Check foss-2019a for debian

foss-2018b/libmo_unpack-3.1.2-foss-2018b.eb

@@ -15,6 +15,8 @@ builddependencies = [('CMake', '3.11.4')]
 
 separate_build_dir = True
 
+configopts = '-DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -lsubunit"'
+
 sanity_check_paths = {
     'files': ['lib/libmo_unpack.%s' % SHLIB_EXT],
     'dirs': [],

foss-2019a/ELIC_R-2-foss-2019a-R-3.6.0.eb

@@ -1,112 +0,0 @@
-easyblock = 'Bundle'
-
-name = 'ELIC_R'
-version = '2'
-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': '2019a'}
-
-dependencies = [
-    ('R', '3.6.0'),
-    ('GEOS', '3.7.2', '-Python-3.7.2'),
-    ('GDAL', '3.0.0', '-Python-3.7.2'),
-]
-
-exts_default_options = {
-    'source_urls': [
-        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
-        'https://cran.r-project.org/src/contrib/',  # current version of packages
-        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
-    ],
-    'source_tmpl': '%(name)s_%(version)s.tar.gz'
-}
-
-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 Sept 25th 2018
-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'),
-    ('gstat', '2.0-2'),
-    ('RNetCDF', '1.9-1'),
-    ('automap', '1.0-14'),
-    ('clhs', '0.7-2'),
-    ('rasterVis', '0.45'),
-    ('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'),
-    ('treemap', '2.4-2'),
-    ('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'),
-    ('ggmap', '3.0.0'),
-    ('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', '0.1.4'),
-    ('refinr', '0.3.1'),
-    ('x13binary', '1.1.39-2'),
-    ('seasonal', '1.7.0'),
-    ('mitools', '2.4'),
-    ('survey', '3.36'),
-    ('hts','5.1.5'),
-    ('thief', '0.3'),
-    ('forecastHybrid', '4.2.17'),
-    ('ggseas', '0.5.4'),
-    ('sysfonts', '0.8'),
-    ('showtextdb', '2.0'),
-    ('showtext', '0.7'),
-    ('BiocManager', '1.30.4'),
-    ('rvcheck', '0.1.5'),
-    ('scatterpie', '0.1.3'),
-    ('velox', '0.2.0'),
-    ('rlist', '0.4.6.1'),
-    ('measurements', '1.4.0'),
-]
-
-modextrapaths = {'R_LIBS': ''}
-
-sanity_check_paths = {
-    'files': [],
-    'dirs': ['ncdf4', 'sf', 'mapview'],
-}
-
-moduleclass = 'numlib'

foss-2019a/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb

@@ -31,7 +31,7 @@ dependencies = [
     ('zlib', '1.2.11'),
     ('cURL', '7.63.0'),
     ('PCRE', '8.43'),
-    ('PROJ', '6.1.0'),
+    ('PROJ', '6.2.0'),
     ('libgeotiff', '1.5.1'),
 ]
 

