{lang}[foss/2021a] R v4.1.0 #13032

branfosj · 2021-06-03T17:44:43Z

(created using eb --new-pr)

Requires:

ICU (~~{lib}[GCCcore/10.3.0] ICU v69.1 #13022~~)
Tk (~~{vis}[GCCcore/10.3.0] Tk v8.6.11 #13023~~)
GSL (~~{numlib}[GCC/10.3.0] GSL v2.7 #13024~~)
nodejs (~~{lang}[GCCcore/10.3.0] nodejs v14.17.0 #13025~~)
UDUNITS (~~{phys}[GCCcore/10.3.0] UDUNITS v2.2.28 #13026~~)
Ghostscript, ImageMagick, LittleCMS (~~{vis}[GCCcore/10.3.0] Ghostscript v9.54.0, ImageMagick v7.0.11-14, LittleCMS v2.12 #13027~~)
GDAL and deps (~~{data}[foss/2021a] GDAL v3.3.0, GEOS v3.9.1, HDF v4.2.15, ... w/ Python 3.9.5 #13030~~)
Xvfb (~~{vis}[GCCcore/10.3.0] Xvfb v1.20.11 #13031~~)

…fy-flexiblas-in-configure.patch

branfosj · 2021-06-03T18:08:49Z

Test report by @branfosj
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/0be77ecd737f4e99facb84e6dba92ca6 for a full test report.

branfosj · 2021-06-03T20:19:34Z

Error: package or namespace load failed for mclust in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/library/00LOCK-mclust/00new/mclust/libs/mclust.so':
  /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/library/00LOCK-mclust/00new/mclust/libs/mclust.so: undefined symbol: _ZGVbN2v_log

Also seen in #11455 (comment)

This looks like a -lm is missing from the build of this package.

branfosj · 2021-06-04T08:41:10Z

Setting

preconfigopts = 'export FLIBS="$FLIBS -lm" && '

in the ec solves the issue - that is putting that on the main R install. I've not found an equivalent for the individual extension to solve the issue.

branfosj · 2021-06-04T18:47:48Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/0367320c6b08701dc8d8c1dc7c033b05 for a full test report.

…asyconfigs into 20210603184437_new_pr_R410

boegel · 2021-06-06T10:53:01Z

Setting
preconfigopts = 'export FLIBS="$FLIBS -lm" && '
in the ec solves the issue - that is putting that on the main R install. I've not found an equivalent for the individual extension to solve the issue.

What about a patch file for mclust, similar to the ones we have for other extensions, see for example https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/r/R/optmatch-0.9-10_icpc-wd308.patch ?

boegel · 2021-06-06T10:53:53Z

easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb

+    ('OpenSSL', '1.1', '', True),
+]
+
+preconfigopts = 'export FLIBS="$FLIBS -lm" && '


At the very least a comment should be added above to explain why this is needed, but it should be possible to come up with something specific to mclust...

I've removed this line and gone with the patch option, as per #13032 (comment) - done in cd4cd5e and c0a7dea

Scratch that. We hit a similar error on quantreg and waveslim. I'd expect it for other extensions as well. I've reverted and added a comment in 88c0e22.

@branfosj I tried installing this easyconfig without the top-level preconfigopts, and it works fine for me...

Can you share the error output you're getting for one of these extensions, along with the failing command, so I can compare?

On which OS are you seeing trouble?

RHEL 8.3

Error is: /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/library/00LOCK-mclust/00new/mclust/libs/mclust.so: undefined symbol: _ZGVbN2v_log

Build for mclust is:

== 2021-06-03 19:08:22,248 filetools.py:1775 INFO Creating directory /dev/shm/build-branfosj-admin/branfosj-admin-up/R/4.1.0/foss-2021a/mclust (parents: True, set_gid: False, sticky: False) == 2021-06-03 19:08:22,248 run.py:226 INFO running cmd: tar xzf /rds/bear-sysadmin/configmgmt/easybuild/sources/r/R/extensions/mclust_5.4.7.tar.gz == 2021-06-03 19:08:22,349 run.py:226 INFO running cmd: R CMD INSTALL /dev/shm/build-branfosj-admin/branfosj-admin-up/R/4.1.0/foss-2021a/mclust/mclust --library=/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/library --no-clean-on-error == 2021-06-03 19:08:45,924 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd " R CMD INSTALL /dev/shm/build-branfosj-admin/branfosj-admin-up/R/4.1.0/foss-2021a/mclust/mclust --library=/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/library --no-clean-on-error " exited with exit code 1 and output: * installing *source* package mclust ... ** package mclust successfully unpacked and MD5 sums checked ** using staged installation ** libs gfortran -fno-optimize-sibling-calls -fpic -O2 -ftree-vectorize -march=native -fno-math-errno -c dmvnorm.f -o dmvnorm.o gcc -I"/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/include" -DNDEBUG -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/OpenSSL/1.1/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GDAL/3.3.0-foss-2021a/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/nodejs/14.17.0-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GLPK/5.0-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ImageMagick/7.0.11-14-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GSL/2.7-GCC-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/UDUNITS/2.2.28-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/HDF5/1.10.7-gompi-2021a/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ICU/69.1-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libsndfile/1.0.31-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/FFTW/3.3.9-gompi-2021a/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/NLopt/2.7.0-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GMP/6.2.1-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libxml2/2.9.10-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/cURL/7.76.0-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Tk/8.6.11-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Java/11.0.2/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/LibTIFF/4.2.0-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libjpeg-turbo/2.0.6-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libpng/1.6.37-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/PCRE2/10.36-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/SQLite/3.35.4-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/zlib/1.2.11-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/XZ/5.2.5-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/bzip2/1.0.8-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ncurses/6.2-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libreadline/8.1-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/cairo/1.16.0-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libGLU/9.0.1-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Mesa/21.1.1-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/X11/20210518-GCCcore-10.3.0/include -I/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/FlexiBLAS/3.0.4-GCC-10.3.0/include -fpic -O2 -ftree-vectorize -march=native -fno-math-errno -c init.c -o init.o gfortran -fno-optimize-sibling-calls -fpic -O2 -ftree-vectorize -march=native -fno-math-errno -c mclust.f -o mclust.o gfortran -fno-optimize-sibling-calls -fpic -O2 -ftree-vectorize -march=native -fno-math-errno -c mclustaddson.f -o mclustaddson.o gcc -shared -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/OpenSSL/1.1/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/OpenSSL/1.1/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GDAL/3.3.0-foss-2021a/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GDAL/3.3.0-foss-2021a/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/nodejs/14.17.0-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/nodejs/14.17.0-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GLPK/5.0-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GLPK/5.0-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ImageMagick/7.0.11-14-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ImageMagick/7.0.11-14-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GSL/2.7-GCC-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GSL/2.7-GCC-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/UDUNITS/2.2.28-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/UDUNITS/2.2.28-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/HDF5/1.10.7-gompi-2021a/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/HDF5/1.10.7-gompi-2021a/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ICU/69.1-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ICU/69.1-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libsndfile/1.0.31-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libsndfile/1.0.31-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/FFTW/3.3.9-gompi-2021a/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/FFTW/3.3.9-gompi-2021a/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/NLopt/2.7.0-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/NLopt/2.7.0-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GMP/6.2.1-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GMP/6.2.1-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libxml2/2.9.10-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libxml2/2.9.10-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/cURL/7.76.0-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/cURL/7.76.0-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Tk/8.6.11-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Tk/8.6.11-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Java/11.0.2/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Java/11.0.2/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/LibTIFF/4.2.0-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/LibTIFF/4.2.0-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libjpeg-turbo/2.0.6-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libjpeg-turbo/2.0.6-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libpng/1.6.37-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libpng/1.6.37-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/PCRE2/10.36-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/PCRE2/10.36-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/SQLite/3.35.4-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/SQLite/3.35.4-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/zlib/1.2.11-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/zlib/1.2.11-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/XZ/5.2.5-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/XZ/5.2.5-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/bzip2/1.0.8-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/bzip2/1.0.8-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ncurses/6.2-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ncurses/6.2-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libreadline/8.1-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libreadline/8.1-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/cairo/1.16.0-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/cairo/1.16.0-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libGLU/9.0.1-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/libGLU/9.0.1-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Mesa/21.1.1-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Mesa/21.1.1-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/X11/20210518-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/X11/20210518-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Xvfb/1.20.11-GCCcore-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/Xvfb/1.20.11-GCCcore-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ScaLAPACK/2.1.0-gompi-2021a-fb/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/ScaLAPACK/2.1.0-gompi-2021a-fb/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/FlexiBLAS/3.0.4-GCC-10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/FlexiBLAS/3.0.4-GCC-10.3.0/lib -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GCCcore/10.3.0/lib64 -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/GCCcore/10.3.0/lib -o mclust.so dmvnorm.o init.o mclust.o mclustaddson.o -lflexiblas -lgfortran -lgfortran -lgfortran -L/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/lib -lR installing to /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/library/00LOCK-mclust/00new/mclust/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for mclust in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/library/00LOCK-mclust/00new/mclust/libs/mclust.so': /rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/R/4.1.0-foss-2021a/lib64/R/library/00LOCK-mclust/00new/mclust/libs/mclust.so: undefined symbol: _ZGVbN2v_log Error: loading failed Execution halted ERROR: loading failed (at easybuild/tools/run.py:565 in parse_cmd_output)

