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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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which version of R is needed for the installation of infercnv? 3.6.0 is the only version? #511

Open tingxie2020 opened 1 year ago

tingxie2020 commented 1 year ago

Hi, I have issue on install infercnv in R4.2.2, I tried BiocManager::install("infercnv"), it showed ERROR: dependencies ‘ape’, ‘phyclust’, ‘parallelDist’, ‘HiddenMarkov’, ‘edgeR’, ‘coin’, ‘rjags’ are not available for package ‘infercnv’ and I am not be able to install any of the dependencies.

I tried sudo docker pull trinityctat/infercnv:latest, but library(infercnv) it shows Error in library("infercnv") : there is no package called ‘infercnv’

Please help. Thanks

GeorgescuC commented 1 year ago

Hi @tingxie2020 ,

Before running the install command, have you tried updating BiocManager itself?

install.packages("BiocManager")

Are you able to install any of the mentioned libraries using install.packages("")?

For the docker image, that is surprising. Do you perhaps have an argument or option when running the image that sets your system's HOME directory as the one inside the image? Singularity does that by default and is the only instance where I encountered such an issue.

Regards, Christophe.