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 han...@depauw.edu profbryanhan...@gmail.com Nerdy blog: ChemoSpec.org I’m at GMT -7 year round [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
