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?
You can use sessionInfo() to accomplish that.
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] graphics grDevices utils datasets stats grid methods base
other attached packages:
[1] ggplot2_0.9.0 reshape2_1.2.1 plyr_1.7.1
loaded via a namespace (and not attached):
[1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 MASS_7.3-18 memoise_0.1 munsell_0.3
[7] proto_0.3-9.2 RColorBrewer_1.0-5 scales_0.2.0 stringr_0.6
>
However, as per comments and the answer below, there are better options
> packageVersion("snow")
[1] ‘0.3.9’
Or:
"Rmpi" %in% loadedNamespaces()
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
To check the version of R execute : R --version
Or after you are in the R shell print the contents of version$version.string
EDIT
To check the version of installed packages do the following.
After loading the library, you can execute sessionInfo ()
But to know the list of all installed packages:
packinfo <- installed.packages(fields = c("Package", "Version"))
packinfo[,c("Package", "Version")]
OR to extract a specific library version, once you have extracted the information using the installed.package function as above just use the name of the package in the first dimension of the matrix.
packinfo["RANN",c("Package", "Version")]
packinfo["graphics",c("Package", "Version")]
The above will print the versions of the RANN library and the graphics library.
You can try something like this:
package_version(R.version)getRversion()
Technically speaking, all of the answers at this time are wrong. packageVersion does not return the version of the loaded package. It goes to the disk, and fetches the package version from there.
This will not make a difference in most cases, but sometimes it does. As far as I can tell, the only way to get the version of a loaded package is the rather hackish:
asNamespace(pkg)$`.__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)
GUI solution:
If you are using RStudio then you can check the package version in the Packages pane.
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"))
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"
Simply use help(package="my_package") and look at the version shown.
This assumes there are no other package versions in the same .libPaths.
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"
来源：https://stackoverflow.com/questions/11103189/how-to-find-out-which-package-version-is-loaded-in-r