Closed vladsavelyev closed 6 years ago
Hmm, I started to have the same error in another unrelated project: https://travis-ci.org/umccr/umccrise/builds/380012172 Probably some R package was updated recently and causing this issue.
UPD: and also here https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897540
Hoping updating of variantannotation
https://github.com/bioconda/bioconda-recipes/pull/8942 will fix it.
UPD: Updating just variantannotation
requires updating of its dependencies, which ultimately requires updates for the whole bioconductor... and I'm not ready to do that manually for over a hundred packages :( So I'll just forget output conda, I guess
Thanks, we'll look into this. IRanges is a standard Bioconductor package and should install with conda cleanly. Maybe the bioconductor-iranges recipe needs some tweaking.
Guys, this PR was the source of the error: https://github.com/bioconda/bioconda-recipes/pull/8925#issuecomment-389606748
So need to either pin bioconductor-s4vectors<0.18
, or wait for CI to ok in my PR above, and risk to merge it. I'll let you know if either works.
The PR fixed that, and
conda update -y bioconductor-iranges
resolves the problem!
Closing the issue.
Hah, now having this:
Error: package or namespace load failed for ‘GenomicRanges’:
Function found when exporting methods from the namespace ‘XVector’ which is not S4 generic: ‘endoapply’
Error: package ‘GenomicRanges’ could not be loaded
Execution halted
Will play a bit more, bit It's likely we'd have to downgrade packages, after all.
Resolved that; just needed to
conda update -y bioconductor-genomicranges bioconductor-xvector
As well.
Now getting to this one:
Error: package or namespace load failed for 'bcbioRNASeq' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'DEGreport' 1.12.0 is being loaded, but >= 1.14 is required
Just updated bioconductor-degreport
(1.14 was already the latest on bioconda), and all works!
For reference, the conda issue with IRanges seems to be related to accidental PR merges of Bioconductor 3.7 packages. conda doesn't support Bioc 3.7 yet because it requires R 3.4.
Hey,
I've installed the package through conda on a linux machine, into a clean conda installation:
But when I load the library, it crashes with the following error:
Am I doing anything wrong?