To round this off, R-patched has the NEWS item
? Setting environment variable _R_CHECK_RD_VALIDATE_RD2HTML_ to a
false value will override R CMD check --as-cran and turn off HTML
validation. This provides a way to circumvent a problematic
tidy.
The 2006 version that ships with macOS is always skipped.
and R-admin now says
R CMD check --as-cran also makes use of ?HTML Tidy?. macOS has a version
in /usr/bin/tidy dating from 2006 which is far too old and is skipped.
Up-to-date versions can be installed from http://binaries.html-tidy.org/.
The current version there is 5.8.0, later than Debian's 5.6.0 used in
developing this and detecting further issues in Rd2HTML that have since
been addressed.
So the simplest thing for someone wanting to do an -as-cran check is to
install html-tidy 5.8.0.
Unfortunately there is nothing we can do about 4.2.0.
On 26/04/2022 16:22, Prof Brian Ripley wrote:
On 26/04/2022 15:43, peter dalgaard wrote:
Yes, I think this should go to r-package-devel or maybe even file a
bug report against "R CMD check". Looks like we "just" need to revise
the logic at the start of check_Rd2HTML():
???? check_Rd2HTML <- function(pkgdir) {
???????? if(!nzchar(Sys.which("tidy")) ||
??????????? !startsWith(system2("tidy", "--version", stdout = TRUE),
??????????????????????? "HTML Tidy"))
???????????? return()
to either
- look for a version number (which the Apple builds don't have)
- explicitly reject the 2006 Apple builds
- somehow allow for an override using an environment variable
This is switched on by _R_CHECK_RD_VALIDATE_RD2HTML_=true or --as-cran. ?I plan to at least let _R_CHECK_RD_VALIDATE_RD2HTML_=false override --as-cran. There seems to have been a report on r-package-devel not mentioning macOS: https://stat.ethz.ch/pipermail/r-package-devel/2022q1/007804.html https://stat.ethz.ch/pipermail/r-package-devel/2022q2/007932.html but I don't think anyone had a clue that the macOS 'tidy' might be insufficient.
or thereabouts... - pd
On 26 Apr 2022, at 16:25 , John Fox <jfox at mcmaster.ca> wrote: Dear Brian, Thank you very much for the explanation. Please see interline below: On 2022-04-25 4:51 p.m., Prof Brian Ripley wrote:
On 25/04/2022 20:04, John Fox wrote:
Dear R-sig-mac list members, When checking packages --as-cran with R 4.2.0 (and R 4.2.0 patched), I'm seeing multiple warnings (and a NOTE) concerning the HTML version of the package help-page manuals. The warning appears for every .Rd file in all of the packages that I've checked. I didn't see this problem before R 4.2.0. I'm writing to the r-sig-mac list rather than r-package-devel because I
Unfortunately the authors of this are not on r-sig-mac.
Should I mention this as well on r-package-devel?
don't encounter the same problem under Windows. Nor does it appear on the CRAN check pages for the packages.
This check is only done if you have 'tidy' on the path.? My Monterey M1 MBP has auk2% tidy --version HTML Tidy for Mac OS X released on 31 October 2006 - Apple Inc. build 2649
That's exactly the version installed on my MacBook Pro. Is this standard for Monterey? If not, would it be best simply to remove tidy (and how did it get there?).
I think that is far too old.? The short answer is to ignore these, or update tidy (from http://binaries.html-tidy.org/) which (5.8.0) finds different issues for car that I do not see on Fedora (with 5.7.16).
I saw these warnings for every .Rd file in all of the packages I checked, not just for the car package. The HTML is presumably generated from the .Rd files by the R installation process. If tidy is general, or common, on Monterey Macs, I wonder why others aren't reporting similar warnings on R CMD check --as-cran.
Probably your Windows machine does not have tidy installed.
I know that there's been discussion of adding an HTML manual, which seems a good idea, but I didn't realize that this has apparently already been implemented. Has anyone else experienced this problem or does anyone understand its source? AFAIK, there's nothing unusual about the R installation on my Mac, but of course there may be some setting that inadvertently turned on checking the HTML manual.
--as-cran turned it on ((f tidy is available).
Again, thank you for the explanation. Best, John
Here's an example (with many lines elided, . . .): ------ snip ------ Johns-MacBook-Pro:car johnfox$ R CMD check --as-cran car_3.0-13.tar.gz * using log directory '/Users/johnfox/Documents/R-package-sources/car/car.Rcheck' * using R version 4.2.0 Patched (2022-04-24 r82246) * using platform: aarch64-apple-darwin20 (64-bit) * using session charset: UTF-8 * using option '--as-cran' * checking for file 'car/DESCRIPTION' ... OK * this is package 'car' version '3.0-13' * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: 'John Fox <jfox at mcmaster.ca>' * checking package namespace information ... OK . . . * checking PDF version of manual ... OK * checking HTML version of manual ... NOTE Found the following problems: Anova.Rd:4:1: Warning: <link> inserting "type" attribute Anova.Rd:12:1: Warning: <script> proprietary attribute "onload" Anova.Rd:12:1: Warning: <script> inserting "type" attribute Anova.Rd:17:1: Warning: <table> lacks "summary" attribute Anova.Rd:135:1: Warning: <table> lacks "summary" attribute Anova.Rd:285:1: Warning: <table> lacks "summary" attribute Boot.Rd:4:1: Warning: <link> inserting "type" attribute Boot.Rd:12:1: Warning: <script> proprietary attribute "onload" Boot.Rd:12:1: Warning: <script> inserting "type" attribute Boot.Rd:17:1: Warning: <table> lacks "summary" attribute Boot.Rd:56:1: Warning: <table> lacks "summary" attribute . . . which.names.Rd:12:1: Warning: <script> proprietary attribute "onload" which.names.Rd:12:1: Warning: <script> inserting "type" attribute which.names.Rd:17:1: Warning: <table> lacks "summary" attribute which.names.Rd:44:1: Warning: <table> lacks "summary" attribute * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE See '/Users/johnfox/Documents/R-package-sources/car/car.Rcheck/00check.log' for details. ------ snip ------ Any help would be appreciated. Thanks, ?? John
-- John Fox, Professor Emeritus McMaster University Hamilton, Ontario, Canada web: https://socialsciences.mcmaster.ca/jfox/
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Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford