[R-SIG-Mac] R CMD check "HTML version of manual" NOTE/Warnings

[John Fox]

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 using 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/