(forwarding to R-devel) Prof. Ripley
Thanks a lot for the help. I greatly appreciate the clarification that R does indeed install the package during the build process. I must have been confused. The error is now fixed and was not related to my (false) claim that R could not locate a dataset in /data. You were not able to replicate the error because you were using the _build_ tarballs available from (I guess) http://bioconductor.org/packages/2.6/bioc/src/contrib/Genominator_1.1.3.tar.gz These tarballs are only put up, when the package passes R CMD build (naturally enough). The version of Genominator I had problems with was 1.1.4 which is only available from subversion (since it did not build when I wrote the email). 1.1.4 ought to be available in a few days when the build system picks up on the changes I just committed. I did mention that I saw that the package did not complete R CMD build, but (semi-passed) R CMD build --no-vignettes Genominator R CMD check Genominator_XXX.tar.gz I have no double checked this, see output below. I am using an R-devel that is a week old or so. What I do below is 1) check out the package from svn 2) R CMD build --no-vignettes 3) R CMD check on the tarball. Looks like it "passes" R CMD check with a warning about missing PDFs 4) verify that the source directory is empty by running svn status 5) R CMD build which fails (as it should) (Note the package - in this svn version - has errors in the vignette) I would have expected that R CMD check failed or at least told me that the vignettes do not build. Of course, given my earlier mistakes with this, I could be messing something up. Output below. Thanks as always, Kasper compute-0-19:~/Work/packages/temp/> echo $BIOCSVN https://hedgehog.fhcrc.org/gentleman/bioconductor/trunk/madman/Rpacks compute-0-19:~/Work/packages/temp/> svn co -r 44843 $BIOCSVN/Genominator <OUTOUR REMOVED> Checked out revision 44843. compute-0-19:~/Work/packages/temp/> R-devel CMD build --no-vignettes Genominator * checking for file 'Genominator/DESCRIPTION' ... OK * preparing 'Genominator': * checking DESCRIPTION meta-information ... OK * removing junk files * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'Genominator_1.1.4.tar.gz' compute-0-19:~/Work/packages/temp/> R-devel CMD check Genominator_1.1.4.tar.gz * checking for working pdflatex ... OK * using log directory '/home/bst/student/khansen/Work/packages/temp/Genominator.Rcheck' * using R version 2.11.0 Under development (unstable) (2010-02-15 r51142) * using session charset: ISO8859-15 * checking for file 'Genominator/DESCRIPTION' ... OK * this is package 'Genominator' version '1.1.4' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking for executable files ... OK * checking whether package 'Genominator' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the name space can be loaded with stated dependencies ... OK * checking whether the name space can be unloaded cleanly ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking data for non-ASCII characters ... OK * checking examples ... OK * checking tests ... OK * checking package vignettes in 'inst/doc' ... WARNING Package vignettes without corresponding PDF: /home/bst/student/khansen/Work/packages/temp/Genominator.Rcheck/00_pkg_src/Genominator/inst/doc/Genominator.Rnw /home/bst/student/khansen/Work/packages/temp/Genominator.Rcheck/00_pkg_src/Genominator/inst/doc/plotting.Rnw /home/bst/student/khansen/Work/packages/temp/Genominator.Rcheck/00_pkg_src/Genominator/inst/doc/withShortRead.Rnw * checking PDF version of manual ... OK WARNING: There was 1 warning, see /home/bst/student/khansen/Work/packages/temp/Genominator.Rcheck/00check.log for details compute-0-19:~/Work/packages/temp/> svn status Genominator compute-0-19:~/Work/packages/temp/> R-devel CMD build Genominator * checking for file 'Genominator/DESCRIPTION' ... OK * preparing 'Genominator': * checking DESCRIPTION meta-information ... OK * installing the package to re-build vignettes * installing *source* package 'Genominator' ... ** R ** data ** inst ** preparing package for lazy loading Loading required package: DBI Attaching package: 'IRanges' The following object(s) are masked from 'package:base': Map, cbind, mapply, order, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, table ** help *** installing help indices ** building package indices ... * DONE (Genominator) * creating vignettes ... ERROR Loading required package: RSQLite Loading required package: DBI Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from 'package:base': cbind, Map, mapply, order, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, table writing regions table: 0.026 sec SQL query: SELECT