[Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Charlotte Soneson ch@r|otte@one@on @end|ng |rom gm@||@com
Sun Apr 26 11:32:12 CEST 2020

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.


> On 25 Apr 2020, at 22:20, Martin Morgan <mtmorgan.bioc using 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-bounces using r-project.org on behalf of lcolladotor using 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
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