[R-pkg-devel] Documenting raw data
Hi Folks,
Looking for some help documenting my raw data (data in inst/extdata).
Is the correct doctype "data"?
The usage of loading this type of data is system.file("extdata", nameoffile,
package="nameofpackage")
Is this the correct string to put in the \usage section? I have tried this,
but get errors such as:
Functions or methods with usage in documentation object 'nameoffile' but not in
code:
'system.file'
Has anyone done this recently and have an example to see where I'm going wrong?
This check seems to be new as in the past I simply had lazydata set to true and
it passed tests.
Thanks for any help.
Cheers,
Alan Cantin
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN-Policies
On 23/04/2020 2:34 p.m., Peter Meissner wrote:
Hello Everyone,
some weeks back I already wrote to CRAN but got no response. So, I post my
question here seeking for advice.
I am trying to publish a package to CRAN. I got rejected once with some
minor change requests. I implemented them and submitted again. This time I
got a whole array of change requests.
The problem is, I am confused since none of the requests is mentioned
anywhere in CRAN policies. So, are those mere suggestions? Are these common
policy now? Has everyone to implement them? How should I proceed?
I'd say that the changes being requested are all things stated in the
Writing R Extensions manual, so this falls under the blanket statement
in the policy that "CRAN hosts packages of publication quality and is
not a development platform."
(In general, I have no problem with complying with CRAN policies, but I am
not sure if these are actually common requirements now or not.)
I'd guess the requests will vary depending on who the reviewer is and
what their mood is, but if you ignore their requests, you're not going
to put them in a better mood.
Duncan Murdoch
Copy of the change requests:
* quote **
Please add \value to all .Rd files for exported functions and explain
the functions results in the documentation.
f.i.: time_stamp.Rd
If a function does not return a value, please document that too, e.g.
\value{None}.
The \description tag in the .Rd files should be one or two sentences on
how the function works and what it's good for. Don't just repeat the
function name.
F.i.: stats_modus_multi.Rd
An .Rd file title should:
- be capitalized
- not end in a period
- be at most 65 characters long
- exist and stand alone (there must be exactly one title)
Please adjust to these standards and again don't simply repeat the name.
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Documenting-functions
F.i.: stats_modus_multi.Rd
Please fix and resubmit, and document what was changed in the submission
comments.
* quote **
Best, Peter
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Package fails on OSX on CRAN but not on rhub
Stuart, As a follow-up, the errors are of the '*** caught illegal operation ***' variety which is frequently seen when different compiled components (and particularly C++ ones) are out of sync with respect to their toolchains. So I would suggest a clean rebuild, but given that it is at CRAN that is out of our hands. Sorry, Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] CRAN-Policies
Hello Everyone,
some weeks back I already wrote to CRAN but got no response. So, I post my
question here seeking for advice.
I am trying to publish a package to CRAN. I got rejected once with some
minor change requests. I implemented them and submitted again. This time I
got a whole array of change requests.
The problem is, I am confused since none of the requests is mentioned
anywhere in CRAN policies. So, are those mere suggestions? Are these common
policy now? Has everyone to implement them? How should I proceed?
(In general, I have no problem with complying with CRAN policies, but I am
not sure if these are actually common requirements now or not.)
Copy of the change requests:
* quote **
Please add \value to all .Rd files for exported functions and explain
the functions results in the documentation.
f.i.: time_stamp.Rd
If a function does not return a value, please document that too, e.g.
\value{None}.
The \description tag in the .Rd files should be one or two sentences on
how the function works and what it's good for. Don't just repeat the
function name.
F.i.: stats_modus_multi.Rd
An .Rd file title should:
- be capitalized
- not end in a period
- be at most 65 characters long
- exist and stand alone (there must be exactly one title)
Please adjust to these standards and again don't simply repeat the name.
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Documenting-functions
F.i.: stats_modus_multi.Rd
Please fix and resubmit, and document what was changed in the submission
comments.
