lmrodriguezr/enveomics/
Full test output:
https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_032029/Windows/00check.log

Thanks!
Miguel.


--
Luis M. Rodriguez-R, Ph.D.
[ https://rodriguez-r.com ]
-
Research Engineer
Georgia Institute of Technology
311 Ferst Drive, ES&T, Room 3324
Atlanta, GA 30332, USA
[ http://enve-omics.gatech.edu/ ]

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Re: [R-pkg-devel] Data docs

2019-10-26 Thread Duncan Murdoch 

On 26/10/2019 11:39 a.m., Luis-Miguel Rodríguez Rojas wrote:

Dear all,

I maintain a package that has data fields, and didn't have any problems
with this before. However, in my latest update, I'm getting the following
error message from the CRAN tests:

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: for code/documentation mismatches, Result: WARNING
   Variables with usage in documentation object 'growth.curves' but not in
code:
 'growth.curves'

   Variables with usage in documentation object 'phyla.counts' but not in
code:
 'phyla.counts'


I'm not seeing those messages when testing your package in the same R 
version as win-builder used, so it could be a transient issue, or a 
problem with the tarball that you submitted.  In either case, I'd 
suggest just trying again:  rebuild and submit.


Duncan Murdoch



The variables are indeed NOT in the code, because they're only to be used
in the examples. In this version I moved my documentation from the old (now
defunct) inlinedocs to ROxygen2. In the previous form, I had to define a
structure in the code including both the function and the example, so
technically the code was using the variables. In the new form, I simply
define the examples with the @examples tag (that ends up in the .rd file
within an \examples{} block).

Does anyone have any idea on how I should define data in the code to avoid
this issue? I could simply add the example lines after the return (so
they're never reached), but that sounds like a horrible hack.

Just in case it's useful:
GitHub repository (inside the enveomics.R folder):
https://github.com/lmrodriguezr/enveomics/
Full test output:
https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_032029/Windows/00check.log

Thanks!
Miguel.


--
Luis M. Rodriguez-R, Ph.D.
[ https://rodriguez-r.com ]
-
Research Engineer
Georgia Institute of Technology
311 Ferst Drive, ES&T, Room 3324
Atlanta, GA 30332, USA
[ http://enve-omics.gatech.edu/ ]

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Re: [R-pkg-devel] Data docs

2019-10-26 Thread Luis-Miguel Rodríguez Rojas 
Hello Duncan,

Thanks for your quick response!

I tried re-building and re-submitting and I'm still getting the same error:
https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_224156/Windows/00check.log
https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_224156/Debian/00check.log

I've made the tarball temporarily available directly in the repository in
case that helps at all:
https://github.com/lmrodriguezr/enveomics/blob/master/enveomics.R_1.5.0.tar.gz

Thanks a lot!
Miguel.

--
Luis M. Rodriguez-R, Ph.D.
[ https://rodriguez-r.com ]
-
Research Engineer
Georgia Institute of Technology
311 Ferst Drive, ES&T, Room 3324
Atlanta, GA 30332, USA
[ http://enve-omics.gatech.edu/ ]



On Sat, Oct 26, 2019 at 1:39 PM Duncan Murdoch 
wrote:

> On 26/10/2019 11:39 a.m., Luis-Miguel Rodríguez Rojas wrote:
> > Dear all,
> >
> > I maintain a package that has data fields, and didn't have any problems
> > with this before. However, in my latest update, I'm getting the following
> > error message from the CRAN tests:
> >
> > Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
> > Check: for code/documentation mismatches, Result: WARNING
> >Variables with usage in documentation object 'growth.curves' but not
> in
> > code:
> >  'growth.curves'
> >
> >Variables with usage in documentation object 'phyla.counts' but not in
> > code:
> >  'phyla.counts'
>
> I'm not seeing those messages when testing your package in the same R
> version as win-builder used, so it could be a transient issue, or a
> problem with the tarball that you submitted.  In either case, I'd
> suggest just trying again:  rebuild and submit.
>
> Duncan Murdoch
>
> >
> > The variables are indeed NOT in the code, because they're only to be used
> > in the examples. In this version I moved my documentation from the old
> (now
> > defunct) inlinedocs to ROxygen2. In the previous form, I had to define a
> > structure in the code including both the function and the example, so
> > technically the code was using the variables. In the new form, I simply
> > define the examples with the @examples tag (that ends up in the .rd file
> > within an \examples{} block).
> >
> > Does anyone have any idea on how I should define data in the code to
> avoid
> > this issue? I could simply add the example lines after the return (so
> > they're never reached), but that sounds like a horrible hack.
> >
> > Just in case it's useful:
> > GitHub repository (inside the enveomics.R folder):
> > https://github.com/lmrodriguezr/enveomics/
> > Full test output:
> >
> https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_032029/Windows/00check.log
> >
> > Thanks!
> > Miguel.
> >
> >
> > --
> > Luis M. Rodriguez-R, Ph.D.
> > [ https://rodriguez-r.com ]
> > -
> > Research Engineer
> > Georgia Institute of Technology
> > 311 Ferst Drive, ES&T, Room 3324
> > Atlanta, GA 30332, USA
> > [ http://enve-omics.gatech.edu/ ]
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
>

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Re: [R-pkg-devel] Data docs

2019-10-26 Thread Duncan Murdoch 

On 26/10/2019 4:54 p.m., Luis-Miguel Rodríguez Rojas wrote:

Hello Duncan,

Thanks for your quick response!

