Re: [Rd] R CMD INSTALL warning for S4 replacement functions on R 4.1.0-alpha
> Sebastian Meyer > on Fri, 23 Apr 2021 23:23:16 +0200 writes: > I can confirm this Rd warning in R-devel (2021-04-23 r80216), but not in > R 4.0.5. It happens when installing the static help (INSTALL option --html). > The following R code reproduces the warning by creating a tiny test > package and then calling relevant internal functions from 'tools': [...] Thanks a lot, Sebastian, for some reason I did not see your reply when I wrote mine... So at least you indirectly solved my puzzlement on that this was not visible with CRAN checks using R-devel : Almost surely they all do *not* create static HTML pages. So this really is a bug in R > 4.0.z and we are happy if you report it, just referring to your R-devel post ... and then we all will be really grateful for whomever provides a (careful, minimal, ..) patch, presumably to src/library/tools/R/Rd2HTML.R Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD INSTALL warning for S4 replacement functions on R 4.1.0-alpha
> Felix Ernst > on Fri, 23 Apr 2021 17:01:05 + writes: > Hi all, > Since R 4.1, R CMD INSTALL throws warning during building the man pages, when installing from source. > We noticed this first on Windows for man pages involving S4 replacement function: > * http://bioconductor.org/checkResults/devel/bioc-LATEST/Modstrings/riesling1-checksrc.html > * http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicAlignments/riesling1-checksrc.html > However, it's also showing up on linux with a slight twist (file not found instead of invalid argument) for other functions: > * https://cran.r-project.org/web/checks/check_results_Matrix.html (right at the end) >> From the messages and the involved offending filenames, we hypothesize that this is triggered by invalid filenames specific to the OS. > Please note, that the warning is not issued during R CMD CHECK for a given package. > Can anyone comment on this? Is more information needed? If it is a bug, I am happy to post on the bug tracker. > Thanks for any advice. > Best regards, > Felix Thanks a lot, Felix, for the heads up -- and for using the pre-release versions of R you should be role model to the many readers of 'R-devel' and other R developers -- even doing it for a living and who are *still* not help the R project by the relatively simple act of starting to work with 'R x.y.0 alpha' To the topic, yes, I think there's something we (the R core team) has not considered when implementing some of the changes in static help page creation. This will now get technical but that should always be ok / even desirable for the R-devel list : The CRAN check on Matrix (with R 4.1.0 alpha, called "R-patched") you mention, here more directly https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/Matrix-00check.html has the relevant lines --- checking whether package ‘Matrix’ can be installed ... WARNING Found the following significant warnings: Rd warning: Previous alias or file overwritten by alias: chol,dsCMatrix-method Rd warning: Previous alias or file overwritten by alias: chol,lsCMatrix-method Rd warning: Previous alias or file overwritten by alias: chol,nsCMatrix-method Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,ddenseMatrix-method.html’: No such file or directory Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,ldenseMatrix-method.html’: No such file or directory Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,ndenseMatrix-method.html’: No such file or directory Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,ddenseMatrix-method.html’: No such file or directory Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,ldenseMatrix-method.html’: No such file or directory Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,ndenseMatrix-method.html’: No such file or directory Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,Matrix-method.html’: No such file or directory Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,Matrix-method.html’: No such file or directory Rd warning: Previous alias or file overwritten by alias: expand Rd warning: Previous alias or file overwritten by alias: crossprod-methods Rd warning: Previous alias or file overwritten by alias: tcrossprod-methods See https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/Matrix-00install.html for details. --- and the (quite large, from many C compilation warnings (from SuiteSparse, not Matrix directly)) 00install.html then gives the details: *** installing help indices converting help for package ‘Matrix’ finding HTML links ... done BunchKaufman-methodshtml CAexhtml [...] bandSparse html bdiag html boolean-matprod html REDIRECT:fileboolean-matprod.html -> boolean-matprod.html [ SUCCESS ] cBind html chol
Re: [Rd] R CMD INSTALL warning for S4 replacement functions on R 4.1.0-alpha
I can confirm this Rd warning in R-devel (2021-04-23 r80216), but not in
R 4.0.5. It happens when installing the static help (INSTALL option --html).
The following R code reproduces the warning by creating a tiny test
package and then calling relevant internal functions from 'tools':
```R
## create test package
dir.create(pkgdir <- tempfile())
tools:::.write_description( # need a DESCRIPTION
unlist(head(packageDescription("tools"), -1)),
file.path(pkgdir, "DESCRIPTION"))
dir.create(file.path(pkgdir, "man"))
cat(r"(\name{test-package}
\title{Test Package}
\alias{\%/\%}
\description{Test alias.}
)", file = file.path(pkgdir, "man", "test-package.Rd"))
## build HTML help
dir.create(outDir <- tempfile())
tools:::.install_package_description(pkgdir, outDir)
tools:::.writePkgIndices(pkgdir, outDir)
tools:::.convertRdfiles(pkgdir, outDir, types = "html")
```
The output is
converting help for package ‘tools’
finding HTML links ... done
test-packagehtml
REDIRECT:topic %/% -> test-package.html [ FAIL ]
REDIRECT:filetest-package.html -> test-package.html [ SUCCESS ]
Rd warning: cannot open file
'/tmp/RtmpasTPyq/fileb3d72f4ea1cf/help/%/%.html': No such file or directory
A workaround (if needed) is to set the environment variable
_R_HELP_LINKS_TO_TOPICS_ to a false value.
Best regards,
Sebastian
Am 23.04.21 um 19:01 schrieb Felix Ernst:
> Hi all,
>
> Since R 4.1, R CMD INSTALL throws warning during building the man pages, when
> installing from source.
>
> We noticed this first on Windows for man pages involving S4 replacement
> function:
>
> *
> http://bioconductor.org/checkResults/devel/bioc-LATEST/Modstrings/riesling1-checksrc.html
> *
> http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicAlignments/riesling1-checksrc.html
>
> However, it's also showing up on linux with a slight twist (file not found
> instead of invalid argument) for other functions:
>
> * https://cran.r-project.org/web/checks/check_results_Matrix.html (right
> at the end)
>
> From the messages and the involved offending filenames, we hypothesize that
> this is triggered by invalid filenames specific to the OS.
> Please note, that the warning is not issued during R CMD CHECK for a given
> package.
>
> Can anyone comment on this? Is more information needed? If it is a bug, I am
> happy to post on the bug tracker.
>
> Thanks for any advice.
>
> Best regards,
> Felix
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
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>
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD INSTALL warning for S4 replacement functions on R 4.1.0-alpha
Hi all, Since R 4.1, R CMD INSTALL throws warning during building the man pages, when installing from source. We noticed this first on Windows for man pages involving S4 replacement function: * http://bioconductor.org/checkResults/devel/bioc-LATEST/Modstrings/riesling1-checksrc.html * http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicAlignments/riesling1-checksrc.html However, it's also showing up on linux with a slight twist (file not found instead of invalid argument) for other functions: * https://cran.r-project.org/web/checks/check_results_Matrix.html (right at the end) >From the messages and the involved offending filenames, we hypothesize that >this is triggered by invalid filenames specific to the OS. Please note, that the warning is not issued during R CMD CHECK for a given package. Can anyone comment on this? Is more information needed? If it is a bug, I am happy to post on the bug tracker. Thanks for any advice. Best regards, Felix [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
