Re: [R-pkg-devel] Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs
On 14/06/2022 01:01, Spencer Graves wrote: > > > On 6/13/22 5:05 PM, Duncan Murdoch wrote: >> On 13/06/2022 5:11 p.m., Spencer Graves wrote: >>> >>> >>> On 6/13/22 1:26 PM, Duncan Murdoch wrote: On 13/06/2022 12:12 p.m., Spencer Graves wrote: > Hello, All: > > >How do I fix "Rd cross-references ... NOTE > Undeclared packages ‘EnvStats’, ‘drc’, ‘zoo’, ‘prodlim’, ‘plyr’, > ‘TRAMPR’, ‘raster’ in Rd xrefs"? > > >This occurs with > "https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecfun-00check.html; > > and with > "https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecdat-00check.html;. > > However, this error is not raised on other platforms. My search for > this note produced essentially the same message for other packages but > no advice on how to fix it. > > >These are references to other packages that I do not use in my > packages but that some users may wish to consider. If needed, I will > add them to "Suggests" for the packages. However, that seems overkill, > because I do not use them myself. ??? Section 2.5 of Writing R Extensions says "Packages referred to by these ‘other forms’ should be declared in the DESCRIPTION file, in the ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields." Of those fields, Suggests looks like the best fit. You'd use Enhances if your package provides "methods for classes from these packages, or ways to handle objects from these packages". >>> >>> >>> GitHub Actions failed after I added those packages to Suggests: >>> >>> >>> https://github.com/sbgraves237/Ecfun/runs/6869516417?check_suite_focus=true >> >> That log doesn't really give much info about what went wrong. Maybe some of the packages in the Suggests list weren't available? > > >Is there a way in GitHub Action to NOT fail when a package is not available -- or at least to give a more useful diagnostic? Hi Spencer and all, Yes, you can set the environment variable _R_CHECK_FORCE_SUGGESTS_. R CMD check will still run even if some suggested packages are missing. Provided no error is raised by your package when one of these Suggests is missing, you should be fine. Best wishes, Hugo > > >There probably is, but I don't know how to find the right manual to read nor any better place to ask for help with that than here. > > >Thanks, sg > >> >> Duncan Murdoch > > __ > 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] Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs
On 13/06/2022 7:01 p.m., Spencer Graves wrote:
[ lots deleted ]
Is there a way in GitHub Action to NOT fail when a package is not
available -- or at least to give a more useful diagnostic?
I don't know the answer to that, but in this case, I'm pretty sure
Github Actions couldn't be more helpful, because the error message was
coming from R in these lines in your Github script:
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE),
".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major,
getRversion()$minor), ".github/R-version")
I have the same lines in my script, so I suspect you copied these from
another package, as I did.
To diagnose that kind of error, just start a clean R session, set the
working directory to your package directory, and try to execute them.
You'll see the same error message as your Github action got. Then you
can debug that the way you debug any other R error message:
- Break it up into separate pieces, and discover it happens in
remotes::dev_package_deps(dependencies = TRUE)
- Run debug(remotes::dev_package_deps), and run just that one command,
tracing through until you can isolate the issue.
There probably is, but I don't know how to find the right manual to
read nor any better place to ask for help with that than here.
Duncan Murdoch
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Re: [R-pkg-devel] Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs
On 13/06/2022 7:01 p.m., Spencer Graves wrote: On 6/13/22 5:05 PM, Duncan Murdoch wrote: On 13/06/2022 5:11 p.m., Spencer Graves wrote: On 6/13/22 1:26 PM, Duncan Murdoch wrote: On 13/06/2022 12:12 p.m., Spencer Graves wrote: Hello, All: How do I fix "Rd cross-references ... NOTE Undeclared packages ‘EnvStats’, ‘drc’, ‘zoo’, ‘prodlim’, ‘plyr’, ‘TRAMPR’, ‘raster’ in Rd xrefs"? This occurs with "https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecfun-00check.html; and with "https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecdat-00check.html;. However, this error is not raised on other platforms. My search for this note produced essentially the same message for other packages but no advice on how to fix it. These are references to other packages that I do not use in my packages but that some users may wish to consider. If needed, I will add them to "Suggests" for the packages. However, that seems overkill, because I do not use them myself. ??? Section 2.5 of Writing R Extensions says "Packages referred to by these ‘other forms’ should be declared in the DESCRIPTION file, in the ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields." Of those fields, Suggests looks like the best fit. You'd use Enhances if your package provides "methods for classes from these packages, or ways to handle objects from these packages". GitHub Actions failed after I added those packages to Suggests: https://github.com/sbgraves237/Ecfun/runs/6869516417?check_suite_focus=true That log doesn't really give much info about what went wrong. Maybe some of the packages in the Suggests list weren't available? Is there a way in GitHub Action to NOT fail when a package is not available -- or at least to give a more useful diagnostic? There probably is, but I don't know how to find the right manual to read nor any better place to ask for help with that than here. Your DESCRIPTION file has a blank line after the list of Suggests packages, and that caused dev_package_deps() to die with the error you saw. I think the blank line is illegal in a DESCRIPTION file: in the DCF format, that separates blocks, and everything is supposed to be in one block. But remotes::dev_package_deps() could perhaps give a more informative message, as R CMD INSTALL does. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs
On 6/13/22 5:05 PM, Duncan Murdoch wrote: On 13/06/2022 5:11 p.m., Spencer Graves wrote: On 6/13/22 1:26 PM, Duncan Murdoch wrote: On 13/06/2022 12:12 p.m., Spencer Graves wrote: Hello, All: How do I fix "Rd cross-references ... NOTE Undeclared packages ‘EnvStats’, ‘drc’, ‘zoo’, ‘prodlim’, ‘plyr’, ‘TRAMPR’, ‘raster’ in Rd xrefs"? This occurs with "https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecfun-00check.html; and with "https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecdat-00check.html;. However, this error is not raised on other platforms. My search for this note produced essentially the same message for other packages but no advice on how to fix it. These are references to other packages that I do not use in my packages but that some users may wish to consider. If needed, I will add them to "Suggests" for the packages. However, that seems overkill, because I do not use them myself. ??? Section 2.5 of Writing R Extensions says "Packages referred to by these ‘other forms’ should be declared in the DESCRIPTION file, in the ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields." Of those fields, Suggests looks like the best fit. You'd use Enhances if your package provides "methods for classes from these packages, or ways to handle objects from these packages". GitHub Actions failed after I added those packages to Suggests: https://github.com/sbgraves237/Ecfun/runs/6869516417?check_suite_focus=true That log doesn't really give much info about what went wrong. Maybe some of the packages in the Suggests list weren't available? Is there a way in GitHub Action to NOT fail when a package is not available -- or at least to give a more useful diagnostic? There probably is, but I don't know how to find the right manual to read nor any better place to ask for help with that than here. Thanks, sg Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs
On 6/13/22 2:22 PM, Ivan Krylov wrote:
On Mon, 13 Jun 2022 13:59:24 -0500
Spencer Graves wrote:
I probably should have just used "Suggests" and not
bothered this list with this issue.
Why not use the \link{foo} form and let the HTML help system resolve
the link at run time? Is it considered bad form to use unqualified
links to help pages in other packages?
The problem is that \link{foo} cannot distinguish between
\link[a]{foo} and \link[b]{foo}. Using "Suggests" sounds to me more
like how how the R Core and CRAN teams probably think the system should
work.
But Duncan or someone else may think differently.
Thanks, Spencer
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