R is a free software environment for statistical computing and graphics.<\/p>\n
From 1st Aug 2024, the only nodes in the iCSF are the 2TB nodes, which received an operating system upgrade. Following this upgrade, some of the older versions of R (and Rstudio) may not run.<\/p>\n
We strongly encourage all users to move to the newer versions of R (see below), which have been built for the new operating system on the iCSF.<\/p>\n
If you only use the iCSF, you can skip this section<\/a>.<\/p>\n New users of the iCSF and CSF3 from June 2025, who run R on both systems, can also skip this section<\/a> (an extra modulefile was needed to fix a compatibility issue with iCSF and CSF3. But this is no longer an issue.)<\/p>\n If you’ve previous used the iCSF AND CSF3 to run R, before the CSF3 upgrade in Feb\/May 2025, you should continue to follow the original instructions below.<\/p>\n Prior to Feb 2025, the operating system on the iCSF nodes was newer than that on CSF3. So any packages you installed in to a “personal” library using So to prevent a package installed on the iCSF from polluting<\/em> your personal library on CSF3, you needed to load the following modulefile:<\/p>\n This will force any subsequent package installs performed on the iCSF into a separate But it does mean that if you install a package on the iCSF, it WON’T be visible to R on the CSF3. You’ll need to login to CSF3 and install it again, for use on CSF3.<\/p>\n In summary:<\/p>\n If you need further information about R packages installs on the iCSF and CSF3, please contact its-ri-team@manchester.ac.uk<\/a>.<\/p>\n Please see the Setup procedure<\/a> section below for the modulefile commands that will make a particular version available to your login session.<\/p>\n The following versions are installed on the iCSF:<\/p>\n These versions are for use on the iCSF nodes, following the operating system upgrade. You are strongly encouraged to begin using version 4.4.0 or newer.<\/strong><\/p>\n This release is missing libRlapack.so<\/em>, so it is unable to use Basic Linear Algebra Subprograms<\/a> (BLAS). This only applies to the optimised installation on iCSF.<\/li>\n Versions below here here may not run correctly on the upgraded iCSF nodes – please use a newer version (see above.) Note that the old incline256 nodes are no longer available (1st Aug 2024.)<\/strong><\/p>\n Bioconductor<\/a> is included in some of the central iCSF installations of R. Not all associated packages may be available, but you can install them to your own home directory using the Adding BioConductor Packages<\/a> instructions below, in conjunction with information from the bioconductor website.<\/p>\n Alternatively, we may be able to add them to the central install – contact its-ri-team@manchester.ac.uk<\/a> .<\/p>\n There are no restrictions on access to R as it is a free piece of software released under a GNU license. All users should familiarise themselves with the licensing information available via the R website<\/a>.<\/p>\n To access the executables please load an appropriate modulefile.<\/p>\n Note, if you wish to use Rstudio, load the R modulefile first, then please see the Rstudio page<\/a> for a list of available modulefiles.<\/p>\n The following versions were installed for the now-retired incline256 nodes. They may not run on the incline 2TB nodes (please try them.)