Hi everyone, Charlotte, thank you very much! I didn't know about that issue on `remotes` and the fix attempts. Thank you for the info Martin!
However, I have to report that it doesn't seem like switching from remotes::install_deps() to BiocManager::install() fixes the issue. I updated my GitHub Actions workflow to obtain the list of dependencies using remotes, but install them with BiocManager::install() instead of remotes::install_deps(). You can see this at https://github.com/leekgroup/derfinderPlot/blob/ea58939ac6bf13cae7d26951732914d96b5f7d07/.github/workflows/check-bioc.yml#L139-L149 although I include the relevant lines of code below: ## Locate the package dependencies deps <- remotes::dev_package_deps(dependencies = TRUE) ## Install any that need to be updated using BiocManager to avoid ## the issues described at ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html ## https://github.com/r-lib/remotes/issues/296 remotes::install_cran("BiocManager") BiocManager::install(deps$package[deps$diff != 0]) This still leads to TxDb.Hsapiens.UCSC.hg19.knownGene failing to install because GenomeInfoDbData is not available on both macOS and Windows (again, this doesn't fail on the Bioconductor devel docker). Here's for example the error on Windows https://github.com/leekgroup/derfinderPlot/runs/620055131?check_suite_focus=true#step:12:1077. Immediately after, GenomeInfoDbData does get installed https://github.com/leekgroup/derfinderPlot/runs/620055131?check_suite_focus=true#step:12:1100 and after it, tibble https://github.com/leekgroup/derfinderPlot/runs/620055131?check_suite_focus=true#step:12:1174. Likely this issue only happens on Windows and macOS because of the availability of some packages in source form and others in binary form, unlike only using source versions in the Bioconductor docker run. However, maybe I need some other code to get all the dependencies of a given package in a different order, though I was hoping that BiocManager::install() would find the right order for me as it seems to try to do so already. Charlotte linked to https://github.com/r-lib/remotes/commit/88f302fe53864e4f27fc7b3897718fea9a8b1fa9. So maybe there's still something else to try to fix in remotes and/or BiocManager instead of the DESCRIPTION files of other packages like I initially thought of in this thread and in https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016671.html. Best, Leo On Sun, Apr 26, 2020 at 10:30 AM Martin Morgan <mtmorgan.b...@gmail.com> wrote: > > 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> 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 > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
