bioconda-recipes: bioconductor-chromvar is broken

Hi,

The recently updated ‘bioconda-chromvar’ bioconda package doesn’t work any more. (Its R package works well so I suppose it has something to do with bioconda)

I’m attaching the R script and datasets here to reproduce the errors. https://www.dropbox.com/sh/ts3a6bjrija6qw7/AAD0ryO5qzXvcyO6NKMJQMera?dl=0

$ conda create -n chromvar_test python=3.6 $ conda activate chromvar_test $ conda install bioconductor-chromvar $ conda install bioconductor-bsgenome.hsapiens.ucsc.hg19 $ Rscript chromVAR.R

Several errors will be reported:

Error1 : libssl.so.1.0.0: cannot open shared object file: No such file or directory
It is caused by library mismatches between r-openssl and openssl Fixed by conda install openssl==1.0.2p

Error2: libgsl.so.19: cannot open shared object file: No such file or directory Fixed by conda install gsl=2.2.1

Error3: Error in library(BSgenome.Hsapiens.UCSC.hg19) : there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ It looks like conda install bioconductor-bsgenome.hsapiens.ucsc.hg19 doesn’t really work Fixed by installing ‘BSgenome.Hsapiens.UCSC.hg19’ within R $ R

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19", version = "3.8")

Error4: Segmentation fault This error happens at the step of ‘kmerdev <- computeDeviations(SE, KmerMatch)’ in R script We tracked down the dependency package 'r-nabor '. Fixed by installing ‘nabor’ within R $ R > install.packages("nabor")

I did my best but it seems beyond my capabilities to fix all the issues. I would be really grateful if you could help fix them. Many thanks!