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

[Duncan Murdoch]

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
>>>>>>
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