R devel - Apr 2013 - vignettes: problems with PDF compaction

[Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET]

Each time I update my heplots package, I get warnings from R CMD check
on R-Forge,

* checking sizes of PDF files under ?inst/doc? ... WARNING
   ?gs+qpdf? made some significant size reductions:
      compacted ?HE-examples.pdf? from 739Kb to 366Kb

and upon submission to CRAN, a message from maintainers:

On CRAN now: but again there were warnings about significant size
reductions in PDF compaction, which should really be fixed on your end.

however, I am unable to find what to do to fix this on my end. In my 
package directory,
I have the vignette sources all under vignettes/, with copies of the 
.pdf and .Rnw
under inst/doc for historical reasons. [Q: can I now safely delete the 
copies under
inst/doc ?]

inst/doc/
HE-examples.pdf
HE-examples.Rnw
vignettes/
HE-examples.pdf
HE-examples.Rnw
HE-examples.bib
fig/
...

I have qpdf installed:
 > Sys.which(Sys.getenv("R_QPDF", "qpdf"))
qpdf
"c:\\Rtools\\bin\\qpdf.exe"
 >

but, if I try to run it on the vignettes/HE-examples.pdf file, nothing 
happens:

 > 
tools::compactPDF("C:/Documents/workspace/heplots/vignettes/HE-examples.pdf")
 >

Since vignettes are re-built from sources and then installed into 
inst/doc, I don't see why
PDF compaction cannot be run as part of the build process. That is, if
R CMD check --as-cran detects a problem, shouldn't there be some option for
R CMD build that would run gs+qpdf to correct it?

The idea of vignettes for R packages is a good thing, but, this problem 
(and others with vignettes) discourages me from using vignettes in 
packages, a bad thing.

-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, Quantitative Methods
York University      Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele Street    Web:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA

On 21.04.2013 19:28, Michael Friendly wrote:
> [Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET]
>
> Each time I update my heplots package, I get warnings from R CMD check
> on R-Forge,
>
> * checking sizes of PDF files under ?inst/doc? ... WARNING
>    ?gs+qpdf? made some significant size reductions:
>       compacted ?HE-examples.pdf? from 739Kb to 366Kb
>
> and upon submission to CRAN, a message from maintainers:
>
> On CRAN now: but again there were warnings about significant size
> reductions in PDF compaction, which should really be fixed on your end.
>
> however, I am unable to find what to do to fix this on my end. In my
> package directory,
> I have the vignette sources all under vignettes/, with copies of the
> .pdf and .Rnw
> under inst/doc for historical reasons. [Q: can I now safely delete the
> copies under
> inst/doc ?]
>
> inst/doc/
> HE-examples.pdf
> HE-examples.Rnw
> vignettes/
> HE-examples.pdf
> HE-examples.Rnw
> HE-examples.bib
> fig/
> ...
>
> I have qpdf installed:
>  > Sys.which(Sys.getenv("R_QPDF", "qpdf"))
> qpdf
> "c:\\Rtools\\bin\\qpdf.exe"
>  >
>
> but, if I try to run it on the vignettes/HE-examples.pdf file, nothing
> happens:
>
>  >
>
tools::compactPDF("C:/Documents/workspace/heplots/vignettes/HE-examples.pdf")
>
>  >
>
> Since vignettes are re-built from sources and then installed into
> inst/doc, I don't see why
> PDF compaction cannot be run as part of the build process. That is, if
> R CMD check --as-cran detects a problem, shouldn't there be some option
for
> R CMD build that would run gs+qpdf to correct it?
Yes, see

R CMD build --help


that tells you

   --compact-vignettes=  try to compact PDF files under inst/doc:
                         "no" (default), "qpdf",
"gs", "gs+qpdf", "both"


Best,
Uwe Ligges

>
> The idea of vignettes for R packages is a good thing, but, this problem
> (and others with vignettes) discourages me from using vignettes in
> packages, a bad thing.
>

On 4/21/2013 1:28 PM, Michael Friendly wrote:
> [Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET]
>
> Each time I update my heplots package, I get warnings from R CMD check
> on R-Forge,
>
> * checking sizes of PDF files under ?inst/doc? ... WARNING
>    ?gs+qpdf? made some significant size reductions:
>       compacted ?HE-examples.pdf? from 739Kb to 366Kb
>
To follow up my own post, I did some more checking of whether/how to
compact PDFs on my own system.  My conclusion is that that I am unable
to comply with the request from CRAN maintainers, even though I would
like to.  Once again, I wonder why this cannot be handled on the CRAN
side automatically.

qpdf: running it from a cmd prompt (using the options from 
tools::compactPDF) doesn't do very much compression

C:\R\test>qpdf --stream-data=compress --object-streams=generate 
HE-examples.pdf
HE-examples-comp.pdf

C:\R\test>dir HE-examples*
04/22/2013  10:55 AM           699,191 HE-examples-comp.pdf
04/22/2013  10:28 AM           756,624 HE-examples.pdf

gs:  I have gs installed at C:\Program Files\gs\gs9.07\bin\gswin32.exe,
but the gs installer doesn't put itself on the path, so 
tools::compactPDF sees gs_cmd as empty:

 > gs_cmd = Sys.getenv("R_GSCMD", "")
[1] ""

so it can't run gs+qpdf.  OK, so I try to do it manually:

 > Sys.setenv(R_GSCMD = "C:/Program
Files/gs/gs9.07/bin/gswin32.exe")
 > setwd("test")
 >
 > tools::compactPDF("HE-examples.pdf")
 > tools::compactPDF("HE-examples.pdf",
gs_quality="ebook")

But this doesn't do anything, not even changing the timestamp on the 
file, because the file size doesn't change enough.

C:\R\test>dir HE-examples.pdf
04/22/2013  10:28 AM           756,624 HE-examples.pdf

-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, Quantitative Methods
York University      Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele Street    Web:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA