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Question: Impossible to use goseq package - problem with geneLenDataBase
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gravatar for amyfm
2.1 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:

1: running command '"C:/R/R-32~1.2/bin/i386/R" CMD INSTALL -l "C:\R\R-3.2.2\library" C:\Users\Cristina\AppData\Local\Temp\RtmpsfFYq5/downloaded_packages/geneLenDataBase_1.6.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneLenDataBase’ had non-zero exit status
3: running command '"C:/R/R-32~1.2/bin/i386/R" CMD INSTALL -l "C:\R\R-3.2.2\library" C:\Users\Cristina\AppData\Local\Temp\RtmpsfFYq5/downloaded_packages/GO.db_3.2.2.tar.gz' had status 1 
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

ADD COMMENTlink modified 2.1 years ago by Martin Morgan ♦♦ 20k • written 2.1 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.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Jakub30

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.

ADD REPLYlink written 2.1 years ago by Martin Morgan ♦♦ 20k

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.

ADD REPLYlink written 2.1 years ago by Martin Morgan ♦♦ 20k

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

ADD REPLYlink written 2.1 years ago by amyfm0
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