<\/p>\n If you have problems running any of the following versions, please consider using one of the above newer versions. You’ll need to reinstall any R libraries you’ve installed.<\/p>\n Microsoft R Open with MKL (this is an old version, we recommend the open source versions above.)<\/p>\n Having loaded the appropriate modulefile, simply run:<\/p>\n PLEASE NOTE: If more than one R module file is loaded it will default to the version which has been loaded most recently.<\/p>\n You will now be at the R prompt.<\/p>\n To exit R, type:<\/p>\n To start the GUI, enter If you are using Microsoft Open R then please note that you do not have exclusive access to iCSF compute nodes so it is highly recommended that you set:<\/p>\n to avoid the software trying to use the whole node and interfering with other people’s work.<\/p>\n Packages that provide extra functionality can be added to R by allowing R to save them in to your iCSF home directory. Packages can be downloaded automatically by R (if it can find the package associated with the library you are requesting) or you can supply a source package for R to unpack and install. The download method is preferred. Follow the instructions below:<\/p>\n To add packages that will be downloaded by R from the CRAN (cran.r-project.org):<\/p>\n This problem does NOT occur in recent versions of R (e.g., 4.4.1.) If you do have a problem with R libraries not installing correctly, please read this section.<\/p>\n Some packages fail to install because they depend on the This problem does NOT occur in recent versions of R (e.g., 4.4.1.) If you do have a problem with R libraries not installing correctly, please read this section.<\/p>\n We’ve seen some R packages fail to install due to a failure in R to compile the The solution was to do the In the above instructions replace the If you’ve downloaded an R library source file you can add it to your local workspace using the following commands (which assume the source package is in your home directory on the iCSF):<\/p>\n Alternatively,<\/p>\n The compiled library files will be save in a directory named <\/a><\/p>\n Note: This is NOT the method used for older<\/em> versions of R (3.5 and older). See below for that.<\/p>\n The ‘manager’ for bioconductor has changed in version 3.6.0. Details are given here on how to install BioConductor packages in R 3.6.0 (and up). Please also check the BioConductor installation instructions<\/a> at their website for up-to-date version information.<\/p>\n See below<\/a> for how to then use (load) an installed BioConductor package.<\/p>\n Note: This is NOT the method used for newer versions of R (3.6 and newer). See above for that.<\/p>\n BioConductor packages or packages that rely on bioconductor packages can be installed in to your local R library (in your home directory) as follows (this example assumes use of R 3.2.0):<\/p>\n and when it asks if you want to use a personal library answer <\/a><\/p>\n BioConductor packages have to be loaded like any other package if you’ve previously installed them. For example, assuming you have installed a BioConductor package named To list the installed packages run:<\/p>\n To list loaded packages run:<\/p>\n <\/a><\/p>\n We advice using ‘renv’<\/strong> to install R packages that you need. The renv<\/strong> package helps you create conflict free reproducible environments for your R projects. Using renv you can maintain separate project folder with their own set of R packages and they will not conflict with other R packages in other renv project folders or R modules. This is somewhat similar to using conda virtual environments. Benefit of using renv includes:<\/p>\n The main steps involved are:<\/p>\n Here are the commands needed to perform the steps described above. That’s it, we’ve now created our first For running \/ using the packages installed in a ‘renv’ project folder, or to add more packages, you need to do the following:<\/p>\n You can then load and run your R package or R CMD SCRIPT.