counts,feature FROM counts_tbl INNER JOIN __regions__ ON __regions__.chr = counts_tbl.chr AND counts_tbl.location BETWEEN __regions__.start AND __regions__.end AND (counts_tbl.strand = __regions__.strand OR __regions__.strand = 0 OR counts_tbl.strand = 0) fetching merge table: 0.027 sec splitting by: feature: 0.002 sec matplot: doing 1 plots with col= ("1") pch= ("1" "2" "3" "4" "5" "6" "7" "8" "9" "0" "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" "t" "u" "v" "w" "x" "y" "z" "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" "T" "U" "V" "W" "X" "Y" "Z") ... writing regions table: 0.025 sec SQL query: SELECT __regions__.id, TOTAL(counts) FROM __regions__ LEFT OUTER JOIN counts_tbl ON __regions__.chr = counts_tbl.chr AND counts_tbl.location BETWEEN __regions__.start AND __regions__.end AND (counts_tbl.strand = __regions__.strand OR __regions__.strand = 0 OR counts_tbl.strand = 0) GROUP BY __regions__.id ORDER BY __regions__.id fetching summary table: 0.044 sec fetching summary: 0.016 sec matplot: doing 1 plots with col= ("1") pch= ("1" "2" "3" "4" "5" "6" "7" "8" "9" "0" "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" "t" "u" "v" "w" "x" "y" "z" "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" "T" "U" "V" "W" "X" "Y" "Z") ... writing regions table: 0.026 sec SQL query: SELECT __regions__.id, TOTAL(counts_1), TOTAL(counts_2) FROM __regions__ LEFT OUTER JOIN allcounts ON __regions__.chr = allcounts.chr AND allcounts.location BETWEEN __regions__.start AND __regions__.end AND (allcounts.strand = __regions__.strand OR __regions__.strand = 0 OR allcounts.strand = 0) GROUP BY __regions__.id ORDER BY __regions__.id fetching summary table: 0.048 sec Loading required package: GenomeGraphs Loading required package: biomaRt Loading required package: grid Loading required package: ShortRead Loading required package: Biostrings Loading required package: BSgenome Loading required package: lattice Loading required package: yeastRNASeq Error: no function to return from, jumping to top level Execution halted Thanks again, Kasper 2010/2/26 Prof Brian Ripley <rip...@stats.ox.ac.uk>: > On Wed, 24 Feb 2010, Kasper Daniel Hansen wrote: > >> Based on some testing it seems to me that if I have a package with >> a dataset in /data >> a Sweave vignette in inst/doc (but no associated pdf file) >> the vignette loads the data in /data through >> data(dataset) >> and I do a >> R CMD build >> R will try to build the pdf version of the vignette, but will be >> unable to find the dataset in data because the package is not yet >> installed. However, if I do > > But R CMD build *does* install the package to build vignettes. If I take > the current BioC-2.6 version of Genominator (1.1.3), remove the > inst/doc/*.pdf and any installed versions I see > > gannet% Rdev CMD build Genominator > * checking for file 'Genominator/DESCRIPTION' ... OK > * preparing 'Genominator': > * checking DESCRIPTION meta-information ... OK > * installing the package to re-build vignettes > * installing *source* package ‘Genominator’ ... > ** R > ** data > ** inst > ** preparing package for lazy loading > Loading required package: DBI > Creating a new generic function for "head" in "Genominator" > ** help > *** installing help indices > ** building package indices ... > * DONE (Genominator) > * creating vignettes ... OK > * removing junk files > * checking for LF line-endings in source and make files > * checking for empty or unneeded directories > * building 'Genominator_1.1.3.tar.gz' > > (Well, once I had installed the 307Mb dependency yeastRNASeq.) > > Now, you may be using an unreleased version of Genominator, but your > hypothesis (that the package needs to be installed beforehand) is not > correct. > >> R CMD build --no-vignettes PKGNAME >> R CMD check PKGNAME_VERSION.tar.gz >> the package passes R CMD check! Presumably because R CMD check >> installs the package first. > > Yes, to a temporary library, just as R CMD build does if there are > vignettes. > >> This took me a long time to track down (inspired by a recent addition >> of dataset to the Bioconductor package Genominator and a subsequent >> failed build - specifically the dataset yeastAnno.sources and the >> vignette withShortRead.Rnw). I am using lazy loading (in case it >> matters, which I don't think it does). >> >> It seems like the relevant fix is to include pdf versions of the >> vignette(s) in inst/doc. >> >> On one hand I can see why the build fails. > > So given the evidence that R CMD build does install the package, please > explain. > >> And the fix is easy. But >> just thought I would mention it. >> >> Kasper >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