Linking command looks identical on CentOS 7, no problem there. I'll also check on RHEL8

I'm also seeing this on our Ubuntu 20.04 (singularity container install).

There are other options for placing the -lm - I can add it to LDFLAGS instead and it still works. However, it does look like it needs setting in the R ec for me, as these items get stored in a config file inside the R install.

I can confirm I see the same problem on RHEL8, the -lm needs to be specified explicitly.

I'm not sure whether it makes more sense to add it through LDFLAGS...

The contents of <installdir>/lib/R/etc/Makeconf looks identical on both CentOS 7 and RHEL8 (except for absolute paths).

FLIBS = -lgfortran

Is there in both, yet somehow -lm is added automagically, or not needed at all, when linking mclust on CentOS 7?!

CentOS 7 brings in further differences. The missing symbols (_ZGVbN2v_log) are part of the vectorised math library (libmvec) so something different could be happening there. It confuses me that I've not seen this before.

verdurin · 2021-06-07T14:31:39Z

Test report by @verdurin
FAILED
Build succeeded for 38 out of 41 (1 easyconfigs in total)
easybuild-c7.novalocal - Linux centos linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/d5a35e82aeae16457fc913d03f49335e for a full test report.

verdurin · 2021-06-07T16:05:42Z

Test report by @verdurin
FAILED
Build succeeded for 2 out of 3 (1 easyconfigs in total)
easybuild-c7.novalocal - Linux centos linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/e02ec9d5c6a74e0f6c1f78a2944a960c for a full test report.

boegel · 2021-06-07T16:14:26Z

Checksum verification for extension source rda_1.0.2-2.1.tar.gz failed

@verdurin Is that broken download, or are they really doing in-place updates again in CRAN?

branfosj · 2021-06-07T16:26:40Z

Checksum verification for extension source rda_1.0.2-2.1.tar.gz failed
@verdurin Is that broken download, or are they really doing in-place updates again in CRAN?

:(
Sorry - I missed that the old easyconfigs had an alternative checksum for rda_1.0.2-2.1.tar.gz. I've readded that in 06382ce.

Edit: I've also checked and that was the only alternative checksum in the previous R ec that is still relevant here.

verdurin · 2021-06-07T17:37:09Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
nuc.lan - Linux Fedora 33, x86_64, Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, Python 3.9.4
See https://gist.github.com/606731cbb2383e3f671f979f1e38674e for a full test report.

verdurin · 2021-06-07T19:39:44Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild-c7.novalocal - Linux centos linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/bf4a5372a5388be92b6ab177763d7e32 for a full test report.

verdurin · 2021-06-08T07:15:29Z

@branfosj @boegel could you re-test on RHEL8 systems?

boegel · 2021-06-08T10:26:22Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node2617.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/0887e1332f660a82389d258a1f0f5092 for a full test report.

branfosj · 2021-06-08T11:09:30Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/2e012e1b4f627c2652bb99640f79d0fa for a full test report.

boegel · 2021-06-08T12:17:10Z

@branfosj Looks like the gert extension need git 2.x?

----------------------------- ANTICONF -------------------------------
Configuration failed to find libgit2 library. Try installing:
 * brew: libgit2 (MacOS)
 * deb: libgit2-dev (Debian, Ubuntu, etc)
 * rpm: libgit2-devel (Fedora, CentOS, RHEL)
If libgit2 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libgit2.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: git2.h: No such file or directory
compilation terminated.

see #13073

branfosj · 2021-06-08T12:29:58Z

Added in 35458d4.

