add -lm to mclust build and remove it from being set in the R ec

easybuilders · Jun 6, 2021 · cd4cd5e · cd4cd5e
1 parent 8ec6efc
commit cd4cd5e
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Showing 2 changed files with 13 additions and 3 deletions.
diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb
@@ -53,7 +53,6 @@ dependencies = [
     ('OpenSSL', '1.1', '', True),
 ]
 
-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
@@ -73,7 +72,7 @@ exts_default_options = {
 }
 
 # !! order of packages is important !!
-# packages updated on 03 June 2021
+# packages updated on 3rd June 2021
 exts_list = [
     'base',
     'datasets',
@@ -177,7 +176,11 @@ exts_list = [
         'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'],
     }),
     ('mclust', '5.4.7', {
-        'checksums': ['45f5a666caee5bebd3160922b8655295a25e37f624741f6574365e4ac5a14c23'],
+        'patches': ['mclust-5.4.7_add-lm.patch'],
+        'checksums': [
+            '45f5a666caee5bebd3160922b8655295a25e37f624741f6574365e4ac5a14c23',  # mclust_5.4.7.tar.gz
+            'd41bda861abe2022e1139e85890828c8a97f0fcdb8b2cbe6182871437ce0db81',  # mclust-5.4.7_add-lm.patch
+        ],
     }),
     ('RANN', '2.6.1', {
         'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'],

diff --git a/easybuild/easyconfigs/r/R/mclust-5.4.7_add-lm.patch b/easybuild/easyconfigs/r/R/mclust-5.4.7_add-lm.patch
@@ -0,0 +1,7 @@
+Add -lm to libsto avoid undefined symbol _ZGVbN2v_lo
+Patch by Simon Branford (University of Birmingham)
+--- src/Makevars.orig	2021-06-06 11:55:48.233875000 +0100
++++ src/Makevars	2021-06-06 11:55:58.272198000 +0100
+@@ -1 +1 @@
+-PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
++PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -lm