* quote **
Best, Peter
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Package fails on OSX on CRAN but not on rhub
On 23 April 2020 at 19:06, Stuart Lacy via R-package-devel wrote: | I've been told to fix the problems that my package 'multistateutils' has on | OSX: | https://cran.r-project.org/web/checks/check_results_multistateutils.html | | This is seemingly something to do with my Rcpp code, but I can't debug it | on my local (Linux) machine, as when I check my code using Rhub it passes | the checks: | https://builder.r-hub.io/status/multistateutils_1.2.4.tar.gz-9295de3b93d746eb93983d33269cf08d | | Does anyone have any tips for testing their packages on OSX, or any | OSX-specific issues with Rcpp? Yes -- Rcpp 1.0.4 passed on macOS at CRAN was released there. And only post-release, many macOS users (who could have tested pre-release) made a lot of noise concerning issues on their machines. Eventually, and thanks to careful digging by Winston, it was seen as being caused by a newer (relative to what CRAN has) macOS SDK issued by Apple. And Rcpp 1.0.4.6 was prepared almost three weeks ago, admitted on CRAN about two weeks ago ... but still only has one out of three binaries for macOS built on CRAN as you see at https://cloud.r-project.org/web/packages/Rcpp/index.html Given that the _binary_ package for macOS may be useless for you, you could try to force installation of the _source_ package for your testing. It should work just fine. If you want to see more details, see issue #1060 at the Rcpp GitHub repo. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Package fails on OSX on CRAN but not on rhub
Hi, I've been told to fix the problems that my package 'multistateutils' has on OSX: https://cran.r-project.org/web/checks/check_results_multistateutils.html This is seemingly something to do with my Rcpp code, but I can't debug it on my local (Linux) machine, as when I check my code using Rhub it passes the checks: https://builder.r-hub.io/status/multistateutils_1.2.4.tar.gz-9295de3b93d746eb93983d33269cf08d Does anyone have any tips for testing their packages on OSX, or any OSX-specific issues with Rcpp? Thanks, Stuart -- Stuart Lacy Research Software Engineer Wolfson Atmospheric Chemistry Lab & Information Services *C/G/116* University of York Heslington York YO10 5DD +44 (0)1904 324756 [image: https://www.york.ac.uk/media/abouttheuniversity/supportservices/informationdirectorate/images/cse/CSEUK%20Primary%20(r)%20RGB-80x95.jpg] Disclaimer: https://www.york.ac.uk/about/legal-statements/email-disclaimer/ [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] WARNING Files in the 'vignettes' directory but no files in 'inst/doc':
On 23/04/2020 11:10 a.m., John Lawson wrote: My AQLSchemes package has a pdf vignette created with Rmarkdown. I tried to add a vignette to my daewr package in exactly the same way, by setting the Description file like the AQLSchemes package Description file with the statements Suggests: R.rsp VignetteBuilder: R.rsp. In both packages I put the vignette .Rmd file and output .pdf file in the vignettes directory, and the inst directory is empty When I run the check on the AQLSchemes on my local machine, I see the messages - preparing 'AQLSchemes': v checking DESCRIPTION meta-information ... - installing the package to build vignettes ... checking sizes of PDF files under 'inst/doc' ... NOTE Unable to find GhostScript executable to run checks on size reduction 0 errors v | 0 warnings v | 1 note x and the package builds correctly with the vignette However, when I run the check on daewr I see the messages - preparing 'daewr': (665ms) v checking DESCRIPTION meta-information ... - checking for LF line-endings in source and make files and shell scripts (894ms) - checking for empty or unneeded directories Removed empty directory 'daewr/inst' ... checking files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'ModelRobust.Rmd', 'ModelRobust.pdf' 0 errors v | 1 warning x | 0 notes v Error: R CMD check found WARNINGs Execution halted The two packages are set up in the same way. Any insight as to why one builds with the vignette but the other does not, would be greatly appreciated. As far as I know R.rsp doesn't support Rmd vignettes. I just took a quick look at the code, and it appears to support these formats: .rsp, .pdf.asis, .html.asis, .tex, .ltx, .md, .md.rsp. So you should rename the source file to one of those, or choose a different vignette engine. knitr::rmarkdown is the usual engine to use with R Markdown files. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] WARNING Files in the 'vignettes' directory but no files in 'inst/doc':
