Hi. I can reproduce 2 out of the 3 cases on R version 3.0.0 alpha (2013-03-12 r62224) [Platform: x86_64-w64-mingw32/x64 (64-bit)]. The error does not appear to be in the R vignette machinery but rather in the vignettes themselves (or the packages they're using). Comments below.
On Wed, Mar 13, 2013 at 1:16 PM, Henrik Bengtsson <h...@biostat.ucsf.edu> wrote: > Hi, > > I contributed code to R r62130 which may be responsible for that (not > sure). I'll investigate as soon as got the time. > > /Henrik > > On Wed, Mar 13, 2013 at 10:17 AM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: >> Hello, >> >> I'm seeing three different vignette-related errors with recent >> versions of R-3.0.0 alpha. >> ############################################# # Case #1: BitSeq ############################################# >> 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). >> I failed to reproduce this when running the vignette manually; > setwd("BitSeq/inst/doc/") > Sweave("BitSeq.Rnw") > tools:::find_vignette_product("BitSeq", by="weave") [1] "BitSeq.tex" However, when I look for the files listed in your error message I don't find them in ".", but I do find them in system.file("extdata",package="BitSeq"). Inspecting 'BitSeq.Rnw', I find # move to directory with the data setwd(system.file("extdata",package="BitSeq")); and at the very end # restore the original working directory setwd(old_directory); My guess is that in your case there's an error occurring during Sweave resulting in the current directory being incorrect upon return. This causes the tools:::find_vignette_product() assertion following immediately after to look in the incorrect directory. [ It should be easy to update the R vignette mechanism such that this check for the vignette output is done in the proper directory regardless whether the vignette changes the current working directory or not. ] ############################################# # Case #2: ppiData ############################################# >> 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. Building the vignette manually, I get: > setwd("ppiData/inst/doc/") > Sweave("ppiData.Rnw") Writing to file ppiData.tex Processing code chunks with options ... [...] Loading required package: lattice 2 : echo keep.source term verbatim (label = collectData, ppiData.Rnw:79) Error: chunk 2 (label = collectData) Error in as.list.default(org.Sc.sgdCOMMON2ORF) : no method for coercing this S4 class to a vector Enter a frame number, or 0 to exit 1: Sweave("ppiData.Rnw") 2: driver$runcode(drobj, chunk, chunkopts) 3: RweaveTryStop(err, options) Selection: So, that appears to be the root of the problem. The "Error in vignette_type(Outfile) : Vignette product 'ppiData.tex' does not have a known filename extension ('NA')" occurs after R has temporarily built the package and then tries to install it. It fails to pick up the above Sweave() error during the build process because Sweave() leaves an (incomplete) 'ppiData.tex' file behind the R vignette machinery believes it was successful and keeps going. [ I don't know enough of the inner details of Sweave() and how it's exception handling works, but hopefully it's possible to detect the Sweave error and give a more informative error message earlier on. ] >> >> 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 >> >> ############################################# # Case #3: bumphunter ############################################# >> 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. Yes. The error message occurs as part of an assertion test immediately after running texi2pdf() on the Sweave generated 'bumphunter.tex' file. So, the error message is correct and it occurs as soon as possible. [ I'll see if we could also pick up and report on the (below) warning message produced my 'texi2pdf', because that would help the troubleshooting on the user end. ] I can reproduce this on Windows (session details above), also when building the vignette manually: > setwd("bumphunter/vignettes/") > Sweave("bumphunter.Rnw") # successful [...] > tools::texi2pdf("bumphunter.tex") Warning message: running command '"C:\PROGRA~2\MIKTEX~1.9\miktex\bin\texi2dvi.exe" --quiet --pdf "bumphunter.tex" -I "C:/PROGRA~1/R/R-3.0.0alpha/share/texmf/tex/latex" -I "C:/PROGRA~1/R/R-3.0.0alpha/share/texmf/bibtex/bst"' had status 1 It turns out that the 'bumphunter.tex' file has an active file lock that prevents texi2dvi.exe from compiling the file, e.g. fileLocked <- function(file) { fileT <- sprintf("%s.tmp", file) ok <- file.rename(file, fileT) file.rename(fileT[ok], file[ok]) names(ok) <- file !ok } > files <- list.files() > files <- files[file_test("-f", files)] > fileLocked(files) bumphunter-clusterplot.pdf bumphunter-plotSegments.pdf FALSE FALSE bumphunter.Rnw bumphunter.tex FALSE TRUE So, there is something that holds on to this file. My guess it has to do with the parallel computations via socket connections, e.g. > showConnections() description class mode text isopen can read 5 "<-hb-x201:11372" "sockconn" "a+b" "binary" "opened" "yes" 6 "<-hb-x201:11372" "sockconn" "a+b" "binary" "opened" "yes" 7 "<-hb-x201:11372" "sockconn" "a+b" "binary" "opened" "yes" can write 5 "yes" 6 "yes" 7 "yes" Sure enough, doing: > closeAllConnections() > tools::texi2pdf("bumphunter.tex") Now texi2dvi runs and it produces a PDF (though there is some bibtex error, but that's a different story). Hope this helps /Henrik >> >> 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 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
