Working with custom packages
Working with R packages
Detailed NeSI documentation on working with R packages
Tom Kelly (The University of Otago PhD graduate) developed a number of scripts and examples on how to install R packages on NeSI.
Working with Python packages
Detailed NeSI documentation on working with Python packages
Example of installing a custom R package
First, let’s get onto a build node
[apaw363@login-01 ~]$ ssh build-wm
[apaw363@build-wm ~]$
Now, let’s see which R versions we have available:
module spider R
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R:
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Description:
R is a free software environment for statistical computing and graphics.
Versions:
R/3.0.3-goolf-1.5.14
R/3.1.1-goolf-1.5.14
R/3.1.1-iomkl-6.5.4
R/3.1.2-goolf-1.5.14
R/3.2.1-intel-2015a
R/3.3.0-intel-2015a
R/3.4.0-gimkl-2017a
R/3.4.2-gimkl-2017a
Other possible modules matches:
ANTLR ARCSI Advisor BioConductor Bismark BreakDancer CNVnator DendroPy EMIRGE Elmer FastTree FineMarine FreeBayes FreeSurfer FreeXL ...
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To find other possible module matches do:
module -r spider '.*R.*'
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For detailed information about a specific "R" module (including how to load the modules) use the module's full name.
For example:
$ module spider R/3.4.2-gimkl-2017a
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Some modules are loaded by default. To check that:
$ module list
Currently Loaded Modules:
1) GCCcore/5.4.0 11) PCRE/8.40-gimkl-2017a 21) expat/2.2.0-gimkl-2017a 31) libspatialite/4.3.0a-gimkl-2017a-GEOS-3.5.1
2) binutils/2.26-GCCcore-5.4.0 12) ncurses/6.0-gimkl-2017a 22) libjpeg-turbo/1.5.1-gimkl-2017a 32) netCDF/4.4.1-gimkl-2017a
3) GCC/5.4.0-2.26 13) libreadline/6.3-gimkl-2017a 23) Szip/2.1-gimkl-2017a 33) PostgreSQL/9.6.2-gimkl-2017a
4) impi/2017.1.132-GCC-5.4.0-2.26 14) libpng/1.6.28-gimkl-2017a 24) HDF/4.2.13-gimkl-2017a 34) GDAL/2.2.2-gimkl-2017a-GEOS-3.5.1
5) gimpi/2017a 15) libxml2/2.9.4-gimkl-2017a 25) HDF5/1.8.18-gimkl-2017a 35) NLopt/2.4.2-gimkl-2017a
6) imkl/2017.1.132-gimpi-2017a 16) Tcl/8.6.6-gimkl-2017a 26) KEALib/1.4.6-gimkl-2017a 36) OpenSSL/1.1.0e-gimkl-2017a
7) gimkl/2017a 17) SQLite/3.16.2-gimkl-2017a 27) LibTIFF/4.0.7-gimkl-2017a 37) R/3.4.2-gimkl-2017a
8) zlib/1.2.11-gimkl-2017a 18) cURL/7.52.1-gimkl-2017a 28) PROJ/4.9.3-gimkl-2017a
9) bzip2/1.0.6-gimkl-2017a 19) Java/1.8.0_144 29) libgeotiff/1.4.2-gimkl-2017a
10) XZ/5.2.3-gimkl-2017a 20) GEOS/3.5.1-gimkl-2017a 30) FreeXL/1.0.2-gimkl-2017a
Let’s start R and see if the packages that we need are available:
$ R
....
> library(arules)
Error in library(arules) : there is no package called ‘arules'
Looks like we have to install this library.
> install.packages("arules")
Warning in install.packages("arules") :
'lib = "/gpfs1m/apps/easybuild/RHEL6.3/westmere/software/R/3.4.2-gimkl-2017a/lib64/R/library"' is not writable
Would you like to use a personal library instead? (y/n)
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/3.4
to install packages into? (y/n)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
1: 0-Cloud [https] 2: Algeria [https]
3: Australia (Canberra) [https] 4: Australia (Melbourne 1) [https]
5: Australia (Melbourne 2) [https] 6: Australia (Perth) [https]
7: Austria [https] 8: Belgium (Ghent) [https]
9: Brazil (PR) [https] 10: Brazil (RJ) [https]
11: Brazil (SP 1) [https] 12: Brazil (SP 2) [https]
13: Bulgaria [https] 14: Chile 1 [https]
15: Chile 2 [https] 16: China (Guangzhou) [https]
17: China (Lanzhou) [https] 18: Colombia (Cali) [https]
19: Czech Republic [https] 20: Denmark [https]
21: East Asia [https] 22: Ecuador (Cuenca) [https]
23: Estonia [https] 24: France (Lyon 1) [https]
25: France (Lyon 2) [https] 26: France (Marseille) [https]
27: France (Montpellier) [https] 28: France (Paris 2) [https]
29: Germany (Göttingen) [https] 30: Germany (Münster) [https]
31: Greece [https] 32: Iceland [https]
33: Indonesia (Jakarta) [https] 34: Ireland [https]
35: Italy (Padua) [https] 36: Japan (Tokyo) [https]
37: Malaysia [https] 38: Mexico (Mexico City) [https]
39: Norway [https] 40: Philippines [https]
41: Serbia [https] 42: Spain (A Coruña) [https]
43: Spain (Madrid) [https] 44: Sweden [https]
45: Switzerland [https] 46: Turkey (Denizli) [https]
47: Turkey (Mersin) [https] 48: UK (Bristol) [https]
49: UK (Cambridge) [https] 50: UK (London 1) [https]
51: USA (CA 1) [https] 52: USA (IA) [https]
53: USA (KS) [https] 54: USA (MI 1) [https]
55: USA (OR) [https] 56: USA (TN) [https]
57: USA (TX 1) [https] 58: Vietnam [https]
59: (other mirrors)
Selection:
And then, there is a LOT of output information on your screen to finally arrive to:
** testing if installed package can be loaded
* DONE (arules)
The downloaded source packages are in
‘/tmp/RtmpR64gHN/downloaded_packages’
Indeed now, I can use the package:
> library(arules)
Loading required package: Matrix
Attaching package: ‘arules’
The following objects are masked from ‘package:base’:
abbreviate, write
But let’s see what is in our home directory:
[apaw363@login-01 ~]$ ls R/x86_64-pc-linux-gnu-library/3.4/
arules cli dbplyr hms psych rematch rmarkdown rvest whisker
callr clipr forcats lubridate readr reprex rprojroot selectr xml2
cellranger crayon haven modelr readxl rlang rstudioapi