Update HDF5 from 1.8.5 to 1.10.1

[pmenzel]

The R package Seurat requires at least version 1.8.12.

install.packages('Seurat')
Installing package into ‘/home/kretzmer/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
...
checking for h5cc... /usr/bin/h5cc
checking for HDF5 libraries... yes (version 1.8.5-patch1)
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for H5Fcreate in -lhdf5... yes
checking for hdf5_hl.h... yes
checking for H5LTpath_valid in -lhdf5_hl... no
checking for main in -lhdf5_hl... yes
checking for matching HDF5 Fortran wrapper... no
Found hdf5 with version: 1.8.5-patch1
configure: error: The version of hdf5 installed on your system is not sufficient. Please ensure that at least version 1.8.12 is installed
ERROR: configuration failed for package ‘hdf5r’
* removing ‘/home/kretzmer/R/x86_64-pc-linux-gnu-library/3.5/hdf5r’
ERROR: dependency ‘hdf5r’ is not available for package ‘Seurat’
* removing ‘/home/kretzmer/R/x86_64-pc-linux-gnu-library/3.5/Seurat’

The downloaded source packages are in
    ‘/scratch/local/RtmpJ0SUsa/downloaded_packages’
Warning messages:
1: In install.packages("Seurat") :
  installation of package ‘hdf5r’ had non-zero exit status
2: In install.packages("Seurat") :
  installation of package ‘Seurat’ had non-zero exit status

[thomas]

After some meditation about the 'scientific' libs in the system, I'll opt for building only static libraries.
We don't need to bother about folks that use the libs for their own stuff, and the amount of binaries is/will be rather small, so saving space isn't an issue.

As for the hdf5lib, I''l suggest to build it with autotools and not cmake, 'caus the cmake results (although following a certain logic) look pretty weird:

lrwxrwxrwx root/root         0 2018-08-20 12:15 /usr/lib/libhdf5-shared.so -> libhdf5-shared.so.100.1.0
lrwxrwxrwx root/root         0 2018-08-20 12:15 /usr/lib/libhdf5-shared.so.100.1.0 -> libhdf5-shared.so.1.10.1
-rwxr-xr-x root/root   5401584 2018-08-20 12:15 /usr/lib/libhdf5-shared.so.1.10.1
-rw-r--r-- root/root   9779786 2018-08-20 12:15 /usr/lib/libhdf5-static.a

Or let me put it in other words, this is another attempt of 'smarting-out' each other, 'caus with these names I'm able to give -l hdf5-static to the linker -- oh, what a bargain :)

[donald]

Oops, another hdf5? Sorry, did I merge #886 to early? Is this obsolete now?

[pmenzel]

This can be closed now.