Error When Using biocLite as an installer with rpy2 python library
0
0
Entering edit mode
3.9 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 • 1.2k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1861 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6