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

Duncan Murdoch murdoch@dunc@n @end|ng |rom gm@||@com
Thu Oct 8 18:06:12 CEST 2020 

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
>>>>>>
>>>>>
>>>

More information about the R-package-devel mailing list