I am in a process of figuring out how to use my university cluster. It has 2 versions of R installed. System wide R 2.11 (Debian 6.0) and R 2.14.2 in non-standard location.
I am trying to use MPI together with snow. The code I am trying to run is the following
library(snow)
library(Rmpi)
cl <- makeMPIcluster(mpi.universe.size()-1)
stopCluster(cl)
mpi.quit()
It works without the problems on R 2.11. (I launch the script with mpirun -H localhost,n1,n2,n3,n4 -n 1 R --slave -f code.R
). Now when I try to do it with R 2.14.2, I get the following message:
Error: This is R 2.11.1, package 'snow' needs >= 2.12.1
In addition: Warning message:
So it seems that R loads the package snow version compiled for R 2.11. I've installed snow under R 2.14 into my home folder and I added the following lines to my code:
.libPaths("/soft/R/lib/R/library")
.libPaths("~/R/x86_64-pc-linux-gnu-library/2.11")
print(.libPaths())
print(sessionInfo())
print(version)
And the output before the error confirms that I am indeed running R 2.14.2 and my R packages folder is first in search path. But I still get the error.
So my question is how do I determine which version of package is loaded in R? I can see with installed.packages
all the packages which are installed, so maybe there is some function which lists similar information for loaded packages?
Use the R method packageDescription
to get the installed package description and for version just use $Version
as:
packageDescription("AppliedPredictiveModeling")$Version
[1] "1.1-6"
Use the following code to obtain the version of R packages installed in the system:
installed.packages(fields = c ("Package", "Version"))
You can try something like this:
package_version(R.version)
getRversion()
To check the version of R execute : R --version
Or after you are in the R shell print the contents of version$version.string
EDIT
To check the version of installed packages do the following.
After loading the library, you can execute sessionInfo ()
But to know the list of all installed packages:
packinfo <- installed.packages(fields = c("Package", "Version"))
packinfo[,c("Package", "Version")]
OR to extract a specific library version, once you have extracted the information using the installed.package
function as above just use the name of the package in the first dimension of the matrix.
packinfo["RANN",c("Package", "Version")]
packinfo["graphics",c("Package", "Version")]
The above will print the versions of the RANN library and the graphics library.
Based on the previous answers, here is a simple alternative way of printing the R-version, followed by the name and version of each package loaded in the namespace. It works in the Jupyter notebook, where I had troubles running sessionInfo()
and R --version
.
print(paste("R", getRversion()))
print("-------------")
for (package_name in sort(loadedNamespaces())) {
print(paste(package_name, packageVersion(package_name)))
}
Out:
[1] "R 3.2.2"
[1] "-------------"
[1] "AnnotationDbi 1.32.2"
[1] "Biobase 2.30.0"
[1] "BiocGenerics 0.16.1"
[1] "BiocParallel 1.4.3"
[1] "DBI 0.3.1"
[1] "DESeq2 1.10.0"
[1] "Formula 1.2.1"
[1] "GenomeInfoDb 1.6.1"
[1] "GenomicRanges 1.22.3"
[1] "Hmisc 3.17.0"
[1] "IRanges 2.4.6"
[1] "IRdisplay 0.3"
[1] "IRkernel 0.5"
Search() can give a more simplified list of the attached packages in a session (i.e., without the detailed info given by sessionInfo())
search {base}- R Documentation
Description: Gives a list of attached packages. Search()
search()
#[1] ".GlobalEnv" "package:Rfacebook" "package:httpuv"
#"package:rjson"
#[5] "package:httr" "package:bindrcpp" "package:forcats" #
#"package:stringr"
#[9] "package:dplyr" "package:purrr" "package:readr"
#"package:tidyr"
#[13] "package:tibble" "package:ggplot2" "package:tidyverse"
#"tools:rstudio"
#[17] "package:stats" "package:graphics" "package:grDevices"
#"package:utils"
#[21] "package:datasets" "package:methods" "Autoloads"
#"package:base"
Old question, but not among the answers is my favorite command to get a quick and short overview of all loaded packages:
(.packages())
To see which version is installed of all loaded packages, just use the above command to subset installed.packages()
.
installed.packages()[(.packages()),3]
By changing the column number (3 for package version) you can get any other information stored in installed.packages()
in an easy-to-read matrix. Below is an example for version number and dependency:
installed.packages()[(.packages()),c(3,5)]
Technically speaking, all of the answers at this time are wrong. packageVersion
does not return the version of the loaded package. It goes to the disk, and fetches the package version from there.
This will not make a difference in most cases, but sometimes it does. As far as I can tell, the only way to get the version of a loaded package is the rather hackish:
asNamespace(pkg)$`.__NAMESPACE__.`$spec[["version"]]
where pkg
is the package name.
EDIT: I am not sure when this function was added, but you can also use getNamespaceVersion
, this is cleaner:
getNamespaceVersion(pkg)
You can use packageVersion
to see what version of a package is loaded
> packageVersion("snow")
[1] ‘0.3.9’
Although it sounds like you want to see what version of R you are running, in which case @Justin's sessionInfo
suggestion is the way to go
Simply use help(package="my_package")
and look at the version shown.
This assumes there are no other package versions in the same .libPaths
.
Source: Stackoverflow.com