[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 Apr 26 17:22:05 CEST 2022
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/
>>
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>
--
Brian D. Ripley, ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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