foss-2019a/Mesa-19.0.1-GCCcore-8.2.0.eb

@@ -0,0 +1,73 @@
+# Automatically converted from Mesa-17.2.4-intel-2017b.eb
+# Original message:
+# the purpose of the easyconfig is to build a Mesa for software rendering,
+# not hardware rendering. This means you want at least SSE4.2. We build:
+# - llvmpipe: the high-performance Gallium LLVM driver
+# - swr: Intel's OpenSWR
+# it will try to use the llvmpipe by default. It you want swr, do:
+# GALLIUM_DRIVER=swr
+
+easyblock = 'MesonNinja'
+
+name = 'Mesa'
+version = '19.0.1'
+
+homepage = 'http://www.mesa3d.org/'
+description = """Mesa is an open-source implementation of the OpenGL specification -
+ a system for rendering interactive 3D graphics."""
+
+toolchain = {'name': 'GCCcore', 'version': '8.2.0'}
+# Intel's SWR generates AVX instructions even on CPUs without support for it (ignoring march=native).
+# In that case it is necessary to explicitly set the march of your CPU, for instance for an AMD Opteron 6100
+# toolchainopts = {'optarch': 'march=barcelona'}
+
+source_urls = [
+    'https://mesa.freedesktop.org/archive/',
+    'https://mesa.freedesktop.org/archive/%(version)s',
+    'ftp://ftp.freedesktop.org/pub/mesa/%(version)s',
+    'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s',
+]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = [
+    '6884163c0ea9e4c98378ab8fecd72fe7b5f437713a14471beda378df247999d4',  # mesa-19.0.1.tar.xz
+]
+
+builddependencies = [
+    ('binutils', '2.31.1'),
+    ('Meson', '0.50.0', '-Python-3.7.2'),
+    ('Ninja', '1.9.0'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.0.5'),
+    ('pkg-config', '0.29.2'),
+    ('Mako', '1.0.8'),
+    ('libxml2', '2.9.8'),
+    ('expat', '2.2.6'),
+    ('gettext', '0.19.8.1'),
+]
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('nettle', '3.4.1'),
+    ('libdrm', '2.4.97'),
+    ('LLVM', '7.0.1'),
+    ('X11', '20190311'),
+    ('libunwind', '1.3.1'),
+]
+
+configopts = " -Dplatforms=x11 -Dosmesa=gallium -Ddri3=false -Ddri-drivers='' -Dvulkan-drivers=''"
+configopts += " -Dgbm=false -Dglx-direct=false -Dgallium-drivers='swrast,swr' -Degl=false"
+configopts += " -Dllvm=true -Dshared-llvm=true"
+configopts += " -Dlibunwind=true -Dglx=gallium-xlib"
+
+sanity_check_paths = {
+    'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT,
+              'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT,
+              'include/GL/glext.h', 'include/GL/gl_mangle.h',
+              'include/GL/glx.h', 'include/GL/osmesa.h',
+              'include/GL/gl.h', 'include/GL/glxext.h',
+              'include/GL/glx_mangle.h', 'include/GLES/gl.h',
+              'include/GLES2/gl2.h', 'include/GLES3/gl3.h'],
+    'dirs': []
+}
+
+moduleclass = 'vis'

foss-2019a/NCL-6.6.2-foss-2019a.eb

@@ -37,6 +37,8 @@ dependencies = [
 ]
 builddependencies = [
     ('makedepend', '1.0.6'),
+    ('Bison', '3.0.5'),
+    ('flex', '2.6.4'),
 ]
 
 moduleclass = 'data'

foss-2019a/PROJ-6.2.0-GCCcore-8.2.0.eb

@@ -0,0 +1,37 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2014-2015 The Cyprus Institute
+# Authors:: Thekla Loizou <t.loizou@cyi.ac.cy>
+# License:: MIT/GPL
+#
+##
+easyblock = 'ConfigureMake'
+
+name = 'PROJ'
+version = '6.2.0'
+
+homepage = 'http://trac.osgeo.org/proj/'
+description = """Program proj is a standard Unix filter function which converts 
+geographic longitude and latitude coordinates into cartesian coordinates"""
+
+toolchain = {'name': 'GCCcore', 'version': '8.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['http://download.osgeo.org/proj/']
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+    ('pkg-config', '0.29.2'),
+    ('binutils', '2.31.1'),
+]
+
+dependencies = [('SQLite', '3.27.2')]
+
+sanity_check_paths = {
+    'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo',
+              'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'

foss-2019a/PostgreSQL-11.3-GCCcore-8.2.0-Python-3.7.2.eb

@@ -0,0 +1,48 @@
+easyblock = 'ConfigureMake'
+
+name = 'PostgreSQL'
+version = '11.3'
+versionsuffix = '-Python-%(pyver)s'
+
+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': '8.2.0'}
+
+source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['2a9ff3659e327a4369929478200046942710fd6bc25fe56c72d6b01ee8b1974a']
+
+builddependencies = [
+    ('binutils', '2.31.1'),
+    ('Bison', '3.0.5'),
+    ('flex', '2.6.4'),
+    ('Perl', '5.28.1'),
+]
+
+dependencies = [
+    ('libreadline', '8.0'),
+    ('zlib', '1.2.11'),
+    ('Python', '3.7.2'),
+    # 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')]
+
+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'

foss-2019a/libgeotiff-1.5.1-GCCcore-8.2.0.eb

@@ -19,7 +19,7 @@ builddependencies = [
 dependencies = [
     ('zlib', '1.2.11'),
     ('LibTIFF', '4.0.10'),
-    ('PROJ', '6.1.0'),
+    ('PROJ', '6.2.0'),
     ('libjpeg-turbo', '2.0.2'),
 ]
 

foss-2019a/libmo_unpack-3.1.2-foss-2019a.eb

@@ -15,6 +15,8 @@ builddependencies = [('CMake', '3.13.3')]
 
