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

Tue Apr 26 16:43:25 CEST 2022

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

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/
> 
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-- 
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