Question: (Closed) Installing Bioconductor On Centos6
0
gravatar for syrup16g_TO
5.8 years ago by
syrup16g_TO40
Japan
syrup16g_TO40 wrote:

I'm new to bioinformatics and R.

I have trouble in installing Bioconductor on CentOS6.4.

R version :

R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit)

Error message :

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

Installing package into ‘/home/okuno/R/x86_64-redhat-linux-gnu-library/3.0’ (as ‘lib’ is unspecified) Warning: unable to access index for repository http://www.bioconductor.org/packages/2.12/bioc/src/contrib 'biocLite.R' failed to install 'BiocInstaller', use 'install.packages("BiocInstaller", repos="http://www.bioconductor.org/packages/2.12/bioc")' Warning message : package ‘BiocInstaller’ is not available (for R version 3.0.1)

I have another machine with Windows7OS in the same network, and I could install Bioconductor on the Windows machine. However, I can't do that on CensOS6 machine.

What am I doing wrong?

bioconductor • 2.7k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 5.8 years ago by syrup16g_TO40

what happens when you enter http://www.bioconductor.org/packages/2.12/bioc/src/contrib/PACKAGES into a web browser?

ADD REPLYlink written 5.8 years ago by Martin Morgan1.6k

thank you for your reply.

I entered the URL into a web browser (firefox), and I got 404 error "Server not found".

ADD REPLYlink written 5.8 years ago by syrup16g_TO40

This means that you're not able to reach www.bioconductor.org in your web browser? Then there is something wrong with the some aspect of your computer name server (DNS) configuration or you require use of a proxy; time to speak with a local system administrator guru. For proxy settings, see the help page ?download.file and the high-scoring answers

ADD REPLYlink written 5.8 years ago by Martin Morgan1.6k

thanks a lot! I successed installing bioconductor by DNS configulation using the reference URL.

I did 1.DNS configulation 2.download biocLite.R 3.changing mirror www.bioconductor.org > bioconductor.org

thank you for your kindful helping.

ADD REPLYlink written 5.7 years ago by syrup16g_TO40

did you try as the error message says ? "failed to install 'BiocInstaller',"

"use 'install.packages("BiocInstaller", repos="http://www.bioconductor.org/packages/2.12/bioc")"

ADD REPLYlink written 5.8 years ago by Sudeep1.6k

thank you for your replying.

Yes, I tried it. However I got an error message.

Installing package into ‘~/R/x86_64-redhat-linux-gnu-library/3.0’ (as ‘lib’ is unspecified) Warning: unable to access index for repository http://www.bioconductor.org/packages/2.12/bioc/src/contrib Warning message: package ‘BiocInstaller’ is not available (for R version 3.0.1)

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by syrup16g_TO40

Did you read this thread on bioconductor mailing list ?

ADD REPLYlink written 5.8 years ago by Sudeep1.6k

many thanks to your replying. I read the thread, and I did processes described above.

thank you for your kindful helping.

ADD REPLYlink written 5.7 years ago by syrup16g_TO40

Hello syrup16g_TO!

We believe that this post does is no longer relevant.

This problem might be resolved in the meantime. For questions regarding Bioconductor, you can use its own QA support.bioconductor.org

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Michael Dondrup46k
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1533 users visited in the last hour