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

[Martin Morgan]

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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