<\/p>\n To see the available graphics file formats support, run the The following example generates a histogram and plots it to a Now to view your images while on the iCSF, use the eye of gnome<\/em> ( If you need other image file formats you can then convert your PNG file using the Another example of plotting to file:<\/p>\n If you see the following error when using please try to use the For software documentation and FAQs please consult the R Project website<\/a>.<\/p>\n See also the Bioconductor website<\/a>.<\/p>\n September 2025 – v4.5.1 added Overview R is a free software environment for statistical computing and graphics. incline2000 From 1st Aug 2024, the only nodes in the iCSF are the 2TB nodes, which received an operating system upgrade. Following this upgrade, some of the older versions of R (and Rstudio) may not run. We strongly encourage all users to move to the newer versions of R (see below), which have been built for the new operating system on the iCSF… Read more »<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":43,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-47","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/47","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=47"}],"version-history":[{"count":26,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/47\/revisions"}],"predecessor-version":[{"id":1523,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/47\/revisions\/1523"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=47"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Original Instructions<\/h3>\n
install.packages(\"thing<\/em>\")<\/code>, while you were logged in to the iCSF<\/em>, would very likely NOT run on CSF3, due to older system libraries on that system at the time.<\/p>\n# Additional modulefile for people using R on the iCSF who also use R on\r\n# CSF3. This modulefile is ONLY available on the iCSF nodes!!!\r\n# Load this AFTER loading an 'apps\/gcc\/R\/x.y.x<\/em>' modulefile on the iCSF.\r\n\r\nmodule load apps\/gcc\/R\/incline2000-fix\r\n<\/pre>\n
~\/R\/el9\/<\/code> directory tree, away from the default tree ~\/R\/<\/code> used on the CSF3. It will prevent you breaking your CSF3 package installs.<\/p>\n\n
apps\/gcc\/R\/incline2000-fix<\/code> modulefile will keep your iCSF package installs away from your CSF3 install area. You will still be able to see your CSF3 installs when on the iCSF (they might still work.) But you won’t see your iCSF installs when on CSF3 (they probably won’t work anyway.)<\/li>\n<\/ul>\nVersions available<\/h2>\n
\n
\n
\n
\n
Restrictions on use<\/h2>\n
Setup procedure<\/h2>\n
