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