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
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