# We recommend all users upgrade to using the latest versions of R<\/strong>\r\nmodule load apps\/gcc\/R\/4.5.1\r\n# OR\r\nmodule load apps\/gcc\/R\/4.4.2\r\n\r\n# This installation is unable to use the Basic Linear Algebra Subprograms (BLAS) library\r\nmodule load apps\/gcc\/R\/4.4.1\r\n\r\n# If you experience crashing in 4.4.1<\/strong> (either at the command-line or in Rstudio),\r\n# please try this 'nonopt' version which has been compiled without optimization (-O0)\r\n# to resolve some crashes we've seen in various libraries and functions.\r\nmodule load apps\/gcc\/R\/4.4.1-nonopt\r\n\r\n# Please upgrade to 4.4.2 if using these versions\r\nmodule load apps\/gcc\/R\/4.3.3\r\nmodule load apps\/gcc\/R\/4.1.3\r\nmodule load apps\/gcc\/R\/4.1.2\r\nmodule load apps\/gcc\/R\/4.0.2\r\n\r\n# Additional modulefile to consider loading after loading one of the above:<\/strong>\r\n# If using CSF3 as well as<\/em> iCSF, and you have problems with R libraries not running on CSF3,\r\n# this modulefile will keep your iCSF library installs away from your CSF3 library installs.\r\n# Problems can occur when the CSF tries to use R libraries that were installed on the iCSF.\r\n# (If you do use this, load it before installing any R libraries, and every time you use R.)\r\nmodule load apps\/gcc\/R\/incline2000-fix\r\n<\/pre>\n
# If these versions do not run on the upgraded iCSF nodes, we are unlikely to reinstall them.\r\n# Please move to a newer version of R (see above.) \r\nmodule load apps\/gcc\/R\/4.3.1\r\nmodule load apps\/gcc\/R\/4.1.3-gcc830 \r\nmodule load apps\/gcc\/R\/4.1.2-gcc830\r\nmodule load apps\/gcc\/R\/3.6.1-gcc830\r\nmodule load apps\/gcc\/R\/3.6.1\r\nmodule load apps\/gcc\/R\/3.6.0\r\nmodule load apps\/gcc\/R\/3.5.2\r\nmodule load apps\/gcc\/R\/3.4.2\r\nmodule load apps\/gcc\/R\/3.4.1\r\nmodule load apps\/gcc\/R\/3.3.3\r\nmodule load apps\/gcc\/R\/3.3.0\r\nmodule load apps\/gcc\/R\/3.2.3\r\nmodule load apps\/gcc\/R\/3.2.3-ambs\r\nmodule load apps\/gcc\/R\/3.2.0\r\nmodule load apps\/gcc\/R\/3.1.0 # Fixes a font problem in v3.0.2\r\nmodule load apps\/gcc\/R\/3.0.2\r\nmodule load apps\/gcc\/R\/2.15.3 # Rcmdr not available in this version\r\n<\/pre>\n
module load apps\/gcc\/MRO\/3.2.4\r\n<\/pre>\n
Running the application<\/h2>\n
R\r\n\r\n# To ensure no previously save large objects are loaded, which might cause memory issues\r\n# from previous runs of R if you were processing a large dataset, use:\r\nR --no-restore-data\r\n\r\n# Or use --vanilla, which applies the following flags\r\n# --no-save, --no-restore, --no-site-file, --no-init-file and --no-environ\r\nR --vanilla\r\n<\/pre>\n
q()\r\n<\/pre>\n
library(Rcmdr)<\/code> at the R command line:<\/p>\nlibrary(Rcmdr)\r\n\r\nLoading required package: tcltk\r\nLoading Tcl\/Tk interface ... done\r\n<\/pre>\n
export OMP_NUM_THREADS=4<\/pre>\n
Adding packages<\/h2>\n
Automatically Download from CRAN<\/h3>\n
\n
~\/.Renviron<\/code> file – it may contain some old, out-of-date proxy settings which need to be removed.\n# Note: you may have old proxy settings in an ~\/.Renviron file. You'll need to remove these:\r\ncat ~\/.Renviron\r\n #\r\n # If you see the following, you do not need to do anything!<\/strong>\r\n cat: .Renviron: No such file or directory\r\n\r\n # If you see some lines containing<\/strong>\r\n http_proxy=http:\/\/proxy.man.ac.uk:3128\r\n https_proxy=https:\/\/proxy.man.ac.uk:3128\r\n #\r\n # DELETE these lines or place a # at the start of each line.<\/strong>\r\n\r\n # If your ~\/.Renviron file contains only<\/em> the above proxy lines<\/strong>\r\n # you can delete the file<\/strong>\r\n rm ~\/.Renviron\r\n<\/pre>\n<\/li>\n
module load apps\/gcc\/R\/3.2.0\r\nR\r\n<\/pre>\n<\/li>\n
