[R-pkg-devel] Some, but not all vignettes compressed

[Bryan Hanson]

I have a peculiar problem regarding vignette compaction. Package LearnPCA has 8 vignettes.  I am working on the devel branch with code at https://github.com/bryanhanson/LearnPCA/tree/devel.

The problem is that at CRAN and on win-builder they detect that 5/8 vignettes need to be compacted.  Locally however, 2/8 vignettes, not overlapping with the 5/8 identified at CRAN, are compacted during build.  When I try to compact manually, compactPDF() reports it is not necesssary.

I have looked at a related question by Ben Bolker (https://stat.ethz.ch/pipermail/r-package-devel/2020q4/006086.html) but that doesn't seem resolved.  I am already taking the steps listed in this question: https://stat.ethz.ch/pipermail/r-package-devel/2023q4/009831.html as well as several others.

Regarding versions, I get

gs --version
10.03.0

qpdf --version
qpdf version 11.9.0

Which seem to be the latest.  Note these were installed with HomeBrew but I think R ships with at its own version of qpdf:

Sys.which(Sys.getenv("R_QPDF", "qpdf"))
  /Library/Frameworks/R.framework/Resources/bin/qpdf 
"/Library/Frameworks/R.framework/Resources/bin/qpdf" 

I did not try the HomeBrew versions until I ran into trouble.

Here are the steps I am taking.  I am on MacOS 14.4.1, an M1 chip.

1. Build via a makefile, with this command:

R --no-init-file CMD build --resave-data --compact-vignettes=both $(PKG_NAME)

The build process reports:

* creating vignettes ... OK
* compacting vignettes and other PDF files
    compacted ‘Vig_01_Start_Here.pdf’ from 244Kb to 44Kb
    compacted ‘Vig_08_Notes.pdf’ from 239Kb to 38Kb     

Fine so far.

I also tried to force the path to gs:

export R_GSCMD="/opt/homebrew/bin/gs"; \
export GS_QUALITY="ebook"; \
R --no-init-file CMD build --resave-data --compact-vignettes=both $(PKG_NAME)

With the same result.  I did this because it seems R doesn't see my installation of GhostScript.

And I tried to force a path to both compacting services:

export R_GSCMD="/opt/homebrew/bin/gs"; \
export GS_QUALITY="ebook"; \
export R_QPDF="/opt/homebrew/bin/qpdf"; \
R --no-init-file CMD build --resave-data --compact-vignettes=both $(PKG_NAME)

With the same results.

2. Submit to win-builder (same result seen on actual CRAN submission).  The (partial) report is:

* checking sizes of PDF files under 'inst/doc' ... WARNING
  'gs+qpdf' made some significant size reductions:
     compacted 'Vig_02_Conceptual_Intro_PCA.pdf' from 432Kb to 143Kb
     compacted 'Vig_03_Step_By_Step_PCA.pdf' from 414Kb to 101Kb
     compacted 'Vig_04_Scores_Loadings.pdf' from 334Kb to 78Kb
     compacted 'Vig_06_Math_Behind_PCA.pdf' from 558Kb to 147Kb
     compacted 'Vig_07_Functions_PCA.pdf' from 381Kb to 90Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files,
  or build the source package with --compact-vignettes=both

Note that these are *different* vignettes than those compacted during build, so build seems to have missed some (?).

3. If I expand the tarball locally, point to the inst directory, and run

tools::compactPDF("doc", gs_quality = "ebook", gs_cmd = "/opt/homebrew/bin/gs", verbose = TRUE)

I get this:

qs_quality="ebook" : use_gs=TRUE, use_qpdf=TRUE
#{pdf}s = length(paths) = 8
- doc/Vig_01_Start_Here.pdf:    gs: res=0;  + qpdf: res=0; 
    ==> (new=49942)/(old=45101) = 1.10734 .. not worth using
- doc/Vig_02_Conceptual_Intro_PCA.pdf:    gs: res=0;  + qpdf: res=0; 
    ==> (new=1.00061e+07)/(old=442210) = 22.6275 .. not worth using
- doc/Vig_03_Step_By_Step_PCA.pdf:    gs: res=0;  + qpdf: res=0; 
    ==> (new=5.763e+06)/(old=423484) = 13.6085 .. not worth using
- doc/Vig_04_Scores_Loadings.pdf:    gs: res=0;  + qpdf: res=0; 
    ==> (new=5.41409e+06)/(old=341680) = 15.8455 .. not worth using
- doc/Vig_05_Visualizing_PCA_3D.pdf:    gs: res=0;  + qpdf: res=0; 
    ==> (new=1.23622e+07)/(old=692901) = 17.8412 .. not worth using
- doc/Vig_06_Math_Behind_PCA.pdf:    gs: res=0;  + qpdf: res=0; 
    ==> (new=816690)/(old=571493) = 1.42905 .. not worth using
- doc/Vig_07_Functions_PCA.pdf:    gs: res=0;  + qpdf: res=0; 
    ==> (new=1.36419e+06)/(old=389478) = 3.50262 .. not worth using
- doc/Vig_08_Notes.pdf:    gs: res=0;  + qpdf: res=0; 
    ==> (new=40919)/(old=38953) = 1.05047 .. not worth using

Any suggestions as to what is going on here and how to fix it?

sessionInfo():

R version 4.4.0 RC (2024-04-16 r86468)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.4.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Phoenix
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] foghorn_1.5.2    utf8_1.2.4       R6_2.5.1         rvest_1.0.4      magrittr_2.0.3  
 [6] rappdirs_0.3.3   glue_1.7.0       stringr_1.5.1    tibble_3.2.1     clisymbols_1.2.0
[11] pkgconfig_2.0.3  lifecycle_1.0.4  xml2_1.3.6       cli_3.6.2        fansi_1.0.6     
[16] vctrs_0.6.5      compiler_4.4.0   httr_1.4.7       tools_4.4.0      curl_5.2.1      
[21] pillar_1.9.0     httr2_1.0.1      rlang_1.1.3      crayon_1.5.2     stringi_1.8.3   
[26] selectr_0.4-2   


=============
Bryan A. Hanson
Prof. Emeritus, DePauw University
Chemistry & Biochemistry
hanson using depauw.edu
profbryanhanson using gmail.com
Nerdy blog: ChemoSpec.org
I’m at GMT -7 year round







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