On 04/01/2019 17:44, Dey, John F wrote:
This worked; usetting LIBS is needed.
('HDF5', '1.10.2'), # for hdf5r
('hdf5r', '1.0.1', {
'preinstallopts': "unset LIBS && ",
'checksums':
['32f35dc26809a7e9b9335e0dc24369cf87f4c6deb430b2d9d019450a10164240'],
}),
That's... interesting.
Do you have a version of HDF5 installed in your OS on the system where
you were seeing this problem?
regards,
Kenneth
John Dey
On 1/4/19, 2:55 AM, "[email protected] on behalf of Kenneth Hoste"
<[email protected] on behalf of [email protected]> wrote:
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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FredHutch_easybuild-2Dlife-2Dsciences_blob_master_fh-5Feasyconfigs_R-2D3.5.2-2Dfoss-2D2018b.eb&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=QGNxuXxTfXx0wMipO9xHw0g2BmggdYsdyWCTUppp-OQ&s=-XXzh1wy51rvARZm1ePEQfVBFjWaGJNOONhed1-pVR8&e=
Just for reference, see also PR
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_easybuilders_easybuild-2Deasyconfigs_pull_7355&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=QGNxuXxTfXx0wMipO9xHw0g2BmggdYsdyWCTUppp-OQ&s=ZOg1WjGQX2alrTYqcpzfag2jR2zRQLv-co3WzK83ArE&e=
.
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hhoeflin_hdf5r_issues_111&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=QGNxuXxTfXx0wMipO9xHw0g2BmggdYsdyWCTUppp-OQ&s=5WaVAl1Yc4GVRy-8Q8_xP_kjBIPSsiuetrMXtZ1i80o&e= .
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hhoeflin_hdf5r_blob_master_NEWS.md&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=QGNxuXxTfXx0wMipO9xHw0g2BmggdYsdyWCTUppp-OQ&s=qpayYw9pUTkiiO4Ff-Hcq0A8kdpG1XhYwtSvURYBOas&e=
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
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