forked from UCL-ARC/rcps-buildscripts
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathR-3.6.3_packages_install
executable file
·170 lines (134 loc) · 4.99 KB
/
R-3.6.3_packages_install
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
#!/usr/bin/env bash
###############################################
# Installing UCL needed additional R and Bioconductor
# packages.
#
# This replaces the old ~ccaabaa/Software/R/extra-pkgs-order.txt file from
# previous version of R on Legion etc. It will need to be updated each time
# an extra package is added to the current R installation.
#
# For R 3.6.3
#
# by Brian Alston, June 2016
# Updated Sep 2016 to updated JAGS version
# Updated Nov 2016 for R 3.3.2 and extra modules for rgdal and rgeos packages.
# Updated Dec 2016 to use https://cloud.r-project.org/ as defult repro.
# Updated May 2017 for R 3.4.0 and to add udunits/2.2.20/gnu-4.9.2 module.
# Updated October 2017 for R 3.4.2
# Updated May 2018 for R 3.5.0
# Updated June 2018 to fix MPI support - now using mpi/openmpi/3.0.0/gnu-4.9.2
# Updated September 2018 for R 3.5.1 and ROOT 5.34.36
# Also updated for udunits 2.2.26
# Updated October 2018 to create ~/.R/Makevars to allow installaion of rstan
# Updated April 2019 for R 3.5.3 and PROJ.4 6.0.0
# Updated June 2019 for R 3.6.0, Texinfo 6.6 and TeX Live 2019
# Further updates to get a working set of Geographic packages (PROJ, GDAL etc) July 2019
# Updated April 2020 for R 3.6.3 and GNU 9.2.0 - some packages not currently installed
# - see below
#
# Using Ian's require function to load modules
#
# Will need modules: see list of modules below.
set -e
VERSION=${VERSION:-3.6.3}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/apps/R/R-${VERSION}-OpenBLAS}
export RLIB_MAIN=${RLIB_MAIN:-${INSTALL_PREFIX}/lib64/R/library}
export RLIB_DB=${RLIB_DB:-/home/ccspapp/Scratch/R/R-${VERSION}-OpenBLAS/library}
export REPROS=${REPROS:-https://cloud.r-project.org/}
LOCALDIR=${LOCALDIR:-/shared/ucl/apps/build_scripts/files/R_UCL}
export PATH=$INSTALL_PREFIX/bin:$PATH
dirname=$(dirname $0 2>/dev/null || pwd)
INCLUDES_DIR=${INCLUDES_DIR:-${dirname}/includes}
source ${INCLUDES_DIR}/module_maker_inc.sh
source ${INCLUDES_DIR}/require_inc.sh
require beta-modules
require gcc-libs/9.2.0
require compilers/gnu/9.2.0
require openblas/0.3.7-serial/gnu-9.2.0
require java/1.8.0_92
require fftw/3.3.8/gnu-9.2.0
require ghostscript/9.19/gnu-4.9.2
require texinfo/6.6/gnu-4.9.2
require texlive/2019
require gsl/2.6/gnu-9.2.0
require hdf/5-1.10.5/gnu-9.2.0
require udunits/2.2.26/gnu-9.2.0
require netcdf/4.7.4/gnu-9.2.0
require mpi/openmpi/3.1.5/gnu-9.2.0
# Not currently installed - 15/4/2020
# require jags/4.2.0/gnu.4.9.2-openblas
# require root/5.34.36/gnu-4.9.2-fftw-3.3.6-gsl-2.4
# require glpk/4.60/gnu-4.9.2
require perl/5.22.0
require libtool/2.4.6
require freetype/2.8.1/gnu-4.9.2
require graphicsmagick/1.3.21
require python/2.7.12
require sqlite/3.31.1/gnu-9.2.0
require proj.4/7.0.0/gnu-9.2.0
require sqlite/3.31.1/gnu-9.2.0
require proj.4/7.0.0/gnu-9.2.0
require gdal/3.0.4/gnu-9.2.0
require geos/3.8.1/gnu-9.2.0
require gmt/6.0.0/gnu-9.2.0
# Not currently installed - 15/4/2020
# module load v8/3.15
# module load protobuf/12-2017/gnu-4.9.2
# module load jq/1.5/gnu-4.9.2
require r/3.6.3-openblas/gnu-9.2.0
# Set up ~/.R/Makevars for rstan which needs C++ 2014 stuff
mkdir -p ~/.R
cd ~/.R
cat > Makevars <<EOF
CXX14 = g++ -std=c++1y
CXX14FLAGS = -Wno-unused-variable -Wno-unused-function -fPIC
EOF
# temp_dir=`mktemp -d -p /dev/shm`
temp_dir='/home/ccspapp/Software/R/Packages'
echo "Building in $temp_dir ..."
cd $temp_dir
module list
read -p "Press [Enter] key to start ..."
cd $temp_dir
mkdir -p $RLIB_DB
# Note: some old packages need to be installed from local files that have had minor updates applied eg:
#
# adapt fails to install on R > 3.0.1 with: ERROR: a 'NAMESPACE' file is required
#
# tar xvzf adapt_1.0-4.tar.gz
# cd adapt
# Create NAMESPACE with contents:
#
# exportPattern("^[^\\.]")
#
# cd ..
# tar cvzf adapt_1.0-4-ucl.tar.gz adapt
#
# Do this for all packages that fail with abover error.
R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/adapt_1.0-4-ucl.tar.gz
R_input=${LOCALDIR}/R_packages_UCL_1.R
R --no-save < $R_input
# No longer on CRAN current - July 2013
R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/Design_2.3-0-ucl.tar.gz
# So build of RCurl picks up currect version of libcurl
export PATH=/shared/ucl/apps/curl/7.21.3/bin:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:/shared/ucl/apps/curl/7.21.3/lib
export PKG_LIBS="-L/shared/ucl/apps/curl/7.21.3/lib"
R_input=${LOCALDIR}/R_packages_UCL_2_3.6.3.R
R --no-save < $R_input
R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/OPE_0.7-ucl.tar.gz
R_input=${LOCALDIR}/R_packages_UCL_3.R
R --no-save < $R_input
# No longer on CRAN - Aug 2014
# Removed from packages to be built June 2019 as it fails to build with R 3.6.0
# ${LOCALDIR}/NetworkAnalysis_0.3-1.tar.gz
R_input=${LOCALDIR}/R_packages_UCL_4.R
R --no-save < $R_input
# For Julie Bertrand (j.bertrand@ucl.ac.uk) - added Jan 2014
# No longer on CRAN current - June 2016 - Breaks install with R 3.5.3
# R CMD INSTALL -l $RLIB_MAIN ${LOCALDIR}/ridge_2.1-3.tar.gz
R_input=${LOCALDIR}/R_packages_UCL_5_3.6.3.R
R --no-save < $R_input
# Now to install Bioconductor.
R_input=${LOCALDIR}/Bioconductor_UCL_1_3.6.3.R
R --no-save < $R_input