We see the failure because

Error in curl::curl_download("https://r-lib.github.io/gert/get-libgit2-linux.sh",  : 
          HTTP error 503.

which was when lots of the internet was down.

boegel · 2021-06-08T13:57:39Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3501.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/884387f228414560bd7b3dbc0d336310 for a full test report.

…asyconfigs into 20210603184437_new_pr_R410

boegel · 2021-06-08T18:03:21Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
select-pika-c6gd-2xlarge-0001 - Linux centos linux 8.3.2011, AArch64, ARM UNKNOWN (graviton2), Python 3.6.8
See https://gist.github.com/de19b2d3e7e0497df5f518649fd97cef for a full test report.

edit: failed because ~~the git we include as a dependency doesn't provide the header files~~ we should be using libgit2 rather than git as dependency...

boegel · 2021-06-08T19:05:19Z

easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb

+    ('GLPK', '5.0'),  # for Rglpk
+    ('nodejs', '14.17.0'),  # for V8 (required by rstan)
+    ('GDAL', '3.3.0'),  # for sf
+    ('git', '2.32.0', '-nodocs'),


@branfosj This should be libgit2 rather than git...

('libgit2', '1.1.0'),

boegel · 2021-06-08T19:35:34Z

@boegelbot please test @ generoso

boegelbot · 2021-06-08T19:40:19Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=13032 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_13032 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 17389

Test results coming soon (I hope)...

- notification for comment with ID 857051593 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

branfosj · 2021-06-08T23:03:54Z

Test report by @branfosj
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/5333d9113e8020aa5122cd6a614d9e8b for a full test report.

branfosj · 2021-06-08T23:10:37Z

Test report by @branfosj
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux Ubuntu 20.04, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.8.5
See https://gist.github.com/a7fb85334c5906302bb88103d0a4a992 for a full test report.

boegelbot · 2021-06-08T23:53:32Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/7ea939166322ac3ffbfe7d2661e79d06 for a full test report.

boegel · 2021-06-09T00:10:15Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node2617.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/512bfa21c8d9d2eead05e079ae959adb for a full test report.

boegel · 2021-06-09T01:08:28Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
select-pika-c6gd-2xlarge-0001 - Linux centos linux 8.3.2011, AArch64, ARM UNKNOWN (graviton2), Python 3.6.8
See https://gist.github.com/6a1e9a70a847cad2548452da3c10dc2f for a full test report.

boegel · 2021-06-09T06:23:42Z

Going in, thanks @branfosj!

adding easyconfigs: R-4.1.0-foss-2021a.eb and patches: R-4.1.0_identi…

eb7857c

…fy-flexiblas-in-configure.patch

branfosj added the update label Jun 3, 2021

branfosj added this to the 4.x milestone Jun 3, 2021

branfosj marked this pull request as draft June 3, 2021 18:09

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Add GxEScanR (easybuilders#13039) and add -lm to R FLIBS

9104af5

branfosj mentioned this pull request Jun 4, 2021

{bio,math}[foss/2021a] R-bundle-Bioconductor v3.13, ncdf4 v1.17 #13044

Merged

3 tasks

branfosj marked this pull request as ready for review June 5, 2021 11:40

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

8ec6efc

…asyconfigs into 20210603184437_new_pr_R410

easybuilders deleted a comment from boegelbot Jun 5, 2021

boegel requested changes Jun 6, 2021

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branfosj added 3 commits June 6, 2021 12:50

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

cd4cd5e

fix typo in patch description

c0a7dea

revert to setting FLIBS

88c0e22

add back alternative checksum for rda

06382ce

add git as a dep - for gert

35458d4

easybuilders deleted a comment from boegelbot Jun 8, 2021

boegel and others added 2 commits June 8, 2021 17:18

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

10cd9c6

…asyconfigs into 20210603184437_new_pr_R410

correct git version

76e4859

easybuilders deleted a comment from boegelbot Jun 8, 2021

boegel requested changes Jun 8, 2021

View reviewed changes

libgit2 instead of git

1720ad2

easybuilders deleted a comment from boegelbot Jun 8, 2021

boegel approved these changes Jun 9, 2021

View reviewed changes

boegel merged commit 083968c into easybuilders:develop Jun 9, 2021

branfosj deleted the 20210603184437_new_pr_R410 branch June 9, 2021 06:34

boegel modified the milestones: 4.x, next release (4.4.1) Jun 10, 2021

{lang}[foss/2021a] R v4.1.0 #13032

{lang}[foss/2021a] R v4.1.0 #13032

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