Build environment does not have hdf5. I am now using docker containers for all
my builds. My build environment is extremely limited on purpose, it does not
even have make, pkg-config etc.
FYI, I had to add pkg-config as a builddep to DBus-1.13.6-foss-2018b.eb in
order to have it build.
John Dey
On 1/4/19, 8:51 AM, "easybuild-requ...@lists.ugent.be on behalf of Kenneth
Hoste" <easybuild-requ...@lists.ugent.be on behalf of kenneth.ho...@ugent.be>
wrote:
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, "easybuild-requ...@lists.ugent.be on behalf of
Kenneth Hoste" <easybuild-requ...@lists.ugent.be on behalf of
kenneth.ho...@ugent.be> 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* jf...@fredhutch.org <mailto:jf...@fredhutch.org>
> >
> >
/Users/john/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1817288594
> > *Fred Hutchinson Cancer Research Center*
> > 1100 Fairview Ave. N
> >
<https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3D1100-2BFairview-2BAve.-2BN-26entry-3Dgmail-26source-3Dg&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=QGNxuXxTfXx0wMipO9xHw0g2BmggdYsdyWCTUppp-OQ&s=wZxOOqDbEj2qZnEF8lAijDc4-eMvqn3jCjuySGJGpqM&e=>.,
> > Mail Stop J3-516
> > Seattle, WA 98109
> > *fredhutch.org <http://www.fredhutch.org/>*
> >
>
>
