[R-pkg-devel] is R CMD build --compact-vignettes working as expected?

John Fox j|ox @end|ng |rom mcm@@ter@c@
Thu Oct 8 17:10:30 CEST 2020 

Dear Ben,

Actually, what I used was --compact-vignettes="both", with qpdf and gs 
installed on my Windows and Mac machines, and that apparently didn't 
work for me.

Best,
  John

On 2020-10-07 10:06 p.m., Ben Bolker wrote:
>    OK, I think I see the problem. tl;dr use --compact-vignettes="both" 
> when building the vignettes.
> 
>    --compact-vignettes  by default only tries qpdf.
> 
>    when the R CMD check --as-cran is run, it tries both qpdf and gs. 
> Since gs (apparently, in this case) compresses more aggressively than 
> qpdf, it succeeds in compressing further, and the check complains.
> 
>  From R CMD build --help:
> 
>   --compact-vignettes=  try to compact PDF files under inst/doc:
>                          "no" (default), "qpdf", "gs", "gs+qpdf", "both"
>    --compact-vignettes   same as --compact-vignettes=qpdf
> 
> 
>    I don't know if this is worth documenting somewhere, or modifying the 
> behaviour to make "both" the default for --compact-vignettes ?
> 
> 
> On 10/7/20 8:35 PM, Duncan Murdoch wrote:
>> On 07/10/2020 8:32 p.m., Ben Bolker wrote:
>>>     Thanks for the tip, I'll take a look.
>>>
>>>     Given that three relatively experienced package authors all seem to
>>> have experienced similar issues, it seems that maybe this is worth
>>> figuring out/maybe I'm not just doing something boneheaded.
>>
>> Just to clarify:  I've never noticed the problem you mention.  I just 
>> know how to debug R CMD build.
>>
>> Duncan
>>
>>>
>>>     cheers
>>>       Ben
>>>
>>> On 10/7/20 8:31 PM, Duncan Murdoch wrote:
>>>> I don't know the answer to your question, but you can debug the
>>>> --compact-vignettes option as follows.
>>>>
>>>> debug(tools::compactPDF)
>>>> tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
>>>>
>>>> where "pkgdir" is the directory of the source of your package.  Add
>>>> extra options to the build as separate elements of the argument to
>>>> .build():  this function is called after args have been parsed.
>>>>
>>>> When I do that, I see that it rejects the compaction, because none of
>>>> mine benefit much from it:  it wants at least a 10% and 10K reduction.
>>>> But Ben's example met those criteria.  When I trick it into accepting
>>>> the compaction, it does put the compacted PDF into the tarball.
>>>>
>>>> Duncan Murdoch
>>>>
>>>> On 07/10/2020 6:03 p.m., John Fox wrote:
>>>>> Dear Ben,
>>>>>
>>>>> On 2020-10-07 5:26 p.m., Ben Bolker wrote:
>>>>>>      I hope so too. The (annoying) workaround is to compact the 
>>>>>> vignette
>>>>>> yourself (using qpdf directly or using tools::compactPDF), then use
>>>>>> no-build-vignettes.  The problem there is whatever's supposed to 
>>>>>> happen
>>>>>> with building vignette indices.  The uuuuugly workaround, I guess, 
>>>>>> is to
>>>>>> build the tarball, compact the vignettes oneself, then *replace* 
>>>>>> them in
>>>>>> the tarball.  (Obviously I can automate that, but it seems as 
>>>>>> though it
>>>>>> would be unnecessary if I knew what was going on ...)
>>>>>
>>>>> I've used both of these workarounds and agree that it would be nice to
>>>>> avoid them. After all, what is the --compact-vignettes argument for?
>>>>>
>>>>> Best,
>>>>>     John
>>>>>
>>>>>>
>>>>>>      cheers
>>>>>>       Ben
>>>>>>
>>>>>>
