Error When Using biocLite as an installer with rpy2 python library

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4.3 years ago

BioICoder ▴ 40

Hi All,

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

python3 python R rpy2 • 1.3k views

ADD COMMENT • link updated 4.3 years ago by Ram 44k • written 4.3 years ago by BioICoder ▴ 40

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source('biocLite.R') is deprecated. You need to load use (the equivalent of) BiocManager::install('seqLogo') now

ADD REPLY • link 4.3 years ago by Ram 44k

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@RamRS How would you change that in the code above?

ADD REPLY • link 4.3 years ago by BioICoder ▴ 40

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I don't know rpy2. I've given you the pointer, you should be able to get to the solution using that.

ADD REPLY • link 4.3 years ago by Ram 44k

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