My AQLSchemes package has a pdf vignette created with Rmarkdown. I tried to add a vignette to my daewr package in exactly the same way, by setting the Description file like the AQLSchemes package Description file with the statements Suggests: R.rsp VignetteBuilder: R.rsp. In both packages I put the vignette .Rmd file and output .pdf file in the vignettes directory, and the inst directory is empty When I run the check on the AQLSchemes on my local machine, I see the messages - preparing 'AQLSchemes': v checking DESCRIPTION meta-information ... - installing the package to build vignettes ... > checking sizes of PDF files under 'inst/doc' ... NOTE Unable to find GhostScript executable to run checks on size reduction 0 errors v | 0 warnings v | 1 note x and the package builds correctly with the vignette However, when I run the check on daewr I see the messages - preparing 'daewr': (665ms) v checking DESCRIPTION meta-information ... - checking for LF line-endings in source and make files and shell scripts (894ms) - checking for empty or unneeded directories Removed empty directory 'daewr/inst' ... > checking files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'ModelRobust.Rmd', 'ModelRobust.pdf' 0 errors v | 1 warning x | 0 notes v Error: R CMD check found WARNINGs Execution halted The two packages are set up in the same way. Any insight as to why one builds with the vignette but the other does not, would be greatly appreciated. Sincerely John Lawson [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Non-standard things in the check directory
Just realized that nobody replied to this. So this seems to be a bug in `R CMD check --as-cran`, it does not ignore the arch specific examples and tests directories and files. It happens as well if you run your check on a local windows, not just on R-hub. Should I open a bug for this? There is an env var for it called _R_CHECK_THINGS_IN_CHECK_DIR_, but --as-cran overrides that, so there is not much we can do about it on R-hub. Right now this NOTE does not show up in new package submissions, new package submission probably do not use `--as-cran`, but they set up their own configuration, which might look like this: https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Uwe/make/incoming_env.bat Summary: you'll have to ignore this NOTE for now on R-hub and on your machines. Gabor On Tue, Mar 31, 2020 at 3:37 PM Goldfeld, Keith wrote: > > Good morning - > I am running checks (using devtools::check_rhub) for my package `simstudy`, > and I get one note from one server, Windows Server 2008 R2 SP1, R-devel, > 32/64 bit: > NOTES: > > * checking for non-standard things in the check directory ... NOTE > Found the following files/directories: > 'examples_i386' 'examples_x64' 'simstudy-Ex_i386.Rout' > 'simstudy-Ex_x64.Rout' 'tests_i386' 'tests_x64' > > In my previous submission, I got this note as well. I see that it is likely a > server issue, and not my issue, but is there any way for me to modify my > package to make this go away? > > > - Keith > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] (SOLVED) Warning R-hub Windows Server 2008 : qpdf needed
Hi, Here is the build log showing this warning message: https://builder.r-hub.io/status/graph4lg_0.5.0.tar.gz-31e8935d0c724c4b9d6986f31eeff357 I have just tried again and this warning message does not show up anymore. I thank you Gabor for your help. (new build log: https://builder.r-hub.io/status/graph4lg_0.5.0.tar.gz-6e69d658b38242d0a81efaae5d942be9) Best regards Paul - Mail original - De: "Gábor Csárdi" À: "Paul SAVARY" Cc: "r-package-devel" Envoyé: Mercredi 22 Avril 2020 18:54:32 Objet: Re: [R-pkg-devel] Warning R-hub Windows Server 2008 : qpdf needed Hi, which R version was this? Can you point to a build log? qpdf is definitely installed on R-hub's Windows machines, and it is even on the PATH. Maybe the new toolchain did not find it, I have copied it to a better place now, please try again. Best, Gabor On Wed, Apr 22, 2020 at 5:44 PM Paul SAVARY wrote: > > Hello, > > I'm having trouble checking a package (graph4lg). > > With devtools::check_rhub(), I obtain a warning message on Windows Server 2008 > > *checking data fro ASCII and uncompressed saves ... OK > WARNING > 'qpdf' is needed for checks on size reduction of PDFs > > I checked that qpdf is intalled. It is, because I have Rtools. > Rtools is in my environment path > > That's the first time I obtain this message, although I checked my package > several times on Rhub. > I do not obtain similar messages with other checking platforms. > > I thank you in advance > Regards > Paul Savary > > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