y<\/code> when asked if you wish to create a personal library:\n> install.packages(\"thing\")<\/strong>\r\nWarning in install.packages(\"thing\") :\r\n'lib = \"\/opt\/gridware\/apps\/gcc\/R\/3.2.0\/lib64\/R\/library\"' is not writable\r\nWould you like to create a personal library\r\n~\/R\/x86_64-unknown-linux-gnu-library\/3.0\r\nto install packages into? (y\/n) y<\/strong>\r\n<\/pre>\n<\/li>\n
\n
[https]<\/code> next to it.<\/li>\n<\/ul>\n<\/li>\nlibrary(thing)<\/strong>\r\n<\/pre>\n<\/li>\n<\/ol>\n
nloptr dependency<\/h3>\n
nloptr<\/code> R package. Trying to install that specific package often fails due to a dependency on the nlopt<\/code> library, which R fails to compile. So we have provided this as a separate modulefile. For example:<\/p>\n# This will fail due to a failure to compile nloptr<\/strong>\r\nmodule load apps\/gcc\/R\/4.3.1\r\nR\r\ninstall.packages(\"nloptr\") # Other R packages that depend on this one will also fail\r\nq()\r\n\r\n# The solution is to load an extra modulefile:<\/strong>\r\nmodule load libs\/gcc\/nlopt\/2.7.1\r\nR\r\ninstall.packages(\"nloptr\")\r\n<\/pre>\n
Rcpp dependency<\/h3>\n
Rcpp<\/code> dependency.<\/p>\nRcpp<\/code> package first, then do the package you want to install. For example:<\/p>\n# Install the lme4 packages, which requires nloptr and Rcpp:\r\nmodule load libs\/gcc\/nlopt\/2.7.1\r\nR\r\ninstall.packages(\"nloptr\")\r\ninstall.packages(\"Rcpp\")\r\ninstall.packages(\"lme4\")\r\n\r\n# Test\r\nlibrary(lme4)\r\nq()\r\n<\/pre>\n
module load<\/code> command with the one appropriate to the R version you wish to use.<\/p>\nLibrary from Source<\/h3>\n
\n
module load apps\/gcc\/R\/3.2.0\r\nR CMD INSTALL thing.x.y.z.tar.gz\r\n\r\n* installing to library \u2018\/mnt\/iusers01\/support\/mabcxyz1\/R\/x86_64-unknown-linux-gnu-library\/3.2\u2019\r\n* installing *source* package \u2018thing\u2019 ...\r\n** package \u2018thing\u2019 successfully unpacked and MD5 sums checked\r\n** R\r\n** data\r\n** demo\r\n** preparing package for lazy loading\r\n** help\r\n*** installing help indices\r\n** building package indices\r\n** testing if installed package can be loaded\r\n* DONE (thing)\r\n<\/pre>\n
module load apps\/gcc\/R\/4.3.1\r\nR\r\npackageurl <- \"https:\/\/cran.ma.imperial.ac.uk\/src\/contrib\/Archive\/nloptr\/nloptr_1.2.1.tar.gz\"; install.packages(packageurl, repos=NULL, type=\"source\");\r\ninstall.packages('lme4')\r\n<\/pre>\n<\/li>\nR\r\n> library(thing)\r\n<\/pre>\n<\/li>\n<\/ol>\n
R<\/code> in your home directory. It contains subdirectories for each version of R so if you want to use the library in different versions of R you will have to repeat the above commands for each version.<\/strong><\/p>\nAdding BioConductor Packages – R 3.6.0 and newer<\/h3>\n
# Load your version of R...\r\nmodule load apps\/gcc\/R\/4.4.2\r\n\r\n# Start R\r\nR\r\n\r\n# If we haven't yet installed BiocManager, install it now\r\n# Select from a UK Mirror when prompted (e.g., the UK Bristol mirror)\r\nif (!require(\"BiocManager\", quietly = TRUE))\r\n install.packages(\"BiocManager\")\r\n\r\n# Check the BiocManager version\r\nBiocManager::version()\r\n\r\n# See what is installed (this can be a long list!)\r\nBiocManager::available()\r\n\r\n# Install everything to your home directory\r\nBiocManager::install()\r\n# OR Install a package to your home directory\r\nBiocManager::install(c(\"esATAC<\/em>\"))\r\n #\r\n # Use the name of the package you want to install.\r\n #\r\n # You will be prompted to install to a local directory\r\n # (i.e., your home<\/em> directory) as shown below.