Question: Impossible to use goseq package - problem with geneLenDataBase
0
3.5 years ago by
amyfm0
Ireland
amyfm0 wrote:

Hi,

I am trying to install goseq package in my R studio 3.2.2 doing the following:

source("https://bioconductor.org/biocLite.R")
biocLite("goseq")
library(goseq)


After that, I can't use the package because of a problem with geneLenDataBase. I keep receiving the following messages:

Warning messages:

2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘geneLenDataBase’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
installation of package ‘GO.db’ had non-zero exit status

And I also can't install the package separatedly with: biocLite("geneLenDataBase").It tells me it is not available for my R version, I have tried to do the same with an older R version but it happens the same.

Can anybody help me? thank you very much

modified 3.5 years ago by Martin Morgan ♦♦ 23k • written 3.5 years ago by amyfm0

Hi,

It looks like something went wrong during the installation.

Could you repeat the installation by staring RStudio as an administrator? I just did this with a clean R installation on windows and had no problems.

It is not a good idea to run any program as 'administrator', and it is not necessary to do so to use R and Bioconductor.

It looks like GO.db did not install correctly; try again just installing that package, biocLite("GO.db"). Edit your question to include the complete output of biocLite("GO.db") and post a comment letting us know you've updated the question.