ELIC_R 2020b

foss-2020b/ELIC_R-1-foss-2020b-R-4.0.3.eb

@@ -7,12 +7,12 @@ versionsuffix = '-R-%(rver)s'
 homepage = 'https://gogs.elic.ucl.ac.be'
 description = """This repo provides additional Python and R extensions for ELIC ecosystem."""
 
-toolchain = {'name': 'foss', 'version': '2019b'}
+toolchain = {'name': 'foss', 'version': '2020b'}
 
 dependencies = [
-    ('R', '3.6.2'),
-    ('GDAL', '3.0.2', '-Python-3.7.4'),
-    ('PostgreSQL', '12.2', '-Python-3.7.4'),
+    ('R', '4.0.3'),
+    ('GDAL', '3.2.0', '-Python-3.8.6'),
+    ('PostgreSQL', '12.4'),
 ]
 
 exts_default_options = {
@@ -27,102 +27,11 @@ exts_default_options = {
 exts_defaultclass = 'RPackage'
 exts_filter = ("R -q --no-save", "library(%(ext_name)s)")
 
-# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends
-# !! order of packages is important !!
-# packages updated on Oct 9th 2019
-exts_list = [
-    ('rgdal', '1.4-4'),
-    ('gdalUtils', '2.0.1.14'),
-    ('ncdf4', '1.16.1'),
-    ('gdtools', '0.1.9'),
-    ('leaflet', '2.0.2'),
-    ('satellite', '1.0.1'),
-    ('sf', '0.7-7'),
-    ('svglite', '1.2.2'),
-    ('leafem', '0.0.1'),
-    ('leafpop', '0.0.1'),
-    ('mapview', '2.7.0'),
-    ('MuMIn', '1.43.6'),
-    ('intervals', '0.15.1'),
-    ('spacetime', '1.2-2'),
-    ('gstat', '2.0-3'),
-    ('RNetCDF', '1.9-1'),
-    ('automap', '1.0-14'),
-    ('clhs', '0.7-3'),
-    ('reporttools', '1.1.2'),
-    ('rgeos', '0.4-3'),
-    ('RandomFieldsUtils', '0.5.3'),
-    ('RandomFields', '3.3.6'),
-    ('rworldmap', '1.3-6'),
-    ('rworldxtra', '1.01'),
-    ('colorRamps', '2.3'),
-    ('mapdata', '2.3.0'),
-    ('mapproj', '1.2.6'),
-    ('RPostgreSQL', '0.6-2'),
-    ('getPass', '0.2-2'),
-    ('stringdist', '0.9.5.2'),
-    ('here', '0.1'),
-    ('svMisc', '1.1.0'),
-    ('networkD3', '0.4'),
-    ('cmsaf', '1.9.5'),
-    ('RPostgres', '1.1.1'),
-    ('nzelect', '0.4.0'),
-    ('wordcloud', '2.6'),
-    ('ngram', '3.0.4'),
-    ('rtweet', '0.6.9'),
-    ('lettercase', '0.13.1'),
-    ('xgboost', '0.90.0.2'),
-    ('rts', '1.0-49'),
-    ('RgoogleMaps', '1.4.4'),
-    ('packrat','0.5.0'),
-    ('rsconnect', '0.8.13'),
-    ('rpostgis', '1.4.2'),
-    ('aws.signature', '0.5.2'),
-    ('aws.s3', '0.3.12'),
-    ('geosphere', '1.5-10'),
-    ('fuzzyjoin', '0.1.5'),
-    ('refinr', '0.3.1'),
-    ('x13binary', '1.1.39-2'),
-    ('seasonal', '1.7.0'),
-    ('mitools', '2.4'),
-    ('survey', '3.36'),
-    ('sysfonts', '0.8'),
-    ('showtextdb', '2.0'),
-    ('showtext', '0.7'),
-    ('BiocManager', '1.30.4'),
-    ('rvcheck', '0.1.5'),
-    ('scatterpie', '0.1.4'),
-    ('velox', '0.2.0'),
-    ('rlist', '0.4.6.1'),
-    ('measurements', '1.4.0'),
-    ('qpdf', '1.1'),
-    ('fda', '2.4.8'),
-    ('fda.usc', '1.5.0'),
-    ('gstat', '2.0-3'),
-    ('countrycode', '1.1.0'),
-    ('itcSegment', '0.8'),
-    ('owmr', '0.8.1'),
-    ('rwunderground', '0.1.8'),
-    ('corrplot', '0.84'),
-    ('prettymapr', '0.2.2'),
-    ('prospectr', '0.1.3'),
-    ('rosm', '0.2.5'),
-    ('rpart.plot', '3.0.8'),
-    ('varhandle', '2.0.4'),
-    ('expint', '0.1-6'),
-    ('actuar', '2.3-3'),
-    # NA
-    #('spptest', NA
-    #('package_vector', NA
-    #('countriesHigh', NA
-    #('pdftools', '2.2'), deb: libpoppler-cpp-dev OR rpm: poppler-cpp-devel
-    #('ggExtra', NA
-]
-
 modextrapaths = {'R_LIBS': ''}
 
