Thanks Charlotte for the detective work. Annotation packages (TxDb, org, BSgenome, and GenomeInfoDbData, for instance) are distributed only as source – this was a decision made quite a while (years) ago, to save disk space (some of these packages are large, and hosting macOS and Windows binaries in addition to source triple disk space requirements) and on the rationale that the packages do not have C-level source code so users do not need RTools or XCode (etc) to install from ‘source’. So in this context and in the face of a buggy remotes package, and installation of Bioconductor packages through non-standard approaches (BiocManager::install() for CRAN and Bioconductor packages and their dependencies use base R commands only) I guess the behavior you document is really an (ongoing?) bug in the remotes package?
Over the years the distribution of source-only annotation packages has caused problems, in particular when (usually Windows) users have temporary or library paths with spaces or non-ASCII characters. I believe that this upstream bug (in R’s handling of Windows paths) has been fixed in the 4.0.0 release, but the details are quite complicated and I have not been able to follow the discussion fully. Martin From: Charlotte Soneson <charlottesone...@gmail.com> Date: Sunday, April 26, 2020 at 5:32 AM To: Martin Morgan <mtmorgan.b...@gmail.com> Cc: Leonardo Collado Torres <lcollado...@gmail.com>, Bioc-devel <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble Hi Leo, Martin, it looks like this is related to an issue with the remotes package: 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). 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), 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). 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<mailto: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<mailto:bioc-devel-boun...@r-project.org> on behalf of lcollado...@gmail.com<mailto: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<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org<mailto: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