>>>>>> On 10/7/20 4:10 PM, John Fox wrote:
>>>>>>> Dear Ben,
>>>>>>>
>>>>>>> I was hoping that someone would pick up on this problem, because 
>>>>>>> I've
>>>>>>> experienced the same issue of --compact-vignettes apparently 
>>>>>>> ignored,
>>>>>>> e.g., with the Rcmdr package under R 4.0.2 on both macOS and 
>>>>>>> Windows.
>>>>>>>
>>>>>>> Best,
>>>>>>>     John
>>>>>>>
>>>>>>> John Fox, Professor Emeritus
>>>>>>> McMaster University
>>>>>>> Hamilton, Ontario, Canada
>>>>>>> web: https://socialsciences.mcmaster.ca/jfox/
>>>>>>>
>>>>>>> On 2020-10-05 1:09 p.m., Ben Bolker wrote:
>>>>>>>>      Am I confused, or doing something wrong, or ... ?
>>>>>>>>
>>>>>>>>      I have qpdf installed, and am running R CMD build with
>>>>>>>> --compact-vignettes, but the PDF in the tarball doesn't seem to be
>>>>>>>> compressed despite the fact that the output messages say 
>>>>>>>> "compacting
>>>>>>>> vignettes ..."
>>>>>>>>
>>>>>>>>
>>>>>>>>      $ R CMD build --compact-vignettes lme4
>>>>>>>> * checking for file ‘lme4/DESCRIPTION’ ... OK
>>>>>>>> * preparing ‘lme4’:
>>>>>>>> * checking DESCRIPTION meta-information ... OK
>>>>>>>> * cleaning src
>>>>>>>> * installing the package to process help pages
>>>>>>>> * saving partial Rd database
>>>>>>>> * creating vignettes ... OK
>>>>>>>> Warning: ‘inst/doc’ files
>>>>>>>>        ‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
>>>>>>>>      ignored as vignettes have been rebuilt.
>>>>>>>>      Run R CMD build with --no-build-vignettes to prevent 
>>>>>>>> rebuilding.
>>>>>>>> * compacting vignettes and other PDF files
>>>>>>>> * cleaning src
>>>>>>>> * checking for LF line-endings in source and make files and shell
>>>>>>>> scripts
>>>>>>>> * checking for empty or unneeded directories
>>>>>>>> * building ‘lme4_1.1-24.tar.gz’
>>>>>>>>
>>>>>>>>      The copy of lmer.pdf in the resulting tarball is 900K or so:
>>>>>>>>
>>>>>>>> $ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf
>>>>>>>> -rw-r--r-- bolker/bolker 907022 2020-10-05 12:59
>>>>>>>> lme4/inst/doc/lmer.pdf
>>>>>>>>
>>>>>>>>      The previously built (and manually compacted) version of 
>>>>>>>> lmer.pdf
>>>>>>>> in the tarball is 500K:
>>>>>>>>
>>>>>>>> $ ls -l lme4/inst/doc/lmer.pdf
>>>>>>>> -rw-r--r-- 1 bolker bolker 495199 Oct  3 22:15 
>>>>>>>> lme4/inst/doc/lmer.pdf
>>>>>>>>
>>>>>>>>       Is 'R CMD build' confused by the presence of a pre-built 
>>>>>>>> PDF in
>>>>>>>> the inst/doc directory? Or am I somehow mistaken about how this is
>>>>>>>> supposed to work?
>>>>>>>>
>>>>>>>>       I would just use --no-build-vignettes and submit the 
>>>>>>>> tarball with
>>>>>>>> the previously built/compressed PDF, but I'm trying to avoid a
>>>>>>>> "Package has a VignetteBuilder field but no prebuilt vignette 
>>>>>>>> index"
>>>>>>>> NOTE, which I assume is missing because I built without building
>>>>>>>> vignettes ... ?
>>>>>>>>
>>>>>>>>      As always, enlightenment is welcome.
>>>>>>>>
>>>>>>>>      cheers
>>>>>>>>        Ben Bolker
>>>>>>>>
>>>>>>>> ______________________________________________
>>>>>>>> R-package-devel using r-project.org mailing list
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>
>>>>> ______________________________________________
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>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>
>>>>
>>

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