Comments (4)
openCyto (installing by hand with the R-bundle-Bioconductor/3.5-foss-2016b-fh1 module loaded) ultimately depends on ncdfFlow, which is installed in the bundle, but not loading:
> library('ncdfFlow') Loading required package: flowCore Loading required package: RcppArmadillo Loading required package: BH Error: package or namespace load failed for ‘ncdfFlow’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/app/easybuild/software/R-bundle-Bioconductor/3.5-foss-2016b-R-3.4.0-fh1/ncdfFlow/libs/ncdfFlow.so': /app/easybuild/software/R-bundle-Bioconductor/3.5-foss-2016b-R-3.4.0-fh1/ncdfFlow/libs/ncdfFlow.so: undefined symbol: ompi_mpi_cxx_op_intercept
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@mikejiang Any idea why this might be happening? I requested Sci Comp to install openCyto for use on the rhinos.
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Looks like the ncdfFlow
is linked to hdf5
library that was compiled with mpi
support, which is not necessary for ncdfFlow
. Anyway, it is currently not able to find the open mpi
symbol and is probably due to the runtime LD path setting. Try to add the mpi
library path to LD_LIBRARY_PATH
see if it helps.
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R-bundle-Bioconductor-3.5-foss-2016b-R-3.4.1-fh2.eb
('openCyto', '1.14.0', bioconductor_options),
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