Programming/R - Revision history

Pysdlb: /* Listing packages installed */

2024-06-13T14:22:28Z

‎Listing packages installed

Pysdlb: /* Installing Additional Libraries */

2024-06-13T14:21:03Z

‎Installing Additional Libraries

Pysdlb: /* Listing packages installed */

2023-03-23T10:32:11Z

‎Listing packages installed

Pysdlb: /* Installing Additional Libraries */

2023-03-23T10:31:15Z

‎Installing Additional Libraries

Pysdlb: /* Navigation */

2022-11-16T11:31:17Z

‎Navigation

Pysdlb at 09:18, 24 May 2021

2021-05-24T09:18:14Z

Pysdlb at 15:19, 22 July 2020

2020-07-22T15:19:00Z

Pysdlb at 15:17, 22 July 2020

2020-07-22T15:17:13Z

Pysdlb at 15:13, 22 July 2020

2020-07-22T15:13:27Z

Pysdlb at 10:53, 10 June 2019

2019-06-10T10:53:35Z

@@ Line 296: / Line 296: @@
 ====Listing packages installed====
-If you need a package that will be frequently used frequently raise a [https://support.hull.ac.uk/ support ticket] with your request.
+If you need a package that will be frequently used raise a [https://hull.service-now.com/ support ticket] with your request.
-To view those already installed within R
+To view those already installed within R.
 <pre>

@@ Line 175: / Line 175: @@
 ====Installing Additional Libraries====
-If you need an additional library installed that would be used by more than just yourself, contact the Viper team by raising a [https://support.hull.ac.uk/ support ticket]  with the details of the library and the version of R you require it for.
+If you need an additional library installed that would be used by more than just yourself, contact the Viper team by raising a [https://hull.service-now.com/ support ticket]  with the details of the library and the version of R you require it for.
-Alternatively, you can install an R library into your own personal library.  Within R run the install.packages command with the package you wish to install.
+Alternatively, you can install an R library into your library.  Within R run the install.packages command with the package you wish to install.
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

@@ Line 296: / Line 296: @@
 ====Listing packages installed====
-If you need a package that will be used frequently visit [https://support.hull.ac.uk/ Topdesk] with your request.
+If you need a package that will be frequently used frequently raise a [https://support.hull.ac.uk/ support ticket] with your request.
 To view those already installed within R
@@ Line 334: / Line 334: @@
 ....
 </pre>
 == Further Information ==

@@ Line 175: / Line 175: @@
 ====Installing Additional Libraries====
-If you need an additional library installed that would be used by more than just yourself, contact the Viper team on [https://support.hull.ac.uk/ Topdesk]  with the details of the library and the version of R you require it for.
+If you need an additional library installed that would be used by more than just yourself, contact the Viper team by raising a [https://support.hull.ac.uk/ support ticket]  with the details of the library and the version of R you require it for.
 Alternatively, you can install an R library into your own personal library.  Within R run the install.packages command with the package you wish to install.

← Older revision		Revision as of 11:31, 16 November 2022
Line 343:		Line 343:
	* [https://www.r-project.org/about.html https://www.r-project.org/about.html]		* [https://www.r-project.org/about.html https://www.r-project.org/about.html]

−	~~==Navigation==~~	+	{{Languagespagenav}}
−
−	* [[Main_Page\|Home]]
−	* [[Applications\|Application support]]
−	* [[General\|General]]
−	~~* [[Programming\|Programming support]] *~~

