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I am running into an error when I tried to run the following lines of code, the error at line 3:

1 from rpy2.robjects.packages import importr
2 base = importr('base')
3 base.source("http://www.bioconductor.org/biocLite.R")
4 biocinstaller = importr("BiocInstaller")
5 biocinstaller.biocLite("seqLogo")

rpy2.rinterface_lib.embedded.RRuntimeError: Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

How can I use BiocManager installer instead of biocLite and reflect that on my code? I couldn't find any documentation or source that talk about this error from within Python.

Thank you in advance

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  • $\begingroup$ you need upgrade your R base version. $\endgroup$
    – zorbax
    Commented Aug 28, 2020 at 10:44
  • $\begingroup$ Definitely recommend installation via Conda as @zorbax points out. This normal stuff for installing rpy2 As a word of warning further errors with rpy2 are also normal and as a general rule of thumb rpy2 is a nightmare. For R's ggplot2 via rpy2 is outdated and will not import the full funcationality of the ggplot2 into Python3. This is irregular given have important ggplot2 is as a graphing package. After my experience I would use subprocessing into R rather than deal with rpy2 again $\endgroup$
    – M__ ♦
    Commented Aug 28, 2020 at 12:59

1 Answer 1

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You're using an outdated version of R. You can use the R 4.0 from conda-forge channel, just create an environment with r-base and then install rpy2, the latest version compatible with R 4.0 is available through pip

conda create -n rpy2 -c conda-forge r-base
conda activate rpy2
pip install rpy2

Now you can use rpy2 with R 4.0 in your python code.

import rpy2.robjects as robjects
robjects.r('install.packages("BiocManager", '
           'repos="http://cran.r-project.org")')
robjects.r('BiocManager::install("seqLogo")')
robjects.r('library(seqLogo)')

Remember deactivate your env with conda deactivate.

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  • $\begingroup$ Thank you so much this work! but when I do the same thing for "GenomicAlignments" package I get error: raise embedded.RRuntimeError(_rinterface._geterrmessage()) rpy2.rinterface_lib.embedded.RRuntimeError: Error in (new("nonstandardGenericFunction", .Data = function (expr, envir = parent.frame(), : object 'GenomicAlignments' not found $\endgroup$
    – aBiologist
    Commented Aug 28, 2020 at 19:00
  • $\begingroup$ I can't replicate you error. I did robjects.r('BiocManager::install("GenomicAlignments")') and then robjects.r('library(GenomicAlignments)') and it works. $\endgroup$
    – zorbax
    Commented Aug 30, 2020 at 23:04
  • $\begingroup$ I am unable to do this for pcalg (cran.r-project.org/web/packages/pcalg/pcalg.pdf). Can I see a minimal working example? $\endgroup$
    – S_S
    Commented Oct 27, 2022 at 14:53

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