Hi John,
On 31/12/2018 18:47, Dey, John F wrote:
I’ve started to work on R-3.5.2-foss-2018b. I am having issues with
hdf5r. I could really use some help. HDF5 R issues have consumed weeks
of my time in the past.
My easyconfig is at
https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/R-3.5.2-foss-2018b.eb
Just for reference, see also PR
https://github.com/easybuilders/easybuild-easyconfigs/pull/7355 .
Using HDF5-1.10.2-foss-2018b and hdf5r-1.0.1,
Upadate: I have downgraded hdf5r to 1.0.0 with Kenneth’s patch and it
works with 3.5.2. I have opened an issue with hdf5r.
Issue link: https://github.com/hhoeflin/hdf5r/issues/111 .
I am also open to review of the R-3.5.2 package. It has 182 updates
from 3.5.1 and about 19 new packages were brought in as dependencies.
ImageMagick has been added to support animation.
# I did not know that shared objects could define objects as undefined ?
nm /app/software/R/3.5.2-foss-2018b/lib/R/library/hdf5r/libs/hdf5r.so |
grep H5T_NATIVE_LDOUBLE_g
U H5T_NATIVE_LDOUBLE_g
Well, the problem here is probably that HDF5 1.10.2 which is included as
a dependency doesn't provide this symbol.
That's strange though, since based on
https://github.com/hhoeflin/hdf5r/blob/master/NEWS.md hdf5r 1.0.1
*should* be compatible with HDF5 1.10.2 .
Maybe we should wait a bit until we (hopefully) get a reply from the
hdf5r maintainer?
This is the tail of the 79MB log file.
gcc -shared -L/app/software/R/3.5.2-foss-2018b/lib/R/lib
-L/app/software/GCCcore/7.3.0/lib64 -L/app/software/GCCcore/7.3.0/lib
-L/app/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib
-L/app/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib
-L/app/software/X11/20180604-GCCcore-7.3.0/lib
-L/app/software/Mesa/18.1.1-foss-2018b/lib
-L/app/software/libGLU/9.0.0-foss-2018b/lib
-L/app/software/cairo/1.14.12-GCCcore-7.3.0/lib
-L/app/software/libreadline/7.0-GCCcore-7.3.0/lib
-L/app/software/ncurses/6.1-GCCcore-7.3.0/lib
-L/app/software/bzip2/1.0.6-GCCcore-7.3.0/lib
-L/app/software/XZ/5.2.4-GCCcore-7.3.0/lib
-L/app/software/zlib/1.2.11-GCCcore-7.3.0/lib
-L/app/software/SQLite/3.24.0-GCCcore-7.3.0/lib
-L/app/software/PCRE/8.41-GCCcore-7.3.0/lib
-L/app/software/libpng/1.6.34-GCCcore-7.3.0/lib
-L/app/software/libjpeg-turbo/2.0.0-GCCcore-7.3.0/lib
-L/app/software/LibTIFF/4.0.9-GCCcore-7.3.0/lib
-L/app/software/Java/1.8.0_181/lib
-L/app/software/Tk/8.6.8-GCCcore-7.3.0/lib
-L/app/software/cURL/7.60.0-GCCcore-7.3.0/lib
-L/app/software/libxml2/2.9.8-GCCcore-7.3.0/lib
-L/app/software/GDAL/2.2.3-foss-2018b-Python-3.6.6/lib
-L/app/software/PROJ/5.0.0-foss-2018b/lib
-L/app/software/GMP/6.1.2-GCCcore-7.3.0/lib
-L/app/software/NLopt/2.4.2-GCCcore-7.3.0/lib
-L/app/software/FFTW/3.3.8-gompi-2018b/lib
-L/app/software/libsndfile/1.0.28-GCCcore-7.3.0/lib
-L/app/software/ICU/61.1-GCCcore-7.3.0/lib
-L/app/software/HDF5/1.10.2-foss-2018b/lib
-L/app/software/UDUNITS/2.2.26-foss-2018b/lib
-L/app/software/GSL/2.5-GCC-7.3.0-2.30/lib
-L/app/software/ImageMagick/7.0.8-22-GCCcore-7.3.0/lib -o hdf5r.so
const_export.o datatype_export.o Wrapper_auto_H5A.o Wrapper_auto_H5.o
Wrapper_auto_H5D.o Wrapper_auto_H5DS.o Wrapper_auto_H5E.o
Wrapper_auto_H5F.o Wrapper_auto_H5G.o Wrapper_auto_H5I.o
Wrapper_auto_H5IM.o Wrapper_auto_H5L.o Wrapper_auto_H5LT.o
Wrapper_auto_H5O.o Wrapper_auto_H5P.o Wrapper_auto_H5R.o
Wrapper_auto_H5S.oWrapper_auto_H5TB.o Wrapper_auto_H5T.o
Wrapper_auto_H5Z.o Wrapper_auto_H5FDcore.o Wrapper_auto_H5FDfamily.o
Wrapper_auto_H5FDlog.o Wrapper_auto_H5FDsec2.o Wrapper_auto_H5FDstdio.o
convert.o hdf5r_init.o H5Error.o H5ls.o Wrapper_manual_H5T.o
-L/app/software/R/3.5.2-foss-2018b/lib/R/lib -lR
installing to /app/software/R/3.5.2-foss-2018b/lib/R/library/hdf5r/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for 'hdf5r' in dyn.load(file,
DLLpath = DLLpath, ...):
unable to load shared object
'/app/software/R/3.5.2-foss-2018b/lib/R/library/hdf5r/libs/hdf5r.so':
/app/software/R/3.5.2-foss-2018b/lib/R/library/hdf5r/libs/hdf5r.so:
undefined symbol: H5T_NATIVE_LDOUBLE_g
Error: loading failed
Execution halted
--
*John Dey*
*HPC Operations*
Scientific Computing
*O* _206.667.4308 <tel:(206)%20667-4308>_
*M* _360.649.2731 <tel:(360)%20649-2731>_
*E* [email protected] <mailto:[email protected]>
/Users/john/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1817288594
*Fred Hutchinson Cancer Research Center*
1100 Fairview Ave. N
<https://maps.google.com/?q=1100+Fairview+Ave.+N&entry=gmail&source=g>.,
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*fredhutch.org <http://www.fredhutch.org/>*
