From a2c55efde0d7f57a2d889e8500809f008b5dd259 Mon Sep 17 00:00:00 2001 From: Taras Lazariv Date: Tue, 5 Mar 2024 21:41:21 +0100 Subject: [PATCH 1/5] adding easyconfigs: R-4.3.3-gfbf-2023b.eb --- .../easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 372 ++++++++++++++++++ 1 file changed, 372 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb new file mode 100644 index 00000000000..5ed3ce06c41 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -0,0 +1,372 @@ +name = 'R' +version = '4.3.3' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['80851231393b85bf3877ee9e39b282e750ed864c5ec60cbd68e6e139f0520330'] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20231019'), + ('Mesa', '23.1.9'), + ('libGLU', '9.0.3'), + ('cairo', '1.18.0'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.4'), + ('zlib', '1.2.13'), + ('SQLite', '3.43.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.40'), # for plotting in R + ('libjpeg-turbo', '3.0.1'), # for plottting in R + ('LibTIFF', '4.6.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '8.3.0'), + ('Tk', '8.6.13'), # for tcltk + ('HarfBuzz', '8.2.2'), # for textshaping + ('FriBidi', '1.0.13'), # for textshaping + +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +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', +} + +# !! order of packages is important !! +# packages updated on 5th November 2023 +exts_list = [ + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.3', { + 'checksums': ['24a3424b5dc2c4bd3e5f7c0b54fbe1355028e329181b2d41f4464c8ade28bf0a'], + }), + ('Rcpp', '1.0.12', { + 'checksums': ['0c7359cc43beee02761aa3df2baccede1182d29d28c9cd49964b609305062bd0'], + }), + ('R6', '2.5.1', { + 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], + }), + ('cli', '3.6.2', { + 'checksums': ['4c0749e3711b2b6ae90fd992784303bc8d98039599cac1deb397239a7018e151'], + }), + ('base64enc', '0.1-3', { + 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], + }), + ('rprojroot', '2.0.4', { + 'checksums': ['b5f463fb25a24dac7a4ca916be57dbe22b5262e1f41e53871ca83e57d4336e99'], + }), + ('xfun', '0.42', { + 'checksums': ['07bbfaed212ba1fcb9367624e8bc4936a7884e30e0efc561199acd0fcba5750a'], + }), + ('commonmark', '1.9.1', { + 'checksums': ['9517a13f4ce4a99bb157493453b04419b222cb65a9471cd3b11e5045ac0db53b'], + }), + ('highr', '0.10', { + 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], + }), + ('digest', '0.6.34', { + 'checksums': ['0b737552932f165d4158ac94631f90abfb02c510df14577d7aa900c8fd3d44d9'], + }), + ('desc', '1.4.3', { + 'checksums': ['54468da73dd78fc9e7c565c41cfe3331802c2134b2e61a9ad197215317092f26'], + }), + ('ellipsis', '0.3.2', { + 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], + }), + ('prettyunits', '1.2.0', { + 'checksums': ['f059f27e2a5c82e351fe05b87ad712f7afc273c651450453f59d99af5deeacea'], + }), + ('crayon', '1.5.2', { + 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], + }), + ('stringi', '1.8.3', { + 'checksums': ['1602be8edd1dd8ac5a836f4077cbc9d6a312ca4b2c594a0486370e8c1e314925'], + }), + ('magrittr', '2.0.3', { + 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], + }), + ('evaluate', '0.23', { + 'checksums': ['c9cf9c37502b8fbfa78e4eb96b8c3d1789060e49505c86c07cb7476da804a45c'], + }), + ('ps', '1.7.6', { + 'checksums': ['52c35ffc3d1e1d984a94c7bbd671ef4ad70946990cbcd80e814e17937b056dd2'], + }), + ('processx', '3.8.3', { + 'checksums': ['1ad8c51482b89702fbbb6621b1a179c1ae67b78388b8fd9c841bbc8cf035d831'], + }), + ('callr', '3.7.5', { + 'checksums': ['18a11e8f7324d5b013149af69a32784aea7433863492aaabccd8d227b73b472c'], + 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('lifecycle', '1.0.4', { + 'checksums': ['ada4d3c7e84b0c93105e888647c5754219a8334f6e1f82d5afaf83d4855b91cc'], + }), + ('vctrs', '0.6.5', { + 'checksums': ['43167d2248fd699594044b5c8f1dbb7ed163f2d64761e08ba805b04e7ec8e402'], + }), + ('stringr', '1.5.1', { + 'checksums': ['a4adec51bb3f04214b1d8ef40d3a58949f21b1497cbeaf2ba552e0891eef45de'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), + ('diffobj', '0.3.5', { + 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], + }), + ('rematch2', '2.1.2', { + 'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'], + }), + ('waldo', '0.5.2', { + 'checksums': ['82cdae1ab2c5e7e5dbf5c6bdf832020b46e152732053fb45de7c9a81afdf2e05'], + }), + ('testthat', '3.2.1', { + 'checksums': 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['6c0fbe98ece8a511973263f8e8a35574df0cfc45edea7452b53b8d326436b3bd'], + }), + ('cpp11', '0.4.7', { + 'checksums': ['801d1266824c3972642bce2db2a5fd0528a65ec845c58eb5a886edf082264344'], + }), + ('systemfonts', '1.0.5', { + 'checksums': ['840ffb1d8293739c79cbc868101d9f9a84f4a9de4c7b3625e30af2fb63e15823'], + }), + ('textshaping', '0.3.7', { + 'checksums': ['fa924dbe1fb4138b80d6c26ee42f4203843f1d34f77e2a5e42514e6fcc97ec42'], + }), + ('ragg', '1.2.7', { + 'checksums': ['d77a18662d127881dcb5046033eb809293ad9ad439fa4b217202b8cef4280c9f'], + }), + ('whisker', '0.4.1', { + 