Difference between revisions of "Installing R packages on Freebee"
(Created page with "If you for some reason can't install the necessary packages on your local computer you can try to use R on Freebee. Log on to freebee as normal and type: module load R/3.5.0...") |
(Tag: Visual edit) |
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Line 3: | Line 3: | ||
Log on to freebee as normal and type: | Log on to freebee as normal and type: | ||
− | module load R/3.5.0 | + | <code>module load R/3.5.0</code> |
To start R type: | To start R type: | ||
− | R | + | <code>R</code> |
Then just paste and run all these lines. It will take a long time (probably at least 30 min): | Then just paste and run all these lines. It will take a long time (probably at least 30 min): | ||
− | install.packages("pheatmap") | + | <code>install.packages("pheatmap")</code> |
− | |||
− | |||
− | |||
− | |||
− | |||
− | After it | + | <code>install.packages("repmis")</code> |
+ | |||
+ | <code>install.packages("reshape2")</code> | ||
+ | |||
+ | <code>install.packages("gplots")</code> | ||
+ | |||
+ | <code>install.packages("RColorBrewer")</code> | ||
+ | |||
+ | <code>install.packages("ggplot2")</code> | ||
+ | |||
+ | After it hast finished you can test the installation by <code>typing library(package_name</code>) | ||
If everything worked fine you can type: | If everything worked fine you can type: | ||
− | source("https://bioconductor.org/biocLite.R") | + | |
− | biocLite("DESeq2") | + | <code>source("https://bioconductor.org/biocLite.R")</code> |
+ | |||
+ | <code>biocLite("DESeq2")</code> | ||
This will also take probably 30 minutes. | This will also take probably 30 minutes. | ||
You might get a message after installing DESEq2 saying: | You might get a message after installing DESEq2 saying: | ||
− | installation path not writeable, unable to update packages: coda, doParallel, | + | installation path not writeable, unable to update packages: coda, doParallel,iterators, lme4, mvtnorm, nloptr, Rcpp, RcppEigen, Rmpi, snow, foreign, lattice, MASS, Matrix, mgcv, survival |
− | |||
− | |||
− | |||
This might not be a problem. Try: | This might not be a problem. Try: | ||
− | library(DESeq2) and if it loads without problems you should be fine. | + | |
+ | <code>library(DESeq2)</code> and if it loads without problems you should be fine. | ||
type quit() to exit R. You don't have to save workspace. | type quit() to exit R. You don't have to save workspace. |
Revision as of 21:16, 3 December 2018
If you for some reason can't install the necessary packages on your local computer you can try to use R on Freebee.
Log on to freebee as normal and type:
module load R/3.5.0
To start R type:
R
Then just paste and run all these lines. It will take a long time (probably at least 30 min):
install.packages("pheatmap")
install.packages("repmis")
install.packages("reshape2")
install.packages("gplots")
install.packages("RColorBrewer")
install.packages("ggplot2")
After it hast finished you can test the installation by typing library(package_name
)
If everything worked fine you can type:
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
This will also take probably 30 minutes.
You might get a message after installing DESEq2 saying:
installation path not writeable, unable to update packages: coda, doParallel,iterators, lme4, mvtnorm, nloptr, Rcpp, RcppEigen, Rmpi, snow, foreign, lattice, MASS, Matrix, mgcv, survival
This might not be a problem. Try:
library(DESeq2)
and if it loads without problems you should be fine.
type quit() to exit R. You don't have to save workspace.