Bioconductor version error

Languages R
1

@jeroen, @jimhester
Hi,
I am the maintainer of this scMerge package for Bioconductor. The issue that I am having is that Travis seems to be using Bioconductor version 3.8 rather than the newly released 3.9 (https://travis-ci.org/SydneyBioX/scMerge/jobs/529095216). This caused an installation error for a dependent BioC package M3Drop (scMerge requires M3Drop version >= 1.9.4).

I am unsure if this is a bug or not.

Thanks

1 Like
2

Looking through the code that generates download URLs suggests that ā€œ3.8ā€ comes from the R_BIOC_VERSION envvar.

According to https://bioconductor.org/install/, you can install the latest Bioconductor version with

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

Maybe itā€™s sufficient to set the envvar: the logic suggests that it may be calling the above code in any case.

3

I am being hit by this too for a package of mine: https://travis-ci.org/xrobin/xavamess/jobs/535684539

Did you manage to solve the issue?
I donā€™t set the R_BIOC_VERSION variable anywhere, nor do I install or load BiocManager anywhereā€¦ I assume thatā€™s done in a setup script?

4

I managed to get around this problem by writing up a short R script in the travis.yml file. But I think this is only a short-term patch. https://travis-ci.org/SydneyBioX/scMerge/builds/534666350/config

6
7

@LiNk-NY has stated that this was an upstream problem ā€“ they had an issue updating the BiocManager package at CRAN.

So this should be working now without any workarounds. You may need to clear your cache.

8

@native-api itā€™s working now, thanks a lot!
By the way I didnā€™t have to clean the cache - however I had done it previously, so not sure about it.