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?
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syrup16g_TO •
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what happens when you enter http://www.bioconductor.org/packages/2.12/bioc/src/contrib/PACKAGES into a web browser?
thank you for your reply.
I entered the URL into a web browser (firefox), and I got 404 error "Server not found".
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.fileand the high-scoring answersthanks 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.
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")"
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)
Did you read this thread on bioconductor mailing list ?
many thanks to your replying. I read the thread, and I did processes described above.
thank you for your kindful helping.
Hello syrup16g_TO!
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