Impossible to use goseq package - problem with geneLenDataBase
0
0
Entering edit mode
amyfm ▴ 10
@amyfm-9084
Last seen 5.5 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:

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

goseq geneLenDataBase bioclite rstudio • 2.1k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 195 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