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

Prof Brian Ripley r|p|ey @end|ng |rom @t@t@@ox@@c@uk
Tue May 3 16:07:41 CEST 2022 

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 using 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 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/
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac using r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
> 
> 


-- 
Brian D. Ripley,                  ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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