Hi Leo, Martin, it looks like this is related to an issue with the remotes package: https://github.com/r-lib/remotes/issues/296 <https://github.com/r-lib/remotes/issues/296>. It gets the installation order wrong, and tries to install source packages before binaries. This can be a problem with GenomeInfoDbData (which I think doesn’t have a binary, and which it looks like Leo is installing manually). The TxDb package also doesn’t seem to be available as a binary package, and currently the source package for tibble is newer than the Windows binary.
According to the issue above, it should have been fixed in remotes v2.1.1 (https://github.com/r-lib/remotes/commit/88f302fe53864e4f27fc7b3897718fea9a8b1fa9 <https://github.com/r-lib/remotes/commit/88f302fe53864e4f27fc7b3897718fea9a8b1fa9>). To try things out, I set up a minimal package with the only dependency being TxDb.Hsapiens.UCSC.hg19.knownGene (https://github.com/csoneson/testpkg <https://github.com/csoneson/testpkg>), and checked it with GitHub Actions on macOS and Windows. It fails in both cases, since it’s trying to install TxDb.Hsapiens.UCSC.hg19.knownGene first (e.g. https://github.com/csoneson/testpkg/runs/619407291?check_suite_focus=true#step:7:533 <https://github.com/csoneson/testpkg/runs/619407291?check_suite_focus=true#step:7:533>). If I depend instead on GenomicFeatures, everything builds fine (here we have a binary). It is using remotes v2.1.1 though, so perhaps this needs to be investigated further. Charlotte > On 25 Apr 2020, at 22:20, Martin Morgan <mtmorgan.b...@gmail.com> wrote: > > tibble is not a direct dependency of TxDb*. > >> db = available.packages(repos = BiocManager::repositories()) >> deps = tools::package_dependencies("TxDb.Hsapiens.UCSC.hg19.knownGene", db) >> deps > $TxDb.Hsapiens.UCSC.hg19.knownGene > [1] "GenomicFeatures" "AnnotationDbi" > > but it is an indirect dependency > >> deps = tools::package_dependencies("TxDb.Hsapiens.UCSC.hg19.knownGene", db, >> recursive=TRUE) >> "tibble" %in% unlist(deps) > [1] TRUE > > I did > > deps1 = tools::package_dependencies("TxDb.Hsapiens.UCSC.hg19.knownGene", db, > recursive=TRUE) > > deps2 = tools::package_dependencies("tibble", db, recursive=TRUE, > reverse=TRUE) > > intersect(unlist(deps1), unlist(deps2)) > ## [1] "GenomicFeatures" "biomaRt" "BiocFileCache" "dbplyr" > ## [5] "dplyr" > > I believe R checks for immediate dependencies, found all for TxDb* and > GenomicFeatures available, and didn’t check further. I speculate that you > removed tibble, or installed one of the packages in the above list, without > satisfying the dependencies for that package. Or perhaps what the message is > really trying to say is that it failed to load tibble (because it was > installed in a previous version of the R toolchain?) > > It would be interesting to debug this further on your system, to understand > the problem for other users. > > Martin > > On 4/25/20, 2:48 PM, "Bioc-devel on behalf of Leonardo Collado Torres" > <bioc-devel-boun...@r-project.org on behalf of lcollado...@gmail.com> wrote: > > Hi Bioc-devel, > > I think that there's a potential issue with either GenomicFeatures, > TxDb.Hsapiens.UCSC.hg19.knownGene or an upstream package. > > > On a fresh R 4.0 Windows installation with BioC 3.11, I get the > following error message when installing > TxDb.Hsapiens.UCSC.hg19.knownGene as shown at > > https://github.com/leekgroup/derfinderPlot/runs/618370463?check_suite_focus=true#step:13:1225. > > > 2020-04-25T18:32:26.0765748Z * installing *source* package > 'TxDb.Hsapiens.UCSC.hg19.knownGene' ... > 2020-04-25T18:32:26.0769789Z ** using staged installation > 2020-04-25T18:32:26.1001400Z ** R > 2020-04-25T18:32:26.1044734Z ** inst > 2020-04-25T18:32:26.2061605Z ** byte-compile and prepare package for > lazy loading > 2020-04-25T18:32:30.7296724Z ##[error]Error: package or namespace load > failed for 'GenomicFeatures' in loadNamespace(i, c(lib.loc, > .libPaths()), versionCheck = vI[[i]]): > 2020-04-25T18:32:30.7305615Z ERROR: lazy loading failed for package > 'TxDb.Hsapiens.UCSC.hg19.knownGene' > 2020-04-25T18:32:30.7306686Z * removing > 'D:/a/_temp/Library/TxDb.Hsapiens.UCSC.hg19.knownGene' > 2020-04-25T18:32:30.7307196Z there is no package called 'tibble' > 2020-04-25T18:32:30.7310561Z ##[error]Error: package 'GenomicFeatures' > could not be loaded > 2020-04-25T18:32:30.7311805Z Execution halted > > From looking at the bioc-devel landing pages for both GenomicFeatures > and TxDb.Hsapiens.UCSC.hg19.knownGene, I see that tibble is not listed > as a dependency for either package. > > Best, > Leo > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
