Hello, I'm seeing three different vignette-related errors with recent versions of R-3.0.0 alpha.
First, with the package BitSeq (http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get the following when trying to build the package: Error: processing vignette ’BitSeq.Rnw' failed with diagnostics: Failed to locate the ‘weave’ output file (by engine ‘utils::Sweave’) for vignette with name ‘BitSeq’. The following files exists in directory ‘.’: ‘data-C0.est’, ‘data-C1.est’, ‘data-c0b0.prob’, ‘data-c0b0.rpkm’, ‘data-c0b0.sam’, ‘data-c0b0.thetaMeans’, ‘data-c0b1.rpkm’, ‘data-c1b0.rpkm’, ‘data-c1b1.rpkm’, ‘data.estVar’, ‘data.means’, ‘data.par’, ‘data.pplr’, ‘data.tr’, ‘ensSelect1.fasta’, ‘ensSelect1.tr’, ‘parameters1.txt’ Execution halted My guess is it's looking for BitSeq.tex, but it's not clear where it's looking; the package is pretty straightforward, inst/doc contains BitSeq.Rnw and nothing else (no Makefile). Next, the package ppiData whose source is here: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ppiData (login: readonly password: readonly) As you can see, there is no .tex file in the source of the package, but after running R CMD build on it, the resulting .tar.gz file contains ppiData/inst/doc/ppiData.tex Then the package fails check (excerpt of ppiData.Rcheck/00install.out): Error in vignette_type(Outfile) : Vignette product ‘ppiData.tex’ does not have a known filename extension (‘NA’) ERROR: installing vignettes failed * removing ‘/home/biocbuild/bbs-2.12-data-experiment/meat/ppiData.Rcheck/ppiData’ This package does not have a vignette Makefile either, so I'm not sure why the tex file is included in the .tar.gz. These two errors are with: > sessionInfo() R version 3.0.0 alpha (2013-03-09 r62188) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base I also get another error on windows only ( it builds successfully on Mac and Linux) when trying to build bumphunter http://bioconductor.org/packages/2.12/bioc/html/bumphunter.html Warning: running command '"C:\PROGRA˜2\MIKTEX˜1.9\miktex\bin\texi2dvi.exe" --quiet --pdf "bumphunter.tex" -I "E:/biocbld/bbs-2.12-bioc/R/share/texmf/tex/latex" -I "E:/biocbld/bbs-2.12-bioc/R/share/texmf/bibtex/bst"' had status 1 Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'bumphunter'. The following files exists in directory '.': 'bumphunter-clusterplot.pdf', 'bumphunter-plotSegments.pdf', 'bumphunter.Rnw', 'bumphunter.bib', 'bumphunter.tex' Calls: <Anonymous> -> find_vignette_product Execution halted I guess it's looking for bumphunter.pdf. This is with: > sessionInfo() R version 3.0.0 alpha (2013-03-09 r62188) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base thanks, Dan ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
