[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 19:21:15 CEST 2020 

Dear all,

First, thank you to everyone who responded.

Let me be more specific about what I did, focusing on macOS (since I did 
most of this on Windows too):

(1) I observed the problem with the Rcmdr package, including version 
2.7-1, which is newly on CRAN. Presumably, it wouldn't be hard to 
duplicate what I did.

(2) I previously tried both --compact-vignettes="both", 
--compact-vignettes=both, and also just --compact-vignettes. R CMD build 
says that it's "* compacting vignettes and other PDF files", and R CMD 
check --as-cran doesn't complain, reporting "* checking sizes of PDF 
files under ‘inst/doc’ ... OK."

(3) Nothing changes when, following Duncan's advice, I set GS_QUALITY=screen

In the tarball built by R CMD build, the vignette in 
inst/doc/Getting-Started-with-the-Rcmdr.pdf is 1.6 MB. When I compacted 
the vignette with Adobe Acrobat, it was reduced to 395 KB.

Putting all of this together, I suspect that Acrobat may just do a 
better job than gs and qpdf.

Best,
  John


On 2020-10-08 12:06 p.m., Duncan Murdoch wrote:
> When I tried that on MacOS, it did the gs compression with gs_quality 
> set to "none", which does nothing.  I don't know what quality CRAN uses, 
> but for me setting the environment variable GS_QUALITY=screen made a big 
> difference.
> 
> Duncan Murdoch
> 
> On 08/10/2020 11:10 a.m., John Fox wrote:
>> 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
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> R-package-devel using r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>>>
>>>>>>
>>>>
> 

-- 
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/

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