\r\n\r\n### Select from a UK Mirror when prompted (e.g., the UK Bristol mirror)\r\n\r\nBioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)\r\nInstalling package(s) 'esATAC'\r\nWarning in install.packages(pkgs = doing, lib = lib, repos = repos, ...) :\r\n 'lib = \"\/opt\/gridware2\/el7\/apps\/gcc\/R\/3.6.0\/lib64\/R\/library\"' is not writable\r\nWould you like to use a personal library instead? (yes\/No\/cancel) y<\/strong> # Answer 'y'<\/strong>\r\nWould you like to create a personal library\r\n\u2018~\/R\/x86_64-pc-linux-gnu-library\/3.6\u2019\r\nto install packages into? (yes\/No\/cancel) y<\/strong> # Answer 'y'<\/strong>\r\n<\/pre>\n
Adding BioConductor Packages – R 3.5 and earlier<\/h3>\n
\n
~\/.Renviron<\/code> file – it may contain some old, out-of-date proxy settings which need to be removed.\n# Note: you may have old proxy settings in an ~\/.Renviron file. You'll need to remove these:\r\ncat ~\/.Renviron\r\n #\r\n # If you see the following, you do not need to do anything!<\/strong>\r\n cat: .Renviron: No such file or directory\r\n\r\n # If you see some lines containing<\/strong>\r\n http_proxy=http:\/\/proxy.man.ac.uk:3128\r\n https_proxy=https:\/\/proxy.man.ac.uk:3128\r\n #\r\n # DELETE these lines or place a # at the start of each line.<\/strong>\r\n\r\n # If your ~\/.Renviron file contains only<\/em> the above proxy lines<\/strong>\r\n # you can delete the file<\/strong>\r\n rm ~\/.Renviron\r\n<\/pre>\n<\/li>\n
module load apps\/gcc\/R\/3.2.0\r\n<\/pre>\n<\/li>\n
BiocInstaller<\/code>\n> require('BiocInstaller')\r\nLoading required package: BiocInstaller\r\nBioconductor version 3.1 (BiocInstaller 1.18.1), ?biocLite for help\r\n<\/pre>\n<\/li>\n> biocLite(c(\"WGCNA\"))\r\n<\/pre>\n
y<\/code><\/p>\nWould you like to use a personal library instead? (y\/n) y\r\ntrying URL 'http:\/\/bioconductor.org\/packages\/3.1\/bioc\/src\/contrib\/BiocInstaller_1.18.5.tar.gz'\r\nContent type 'application\/x-gzip' length 14977 bytes (14 KB)\r\n==================================================\r\ndownloaded 14 KB\r\n\r\n* installing *source* package \u2018BiocInstaller\u2019 ...\r\n** R\r\n** inst\r\n** preparing package for lazy loading\r\n** help\r\n*** installing help indices\r\n** building package indices\r\n** testing if installed package can be loaded\r\nBioconductor version 3.1 (BiocInstaller 1.18.5), ?biocLite for help\r\nA newer version of Bioconductor is available for this version of R,\r\n ?BiocUpgrade for help\r\n* DONE (BiocInstaller)\r\n\r\nThe downloaded source packages are in\r\n\t\u2018\/tmp\/RtmpMwCszR\/downloaded_packages\u2019\r\nBioconductor version 3.1 (BiocInstaller 1.18.5), ?biocLite for help\r\nA newer version of Bioconductor is available for this version of R,\r\n ?BiocUpgrade for help\r\n'BiocInstaller' updated to version 1.18.5\r\nBioC_mirror: http:\/\/bioconductor.org\r\nUsing Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.0.\r\nInstalling package(s) \u2018WGCNA\u2019\r\nalso installing the dependencies \u2018impute\u2019, \u2018GO.db\u2019\r\n\r\n------- SNIP ------\r\n<\/pre>\n<\/li>\n
n<\/code> as most of them will be part of the central install which you do not have permission to change.\n------- SNIP ------\r\n* DONE (WGCNA)\r\n\r\nThe downloaded source packages are in\r\n\t\u2018\/tmp\/RtmpMwCszR\/downloaded_packages\u2019\r\nOld packages: 'abind', 'annotate', 'base64', 'BiocInstaller', 'BiocParallel',\r\n 'biomaRt', 'Biostrings', 'boot', 'car', 'class', 'cluster', 'codetools',\r\n 'DBI', 'digest', 'e1071', 'edgeR', 'effects', 'evaluate', 'foreach',\r\n 'foreign', 'formatR', 'futile.logger', 'GenomeInfoDb', 'GenomicAlignments',\r\n 'GenomicFeatures', 'GenomicRanges', 'ggplot2', 'gridExtra', 'gtable',\r\n 'highr', 'Hmisc', 'IRanges', 'iterators', 'KernSmooth', 'knitr', 'lambda.r',\r\n 'lattice', 'latticeExtra', 'limma', 'lme4', 'lmtest', 'MASS', 'Matrix',\r\n 'matrixStats', 'mclust', 'mgcv', 'mime', 'multcomp', 'munsell', 'mvtnorm',\r\n 'nlme', 'nnet', 'nor1mix', 'plyr', 'quantreg', 'Rcmdr', 'RcmdrMisc', 'Rcpp',\r\n 'RcppEigen', 'RCurl', 'registry', 'relimp', 'rgl', 'rJava', 'RODBC', 'rpart',\r\n 'Rsamtools', 'rtracklayer', 'ruv', 'S4Vectors', 'sandwich', 'scales', 'sem',\r\n 'snow', 'SparseM', 'spatial', 'statmod', 'stringi', 'survival', 'TH.data',\r\n 'XLConnect', 'XLConnectJars', 'XML', 'xtable', 'zoo'\r\nUpdate all\/some\/none? [a\/s\/n]: n\r\n<\/pre>\n<\/li>\n
library(\"WGCNA\")\r\n<\/pre>\n<\/li>\n<\/ol>\n
Using BioConductor Packages<\/h3>\n
bioThing<\/code>, to use it in your code use:<\/p>\n# Load\/use a BioConductor package named 'bioThing' previously installed\r\nlibrary(bioThing)\r\n<\/pre>\n
Listing Packages<\/h3>\n
installed.packages();\r\n<\/pre>\n
(.packages())\r\n<\/pre>\n
R Project Environments (renv<\/a>)<\/h2>\n
\n
\n
renv<\/code> for your projects\/pipelines to avoid conflicts.<\/li>\nrenv.lock<\/code>, .Rprofile and renv<\/code>.
\nThese files and folders should not be altered. You can see them when you exit R and run the command ls -al<\/strong><\/code> from that directory later.<\/li>\nrenv<\/code> for the first time after installation.<\/li>\n
\nIn this example we will install only the BiocManager<\/code> package in this renv R Project folder, but you can install as many packages you need in a project.<\/p>\n# Create a new directory for our R project\r\nmkdir ~\/MyFirstRProject\r\n\r\n# Go into that directory. This will become our working renv project, once we've finished the setup\r\ncd ~\/MyFirstRProject\r\nmodule load apps\/gcc\/R\/4.4.2\r\nR\r\ninstall.packages(\"renv\")\r\n # Select the preferred CRAN mirror from the presented list (e.g., Bristol)\r\nrenv::init()\r\n# We now quit R. We'll start it again soon!\r\nq()\r\nn\r\n\r\n# At this point we've exited R and are now back at the CSF login-node prompt.\r\nls -al\r\n\r\n# Start R again - it will now see that we're working in an renv project\r\nR\r\n\r\n# Run commands to install additional R packages if needed (here we install BioCManager)\r\ninstall.packages(\"BiocManager\")\r\nY\r\n# Save the state of our project\r\nrenv::snapshot()\r\n# To exit back to the login node prompt\r\nq()\r\nn\r\n\r\n# At this point we've exited R and are now back at the CSF login-node prompt.\r\n# We create a description of this R project, for our own future reference.\r\ngedit README.txt # Or use an editor such as nano\r\n------------------------------------------------------------\r\n| Project Platform: iCSF |\r\n| Project directory location: ~\/MyFirstRProject |\r\n| Modules used: apps\/gcc\/R\/4.4.2 |\r\n| Packages Installed: BiocManager |\r\n------------------------------------------------------------\r\n<\/pre>\n
renv<\/code> project in a new folder.<\/p>\nRunning a package installed in a ‘renv’ project<\/h3>\n
cd ~\/MyFirstRProject # Use the name of your project folder\r\nmodule load apps\/gcc\/R\/4.4.2 # Use the same version as when you created the renv project\r\n # If you wrote the README.txt file (see above), try:\r\n # cat README.txt to read it.\r\nR # Run R\r\n<\/pre>\n
