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

John Fox j|ox @end|ng |rom mcm@@ter@c@
Tue Apr 26 18:01:52 CEST 2022 

Dear Brian and Peter,

As Brian mentioned, I still get warnings (though different ones) from 
the updated tidy. For example, for the car package:

------ snip -------

* 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

------ snip -------

As before, these warnings are generated for all of the .Rd files in the 
package.

I'm cc'ing the r-package-devel list (with apologies for cross-posting) 
so that there will be a record there.

Best,
  John

On 2022-04-26 11:22 a.m., 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
>>
> 
>

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