@@ Line 1: / Line 1: @@
 == Programming Details ==
-R is a programming language and software environment for statistical analysis, graphics representation and reporting.
+R is a programming language and software environment for statistical analysis, graphics representation, and reporting.
-R is freely available under the GNU General Public License, and can be loaded as a module on  Viper (with Linux), Windows (PC) and Mac.
+R is freely available under the GNU General Public License and can be loaded as a module on  Viper (with Linux), Windows (PC), and Mac.
 * R has versions 3.5.1 and R/4.0.2. (Earlier versions will be retired)
@@ Line 35: / Line 35: @@
 ====Batch Mode====
-The SLURM batch file would typical look like the one below, in this case it would be named ''''rscript.job''''.
+The SLURM batch file would typically look like the one below, in this case, it would be named ''''rscript.job''''.
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
@@ Line 47: / Line 47: @@
 #SBATCH -e %N.%j.%a.err
 #SBATCH -p compute
 echo $SLURM_JOB_NODELIST
@@ Line 127: / Line 128: @@
                          including modifying them to follow a particular
                          naming style
-GenomeInfoDbData        Species and taxonomy ID look up tables used by
+GenomeInfoDbData        Species and taxonomy ID lookup tables used by
                          GenomeInfoDb
 GenomicAlignments       Representation and manipulation of short
@@ Line 156: / Line 157: @@
 Rhtslib                 HTSlib high-throughput sequencing library as an
                          R package
-Rsamtools               Binary alignment (BAM), FASTA, variant call
+Rsamtools               Binary alignment (BAM), FASTA, variant calling
                          (BCF), and tabix file import
 S4Vectors               Foundation of vector-like and list-like
@@ Line 176: / Line 177: @@
 If you need an additional library installed that would be used by more than just yourself, contact the Viper team on [https://support.hull.ac.uk/ Topdesk]  with the details of the library and the version of R you require it for.
-Alternatively, you can install a R library into your own personal library.  Within R run the install.packages command with the package you wish to install.
+Alternatively, you can install an R library into your own personal library.  Within R run the install.packages command with the package you wish to install.
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

@@ Line 295: / Line 295: @@
 ====Listing packages installed====
-If you need a package that will be used frequently email help@hull.ac.uk with your request.
+If you need a package that will be used frequently visit [https://support.hull.ac.uk/] with your request.
 To view those already installed within R
@@ Line 302: / Line 302: @@
 > installed.packages()
-                  Package
+AnnotationDbi               "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-abind            "abind"
+BH                          "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-acepack          "acepack"
+Biobase                     "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-ADGofTest        "ADGofTest"
+BiocFileCache               "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-ape              "ape"
+BiocGenerics                "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-assertthat       "assertthat"
+BiocManager                 "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-backports        "backports"
+BiocParallel                "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-base             "base"
+BiocStyle                   "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-base64enc        "base64enc"
+BiocVersion                 "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-BH               "BH"
+Biostrings                  "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-bindr            "bindr"
+DBI                         "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-bindrcpp         "bindrcpp"
+DelayedArray                "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-Biobase          "Biobase"
+GenomeInfoDb                "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-BiocGenerics     "BiocGenerics"
+GenomeInfoDbData            "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-BiocInstaller    "BiocInstaller"
+GenomicAlignments           "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-bit              "bit"
+GenomicFeatures             "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
-bit64            "bit64"
+GenomicRanges               "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
 ....
 </pre>

@@ Line 71: / Line 71: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@login01 ~]$ module add R/3.4.1
+[pysdlb@login01 ~]$ interactive
-[username@login01 ~]$ R
+salloc: Granted job allocation 3039458
-R version 3.4.1 (2017-06-30) -- "Single Candle"
+R version 4.0.2 (2020-06-22) -- "Taking Off Again"
-Copyright (C) 2017 The R Foundation for Statistical Computing
+Copyright (C) 2020 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
@@ Line 81: / Line 84: @@
 You are welcome to redistribute it under certain conditions.
 Type 'license()' or 'licence()' for distribution details.
 R is a collaborative project with many contributors.
@@ Line 92: / Line 93: @@
 Type 'q()' to quit R.
+[Previously saved workspace restored]
 </pre>
@@ Line 102: / Line 105: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-Packages in library ‘/trinity/clustervision/CentOS/7/apps/R/3.3.0/lib64/R/library’:
+Packages in library '/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library':
 </pre>
@@ Line 133: / Line 182: @@
 > install.packages("R.matlab")
 Warning in install.packages("R.matlab") :
-   'lib = "/trinity/clustervision/CentOS/7/apps/R/3.3.0/lib64/R/library"' is not writable
+   'lib = "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"' is not writable
 Would you like to use a personal library instead?  (y/n) y
 Would you like to create a personal library

@@ Line 4: / Line 4: @@
 R is freely available under the GNU General Public License, and can be loaded as a module on  Viper (with Linux), Windows (PC) and Mac.
 [[Applications/RStudio|R-Studio]] is also provided as an interactive session on Viper for R-Studio.
@@ Line 278: / Line 280: @@
 * [https://www.udemy.com/r-basics/ https://www.udemy.com/r-basics/]
 * [https://www.r-project.org/about.html https://www.r-project.org/about.html]
-{|
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
+==Navigation==
-|style="width:95%; border-width: 0" |
 * [[Main_Page|Home]]
 * [[Applications|Application support]]
 * [[General|General]]
-* [[Training|Training]]
+* [[Programming|Programming support]] *