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], + }), + ('pkgdown', '2.0.7', { + 'checksums': ['f33872869dfa8319182d87e90eab3245ff69293b3b791471bf9538afb81b356a'], + }), + ('htmlwidgets', '1.6.4', { + 'checksums': ['7cb08f0b30485dac26f72e4056ec4ed8825d1398e8b9f25ed63db228fe3a0ed0'], + }), + ('profvis', '0.3.8', { + 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), + ('later', '1.3.2', { + 'checksums': ['52f5073d33cd0d3c12e56526c9c53c323ebafcc79b22cc6e51fb0c41ee2b561e'], + }), + ('promises', '1.2.1', { + 'checksums': ['3ce0a26df39ea27536877ec6db13083b2952108245024baa8b40ae856d2ce5be'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('httpuv', '1.6.14', { + 'checksums': ['4026acae26bd99873e269b062f343f2239131130b43fdfd6a1a5a89b913cd181'], + }), + ('sourcetools', '0.1.7-1', { + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], + }), + ('shiny', '1.8.0', { + 'checksums': ['f28740ba28707e8b3dabb2ad27b002dae555317010660702163bb0daefe04641'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('brew', '1.0-10', { + 'checksums': ['4181f7334e032ae0775c5dec49d6137eb25d5430ca3792d321793307b3dda38f'], + }), + ('roxygen2', '7.3.1', { + 'checksums': ['215e9fa9c0e73cb33f9870854c97b25c1a6386f519f69f397123f1a66656e2c8'], + }), + ('rversions', '2.1.2', { + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.4.2.1', { + 'checksums': ['7ba8ca9a652d60bcdea25dbd43bd1e055e97b031c05e0bc3fac43bf245c1209d'], + }), + ('clipr', '0.8.0', { + 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.2', { + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], + }), + ('httr2', '1.0.0', { + 'checksums': ['cb852d6f560c329a7dc17aa760f09a0950413513dc8abfc3facb6418b2934a49'], + }), + ('gh', '1.4.0', { + 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], + }), + ('credentials', '2.0.1', { + 'checksums': ['2c7cfc45bd4afa9a2c2b85d43e907b212da3468781e1b617737bd095253c358b'], + }), + ('zip', '2.3.1', { + 'checksums': ['83754408781c525917f36535865d28214893de0778b5f337e050cb543cacc28f'], + }), + ('gert', '2.0.1', { + 'checksums': ['0ed784837809ce89797ea77834d420e89351728f70d8d2f4b34487df813cd092'], + }), + ('usethis', '2.2.3', { + 'checksums': ['8d0c98995c23b5f4b5b95cd453557d2d15faa7399cc01bff304f5b15cb0cdeb3'], + }), + ('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' From 1537e7723b313b2a5ea84612a19dde703f0d15a1 Mon Sep 17 00:00:00 2001 From: lazariv Date: Wed, 6 Mar 2024 11:12:47 +0100 Subject: [PATCH 2/5] Update easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb index 5ed3ce06c41..74dc215f575 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -37,7 +37,6 @@ dependencies = [ ('Tk', '8.6.13'), # for tcltk ('HarfBuzz', '8.2.2'), # for textshaping ('FriBidi', '1.0.13'), # for textshaping - ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. From a499c022e1f468f15dc356afefa9e8fff8ad4fd2 Mon Sep 17 00:00:00 2001 From: lazariv Date: Thu, 7 Mar 2024 16:36:19 +0100 Subject: [PATCH 3/5] Update R-4.3.3-gfbf-2023b.eb Updated date the package extensions have been checked --- easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb index 74dc215f575..27db2723983 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -62,7 +62,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 5th November 2023 +# packages updated on 4th March 2024 exts_list = [ 'base', 'compiler', From 628b0e31c95bac64d3095223662dbbb73196c532 Mon Sep 17 00:00:00 2001 From: Taras Lazariv Date: Fri, 8 Mar 2024 16:11:16 +0100 Subject: [PATCH 4/5] Update brio package installation --- easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb index 27db2723983..801efed656f 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -162,6 +162,9 @@ exts_list = [ ('rstudioapi', '0.15.0', { 'checksums': ['935bc81dca37d3d6e77982bfe6e7fbd779e8606e5b7e00d0ba4c80fec0416ccf'], }), + ('brio', '1.1.4', { + 'checksums': ['0cbbf38948682b2435eea69b04be59187b149183dc7562df71dc0d3e260e18e8'], + }), ('pkgload', '1.3.4', { 'checksums': ['60b04b948cda4dc56257b1e89f9b0a4b1273cacecdb2bd995d66dd76e89926ce'], }), @@ -183,9 +186,6 @@ exts_list = [ ('praise', '1.0.0', { 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], }), - ('brio', '1.1.4', { - 'checksums': ['0cbbf38948682b2435eea69b04be59187b149183dc7562df71dc0d3e260e18e8'], - }), ('jsonlite', '1.8.8', { 'checksums': ['7de21316984c3ba3d7423d12f43d1c30c716007c5e39bf07e11885e0ceb0caa4'], }), From 72559bc55c7cf95828c6e92d14ba1c569a6c57f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 11 Mar 2024 17:59:35 +0100 Subject: [PATCH 5/5] Update easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb Add back description of base of include packages --- easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb index 801efed656f..df95c0aaa55 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -64,6 +64,9 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 4th March 2024 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets',