hbc / bcbioRNASeq

R package for bcbio RNA-seq analysis.
https://bioinformatics.sph.harvard.edu/bcbioRNASeq
GNU Affero General Public License v3.0
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Error: package or namespace load failed for ‘IRanges’ #100

Closed vladsavelyev closed 6 years ago

vladsavelyev commented 6 years ago

Hey,

I've installed the package through conda on a linux machine, into a clean conda installation:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p ./miniconda
export PATH=$(pwd)/miniconda/bin:$PATH
conda create -n bcbio_rnaseq -c bioconda r-bcbiornaseq -y
source activate bcbio_rnaseq

But when I load the library, it crashes with the following error:

R -e "library(bcbioRNASeq)"
...
Error: package or namespace load failed for ‘IRanges’:
 Functions found when exporting methods from the namespace ‘IRanges’ which are not S4 generic: ‘endoapply’, ‘mendoapply’
Execution halted

Am I doing anything wrong?

vladsavelyev commented 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

vladsavelyev commented 6 years ago

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

mjsteinbaugh commented 6 years ago

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.

vladsavelyev commented 6 years ago

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.

vladsavelyev commented 6 years ago

The PR fixed that, and

conda update -y bioconductor-iranges

resolves the problem!

Closing the issue.

vladsavelyev commented 6 years ago

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.

vladsavelyev commented 6 years ago

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
vladsavelyev commented 6 years ago

Just updated bioconductor-degreport (1.14 was already the latest on bioconda), and all works!

mjsteinbaugh commented 6 years ago

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.

https://github.com/bioconda/bioconda-recipes/issues/8947