It's just waiting for someone to finish off https://github.com/timholy/HDF5.jl/pull/152
--Tim On Wednesday, November 19, 2014 11:34:10 AM Lanfeng Pan wrote: > The rhdf5 package > [http://www.bioconductor.org/packages/release/bioc/html/rhdf5.html ] in R > contains a hdf5small.tgz which is only 2.3MB. I don't know the difference > but maybe you can consider to include a hdf5 source file in HDF5, too. Then > you can choose the best version for users. The rhdf5 package is much easier > to install without root privilege. > > Best, > Lanfeng > > On Wednesday, November 19, 2014 1:00:07 PM UTC-6, Tim Holy wrote: > > Upstream bugs are rough. If you decide to report it to the libhdf5 > > developers, > > note that even 1.8.13 has a new bug: > > https://github.com/timholy/HDF5.jl/issues/172 > > > > Seems to be getting worse with each release. > > > > --Tim > > > > On Wednesday, November 19, 2014 10:35:47 AM Lanfeng Pan wrote: > > > Wow, 1.8.13 works! I have been fighting with it for a whole night. > > > Thanks! > > > > > > On Wednesday, November 19, 2014 12:15:16 PM UTC-6, Tim Holy wrote: > > > > For the binary, which library version are you using? Can you test > > > > something > > > > different from 1.8.14? (I don't have any particular reason to suspect > > > > 1.8.14 is > > > > bad, I am just wondering...) > > > > > > > > --Tim > > > > > > > > On Wednesday, November 19, 2014 10:08:41 AM Lanfeng Pan wrote: > > > > > Hi guys, > > > > > > > > > > I installed hdf5 manually on a linux server which I have no root > > > > > > > > privilege. > > > > > > > > > Pkg.add("HDF5") is fine but `using HDF5` will give me the following > > > > > > > > errors: > > > > > julia> Pkg.add("HDF5") > > > > > INFO: Installing BinDeps v0.3.6 > > > > > INFO: Installing HDF5 v0.4.6 > > > > > INFO: Installing SHA v0.0.3 > > > > > INFO: Installing URIParser v0.0.3 > > > > > INFO: Building HDF5 > > > > > INFO: Package database updated > > > > > > > > > > julia> using HDF5 > > > > > > > > > > HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0: > > > > > #000: H5P.c line 299 in H5Pcreate(): not a property list class > > > > > > > > > > major: Invalid arguments to routine > > > > > minor: Inappropriate type > > > > > > > > > > HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0: > > > > > #000: H5Pstrcpl.c line 159 in H5Pset_char_encoding(): can't find > > > > > > > > object > > > > > > > > > for ID > > > > > > > > > > major: Object atom > > > > > minor: Unable to find atom information (already closed?) > > > > > > > > > > #001: H5Pint.c line 3381 in H5P_object_verify(): property list is > > > > not > > > > > > a > > > > > > > > > member of the class > > > > > > > > > > major: Property lists > > > > > minor: Unable to register new atom > > > > > > > > > > #002: H5Pint.c line 3331 in H5P_isa_class(): not a property list > > > > > > > > > > major: Invalid arguments to routine > > > > > minor: Inappropriate type > > > > > > > > > > ERROR: Error setting char encoding > > > > > > > > > > in h5p_set_char_encoding at > > > > > > > > /home/pan/.julia/v0.3/HDF5/src/plain.jl:1848 > > > > > > > > > in include at ./boot.jl:245 > > > > > in include_from_node1 at ./loading.jl:128 > > > > > in include at ./boot.jl:245 > > > > > in include_from_node1 at ./loading.jl:128 > > > > > in reload_path at loading.jl:152 > > > > > in _require at loading.jl:67 > > > > > in require at loading.jl:51 > > > > > > > > > > while loading /home/pan/.julia/v0.3/HDF5/src/plain.jl, in expression > > > > > starting on line 2102 > > > > > while loading /home/pan/.julia/v0.3/HDF5/src/HDF5.jl, in expression > > > > > starting on line 1 > > > > > > > > > > julia> dlopen("libhdf5") > > > > > Ptr{Void} @0x00000000057e89b0 > > > > > > > > > > > > > > > > > > > > > > > > > I also tried to use the binary hdf5 files, but the error persists. > > > > The > > > > > > > system information: > > > > > > > > > > $ cat /etc/redhat-release > > > > > CentOS release 6.6 (Final) > > > > > > > > > > $ gcc --version > > > > > gcc (GCC) 4.8.2 20140120 (Red Hat 4.8.2-15) > > > > > > > > > > $which gcc > > > > > ~/gcc-4.8.2/bin/gcc > > > > > > > > > > $ julia --version > > > > > julia version 0.3.2
