Question

Error in upgrading bioconductor

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laksharikrish • 0

@laksharikrish-9680

Last seen 6.5 years ago

I need to work with edgeR and im trying to upgrade Bioconductor but im getting the error

1. source("http://bioconductor.org/biocLite.R")

Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help

2. biocLite("BiocUpgrade")

Error: Bioconductor version 3.2 cannot be upgraded with R version 3.2.2

Which version of R need to be installed? Could anyone help.

bioconductor biocupgrade • 1.7k views

ADD COMMENT • link updated 8.2 years ago by Martin Morgan 25k • written 8.2 years ago by laksharikrish • 0

Martin Morgan · Answer 1 · 2016-02-08

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 day ago

United States

You should use the 'Ask Question' link to ask questions. The 'Tutorials' link is for people who have generated a tutorial, not those looking for a tutorial.

If you want to work with edgeR, you need to do

library(BiocInstaller)

biocLite("edgeR")

There is no need to upgrade, as you are using the current versions of R and Bioconductor.

ADD COMMENT • link 8.2 years ago James W. MacDonald 65k

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Firstly sorry for posting in the wrong place.

But when I try to do biocLite("edgeR"). I get many fatal errors like

base.h:28:15: fatal error: S.h: No such file or directory
compilation terminated.
/usr/lib64/R/etc/Makeconf:134: recipe for target 'corStruct.o' failed
make: *** [corStruct.o] Error 1
ERROR: compilation failed for package ‘nlme’

Are there any additional packages need to be installed?

ADD REPLY • link updated 8.2 years ago by Martin Morgan 25k • written 8.2 years ago by laksharikrish • 0

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You seem to have edited something, as the email I got is different than what I see above. Anyway, in the email you have this:

Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar

Which implies that you are missing the headers required to build R packages from source. How you install that is dependent on your distro, and whether or not you have sudo privileges. On an RPM based system (Red Hat, for example) you would do

sudo yum install R-core-devel

On a Debian style distro (Debian, Ubuntu, etc) you would instead do

sudo apt-get install r-base-dev

If you don't have sudo privileges, you need to ask your sysadmin to do that for you.