Hints and Tips (let us know yours)<\/h2>\n
Plotting Graphs and Graphics<\/h3>\n
capabilities()<\/code> function in R. Note that newer versions of R (e.g., 3.6.0-gcc830) have more graphics formats supported – we recommend you use the latest version of R available on the iCSF:<\/p>\nssh username<\/em>@incline2000.itservices.manchester.ac.uk\r\n[mabcxyz1@incline31 ~]$ module load apps\/gcc\/R\/3.6.1-gcc830\r\n[mabcxyz1@incline31 ~]$ R\r\n> capabilities()\r\n jpeg png tiff tcltk X11 aqua \r\n TRUE TRUE TRUE TRUE TRUE FALSE \r\n<\/pre>\n
.png<\/code> file and a .jpg<\/code> file. It has been tested on the incline256<\/code> nodes.<\/p>\n# R script to demonstrate plotting to image files on the iCSF\r\n\r\n# Enable cairo device - MAC USER: THIS MIGHT FIX SOME FONT PROBLEMS.<\/strong>\r\noptions(bitmapType='cairo')\r\n\r\n# Initialize some data to plot\r\nx = rnorm(100)\r\n\r\n# Save a png plot\r\npng(file=\"hist.png\")\r\nhist(x)\r\nrug(x,side=1)\r\ndev.off()\r\n\r\n# How about jpg\r\njpeg(file=\"hist.jpg\")\r\nhist(x)\r\nrug(x,side=1)\r\ndev.off()\r\n\r\n# R 3.6.1 can also do tiff\r\ntiff(file=\"hist.tif\")\r\nhist(x)\r\nrug(x,side=1)\r\ndev.off()\r\n\r\n# Exit\r\nq();\r\n<\/pre>\n
eog<\/code>) image viewer:<\/p>\n# List the image files created by the above example\r\nls hist.*\r\nhist.jpg hist.png hist.tif\r\n\r\n# Use the image viewer name 'eog' (Eye of Gnome)\r\neog hist.png\r\n<\/pre>\n
convert<\/code> command-line tool, available on the login node or can be run in your jobscript (note that convert<\/code> is a linux command-line program, not an R function):<\/p>\n# Using the hist.png example file from the above R script, convert it to another format:\r\nconvert hist.png hist.tif # R 3.6.1 can write tif files directly (see above) but older versions can't\r\n\r\n# How about a .pdf\r\nconvert hist.png hist.pdf\r\n\r\n# View the PDF file\r\nevince hist.pdf\r\n<\/pre>\n
png(file = \"myplot.png\", bg = \"transparent\")\r\nplot(1:10)\r\nrect(1, 5, 3, 7, col = \"white\")\r\ndev.off()\r\n\r\n## will make myplot1.jpeg and myplot2.jpeg\r\njpeg(file = \"myplot%d.jpeg\")\r\nexample(rect)\r\ndev.off()\r\n<\/pre>\n
Adobe Helvetica Font Problem<\/h3>\n
ggplot2<\/code>,<\/p>\nError in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) : \r\n X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 9 could not be loaded\r\n<\/pre>\n
showtext<\/code> package as follows:<\/p>\ninstall.packages(showtext)\r\nlibrary(showtext)\r\nshowtext_auto()\r\n\r\nlibrary(ggplot2)\r\ntest_data <- data.frame(x=rnorm(100),y=rnorm(100))\r\nggplot(test_data, aes(x=x, y=y)) + ggtitle(\"test plot\")\r\n<\/pre>\n
Further info<\/h2>\n
Updates<\/h2>\n
\nAugust 2024 – Only the 2TB nodes remain and have been upgraded to an EL9 O\/S. R 4.4.x versions installed. Older versions may not run.
\nAugust 2017 – v3.4.1 added
\nJuly 2016 – a version of rjava has been compiled for R version 3.3.0 and has all the java environment variables automatically set. It can be accessed using:module load apps\/gcc\/rjava\/0.9.8-R3.3.0<\/code>.
\n29.01.2016 – v3.2.3-ambs added including the packages: ggplot2, randomForest, dplyr, party, DataCombine, Imtest, Foreign, Hmisc, lattice, survival, Formula.
\n29.01.2016 – v3.2.3 added
\n11 May 2015 – v3.2.0 added
\n9-June-2014 – v3.1.0 added<\/p>\n","protected":false},"excerpt":{"rendered":"