Question: can not install Bioconductor on R studio
1
gravatar for mikysyc2016
9 months ago by
mikysyc201630
mikysyc201630 wrote:

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)

R • 923 views
ADD COMMENTlink modified 9 months ago by Kevin Blighe39k • written 9 months ago by mikysyc201630
4
gravatar for Kevin Blighe
9 months ago by
Kevin Blighe39k
Republic of Ireland
Kevin Blighe39k wrote:

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/]

-----------------------------------------------------------------

-----------------------------------------------------------------

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

ADD COMMENTlink modified 10 weeks ago • written 9 months ago by Kevin Blighe39k

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

ADD REPLYlink written 9 months ago by mikysyc201630

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

Please check the path permission.

ADD REPLYlink written 9 months ago by shenwei3564.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 764 users visited in the last hour