Bioinformatics Asked by aBiologist on September 27, 2020
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
You're using an outdated version of R. You can use the R 4.0 from conda-forge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
.
Answered by zorbax on September 27, 2020
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