 postinstallcmds = [
     "cd %(installdir)s && " +
+    'Rscript -e "install.packages(c(\'rgdal\', \'gdalUtils\', \'ncdf4\', \'gdtools\', \'leaflet\', \'satellite\', \'sf\', \'svglite\', \'leafem\', \'leafpop\', \'mapview\', \'MuMIn\', \'intervals\', \'spacetime\', \'gstat\', \'RNetCDF\', \'automap\', \'clhs\', \'reporttools\', \'rgeos\', \'RandomFieldsUtils\', \'RandomFields\', \'rworldmap\', \'rworldxtra \', \'colorRamps\', \'mapdata\', \'mapproj\', \'RPostgreSQL\', \'getPass\', \'stringdist\', \'here\', \'svMisc\', \'networkD3\', \'cmsaf\', \'RPostgres\', \'nzelect\', \'wordcloud\', \'ngram\', \'rtweet\', \'lettercase\', \'xgboost\', \'rts\', \'RgoogleMaps\', \'packrat\', \'rsconnect\', \'rpostgis\', \'aws.signature\', \'aws.s3\', \'geosphere\', \'fuzzyjoin\', \'refinr\', \'x13binary\', \'seasonal\', \'mitools\', \'survey\', \'sysfonts\', \'showtextdb\', \'showtext\', \'BiocManager\', \'rvcheck\', \'scatterpie\', \'velox\', \'rlist\', \'measurements\', \'qpdf\', \'fda\', \'fda.usc\', \'gstat\', \'countrycode\', \'itcSegment\', \'owmr\', \'rwunderground\', \'corrplot\', \'prettymapr\', \'prospectr\', \'rosm\', \'rpart.plot\', \'varhandle\', \'expint\', \'actuar\'), repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" && ' +
     'Rscript -e "install.packages(c(\'treemap\', \'ggmap\', \'hts\', \'thief\', \'forecastHybrid\', \'ggseas\', \'colourpicker\', \'bsplus\', \'profvis\'), repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" && ' +
     'Rscript -e "library(remotes); install_github(\'myllym/GET\', lib=\'%(installdir)s\')" && ' +
     'Rscript -e "install.packages(c(\'shinyFiles\', \'shinyjs\', \'shinyhelper\', \'shinycssloaders\', \'shinyWidgets\', \'shinyBS\'), repos=\'http://cran.rstudio.com/\', lib=\'%(installdir)s\')" && ' +

foss-2020b/PostgreSQL-12.4-GCCcore-10.2.0.eb

@@ -0,0 +1,51 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'ConfigureMake'
+
+name = 'PostgreSQL'
+version = '12.4'
+
+homepage = 'https://www.postgresql.org/'
+description = """PostgreSQL is a powerful, open source object-relational database system.
+ It is fully ACID compliant, has full support for foreign keys,
+ joins, views, triggers, and stored procedures (in multiple languages).
+ It includes most SQL:2008 data types, including INTEGER,
+ NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP.
+ It also supports storage of binary large objects, including pictures,
+ sounds, or video. It has native programming interfaces for C/C++, Java,
+ .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['9749b891b9d8f984312fe510a7a3613035134cee1e634793dac5568d1e1a5852']
+
+builddependencies = [
+    ('binutils', '2.35'),
+    ('Bison', '3.7.1'),
+    ('flex', '2.6.4'),
+    ('Perl', '5.32.0'),
+    ('Python', '3.8.6'),
+]
+
+dependencies = [
+    ('libreadline', '8.0'),
+    ('zlib', '1.2.11'),
+    # OS dependency should be preferred if the os version is more recent then this version,
+    # it's nice to have an up to date openssl for security reasons
+    # ('OpenSSL', '1.0.2h'),
+]
+
+#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
+osdependencies = [OS_PKG_OPENSSL_DEV]
+
+configopts = '--with-python --with-openssl'
+
+sanity_check_paths = {
+    'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT],
+    'dirs': ['share/postgresql'],
+}
+
+moduleclass = 'data'