I tried re-building and re-submitting and I'm still getting the same error:
https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_224156/Windows/00check.log
https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_224156/Debian/00check.log

I've made the tarball temporarily available directly in the repository 
in case that helps at all:

https://github.com/lmrodriguezr/enveomics/blob/master/enveomics.R_1.5.0.tar.gz



Sorry, I was wrong.  I'm now seeing the error, even on the code I tried 
before.  I think I forget --as-cran last time.


I think this is a bug in R-devel; I'll see if I can confirm that.

Duncan Murdoch

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Re: [R-pkg-devel] License of pre-built vignettes

2019-10-26 Thread Dirk Eddelbuettel 


On 25 October 2019 at 22:45, Mark van der Loo wrote:
| Adding a static PDF vignette is very easy. I have written about it here:
| 
http://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/

And I am doing just that for more and more packages of mine.

It is "wrong" in the sense Mark also alluded elsewhere but also "right"
as it removes variability we sometimes cannot control (changes in
vignette-processing packages fundamentally unrelated to your package,
continued absence of e.g. latex style files on various build machines
such as different rhub flavours) and generally speeds up builds.

As with other things: a trade-off the package maintainer can decide.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] Data docs

2019-10-26 Thread Duncan Murdoch 

I think this is a bug.  It starts to appear in R-devel revision 76780,


r76780 | hornik | 2019-07-04 14:55:52 -0400 (Thu, 04 Jul 2019) | 1 line

Tweaks for c76774.


where the default for a new test is set to TRUE.  The new test was 
introduced in 76774,



r76774 | hornik | 2019-07-03 05:02:40 -0400 (Wed, 03 Jul 2019) | 2 lines

Have codoc() report variables in usages not in the code.
(Optionally for now).


Duncan Murdoch


On 26/10/2019 4:54 p.m., Luis-Miguel Rodríguez Rojas wrote:

Hello Duncan,

Thanks for your quick response!

I tried re-building and re-submitting and I'm still getting the same error:
https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_224156/Windows/00check.log
https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_224156/Debian/00check.log

I've made the tarball temporarily available directly in the repository 
in case that helps at all:

https://github.com/lmrodriguezr/enveomics/blob/master/enveomics.R_1.5.0.tar.gz

Thanks a lot!
Miguel.

--
Luis M. Rodriguez-R, Ph.D.
[ https://rodriguez-r.com  ]
-
Research Engineer
Georgia Institute of Technology
311 Ferst Drive, ES&T, Room 3324
Atlanta, GA 30332, USA
[ http://enve-omics.gatech.edu/ ]



On Sat, Oct 26, 2019 at 1:39 PM Duncan Murdoch > wrote:


On 26/10/2019 11:39 a.m., Luis-Miguel Rodríguez Rojas wrote:
 > Dear all,
 >
 > I maintain a package that has data fields, and didn't have any
problems
 > with this before. However, in my latest update, I'm getting the
following
 > error message from the CRAN tests:
 >
 > Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
 > Check: for code/documentation mismatches, Result: WARNING
 >    Variables with usage in documentation object 'growth.curves'
but not in
 > code:
 >      'growth.curves'
 >
 >    Variables with usage in documentation object 'phyla.counts'
but not in
 > code:
 >      'phyla.counts'

I'm not seeing those messages when testing your package in the same R
version as win-builder used, so it could be a transient issue, or a
problem with the tarball that you submitted.  In either case, I'd
suggest just trying again:  rebuild and submit.

Duncan Murdoch

 >
 > The variables are indeed NOT in the code, because they're only to
be used
 > in the examples. In this version I moved my documentation from
the old (now
 > defunct) inlinedocs to ROxygen2. In the previous form, I had to
define a
 > structure in the code including both the function and the example, so
 > technically the code was using the variables. In the new form, I
simply
 > define the examples with the @examples tag (that ends up in the
.rd file
 > within an \examples{} block).
 >
 > Does anyone have any idea on how I should define data in the code
to avoid
 > this issue? I could simply add the example lines after the return (so
 > they're never reached), but that sounds like a horrible hack.
 >
 > Just in case it's useful:
 > GitHub repository (inside the enveomics.R folder):
 > https://github.com/lmrodriguezr/enveomics/
 > Full test output:
 >

https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_032029/Windows/00check.log
 >
 > Thanks!
 > Miguel.
 >
 >
 > --
 > Luis M. Rodriguez-R, Ph.D.
 > [ https://rodriguez-r.com ]
 > -
 > Research Engineer
 > Georgia Institute of Technology
 > 311 Ferst Drive, ES&T, Room 3324
 > Atlanta, GA 30332, USA
 > [ http://enve-omics.gatech.edu/ ]
 >
 >       [[alternative HTML version deleted]]
 >
 > __
 > R-package-devel@r-project.org
 mailing list
 > https://stat.ethz.ch/mailman/listinfo/r-package-devel
 >



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