can not install Bioconductor on R studio

Question

[mikysyc2016]

Hi all, I can not install Bioconductor on R. Please see below. And I try different method, or use Bioconductor Website command. All of them do not work.

install.packages("bioconductor") Installing package into ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘bioconductor’ is not available (for R version 3.4.4)

Answer 1

[Kevin Blighe]

Update 9th January 2019:

From Bioc 3.8 (I believe), the new way to install Bioconductor base packages is like this:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install()

Individual packages are then installed with:

BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))
BiocManager::install(c("DESeq2"))

et cetera

[source: https://bioconductor.org/install/]

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Old post:

Hello and good evening wherever you are,

Bioconductor is not a package. It is a consortium / environment that maintains many R packages.

When you run R, you can 'connect' to the Bioconductor 'server' with:

source("https://bioconductor.org/biocLite.R")

...or:

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

After that, running biocLite() will update many fundamental R packages to their latest versions.

Running biocLite() with a package name as parameter will search for and install that package. For example:

biocLite("gplots")
biocLite("MASS")

You can then load the package's function into R via:

library(gplots)

...or:

require(gplots)

Packages can also be installed via CRAN with the install.packages() function, but CRAN does not seem to maintain their R packages as well as Bioconductor. On many occasions, CRAN will say that a particular package for your version of R does not exist, when it may already exist via Bioconductor.

Remember that Bioconductor is just a consortium. There are people behind that consortium who work hard to keep packages updated.

Kevin

[mikysyc2016]

Hi, Thank you for your reply. I still can not run.

biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). installation path not writeable, unable to update packages: cluster, foreign, MASS, Matrix, nlme, survival

[shenwei356]

Please read the error log: installation path is not writeable.

Please check the path permission.