Impossible to use goseq package - problem with geneLenDataBase
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amyfm ▴ 10
@amyfm-9084
Last seen 5.8 years ago
Ireland

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

goseq geneLenDataBase bioclite rstudio • 2.2k views
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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.

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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.

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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.

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I don't know what I did but I fixed it! I started to have more problems so I reinstalled everything and now it seems to work. My problem now is how to do the analysis, I have published other post asking about it because I am lost, thank you very much