 separate_build_dir = True
 
+configopts = '-DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -lsubunit"'
+
 sanity_check_paths = {
     'files': ['lib/libmo_unpack.%s' % SHLIB_EXT],
     'dirs': [],

foss-2019a/poppler-0.70.1-foss-2019a.eb

@@ -0,0 +1,53 @@
+# easybuild easyconfig
+#
+# John Dey jfdey@fredhutch.org
+# Fred Hutchinson Cancer Research Center Seattle WA USA
+
+easyblock = 'CMakeMake'
+
+name = 'poppler'
+version = '0.70.1'
+
+homepage = 'https://poppler.freedesktop.org/'
+description = """Poppler is a PDF rendering library based on the xpdf-3.0 code
+ base."""
+
+toolchain = {'name': 'foss', 'version': '2019a'}
+
+source_urls = ['https://poppler.freedesktop.org/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['66972047d9ef8162cc8c389d7e7698291dfc9f2b3e4ea9a9f08ae604107451bd']
+
+separate_build_dir = True
+
+builddependencies = [
+    ('pkgconfig', '1.3.1', '-Python-2.7.15'),
+    ('binutils', '2.30'),
+    ('CMake', '3.11.4'),
+    ('Qt5', '5.10.1'),
+    ('cairo', '1.14.12'),
+    ('GObject-Introspection', '1.54.1', '-Python-2.7.15'),
+    ('libjpeg-turbo', '2.0.0'),
+    ('libpng', '1.6.34'),
+    ('LibTIFF', '4.0.9'),
+    ('NSS', '3.39'),
+    ('OpenJPEG', '2.3.0'),
+]
+
+local_bin_files = ['pdfdetach', 'pdffonts', 'pdfimages', 'pdfinfo', 'pdfseparate',
+                   'pdftocairo', 'pdftohtml', 'pdftoppm', 'pdftops', 'pdftotext',
+                   'pdfunite']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bin_files] +
+             ['lib/libpoppler.%s' % SHLIB_EXT,
+              'lib/libpoppler-cpp.%s' % SHLIB_EXT,
+              'lib/libpoppler-glib.%s' % SHLIB_EXT,
+              'include/poppler/glib/poppler.h'],
+    'dirs': ['bin',
+             'include',
+             'include/poppler/glib',
+             ]
+}
+
+moduleclass = 'vis'

noarch/Java-1.8.0_212.eb

@@ -0,0 +1,20 @@
+# Contribution from the Crick HPC team
+# uploaded by J. Sassmannshausen
+
+name = 'Java'
+version = '1.8.0_212'
+
+homepage = 'http://java.com/'
+description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy
+ Java applications on desktops and servers."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+# download the tar.gz directly from
+# http://www.oracle.com/technetwork/java/javase/downloads/index.html
+(vp, vs) = version.split('_')
+altver = '%su%s' % (vp.split('.')[1], vs)
+sources = ['jdk-%s-linux-x64.tar.gz' % altver]
+checksums = ['62d57a7550c97b534343443475d9afd9']
+
+moduleclass = 'lang'

noarch/Java-1.8.eb

@@ -0,0 +1,18 @@
+# Contribution from the Crick HPC team
+# uploaded by J. Sassmannshausen
+# updated to version 202
+
+easyblock = 'ModuleRC'
+
+name = 'Java'
+version = '1.8'
+
+homepage = 'http://java.com/'
+description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy
+ Java applications on desktops and servers."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+dependencies = [('Java', '%(version)s.0_212')]
+
+moduleclass = 'lang'

noarch/MATLAB-UCL-2015a.eb

@@ -10,7 +10,7 @@ toolchain = {'name': 'dummy', 'version': ''}
 
 sources = [SOURCELOWER_TAR_GZ]
 
-dependencies = [('Java', '1.8.0_192')]
+dependencies = [('Java', '1.8.0_212')]
 
 import os
 license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'matlab-lic-one.sipr.ucl.ac.be')

noarch/MATLAB-UCL-2017a.eb

@@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''}
 # including the hidden files, especially .dvd1 and .dvd2 
 sources = [SOURCELOWER_TAR_GZ]
 
-dependencies = [('Java', '1.8.0_192')]
+dependencies = [('Java', '1.8.0_212')]
 
 import os
 license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'matlab-lic-one.sipr.ucl.ac.be')