Unable to install/use hdf5r due to issues locating libhdf5_hl.so.200

[SuhasSrinivasan]

System Details

Operating System = CentOS Linux release 7.9.2009 (Core)

R = 4.2.0

The hdf5 version available through RPM is 1.8.12-13.el7, which is incompatible with hdf5r 1.3.5.
Then, the following solution was used to compile hdf5 1.12.2 from source.
#115 (comment)

But additional issues follow.

Issue 1 - Installation

However, after successfully verifying hdf5 installation, hdf5r installation still fails.

> install.packages("hdf5r", configure.args="--with-hdf5=/usr/local/hdf5/bin/h5cc")
...
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘hdf5r’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/opt/R/4.2.0/lib/R/library/00LOCK-hdf5r/00new/hdf5r/libs/hdf5r.so':
  libhdf5_hl.so.200: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/R/4.2.0/lib/R/library/hdf5r’

Workaround for Issue 1

1. Verify the location of hdf5

/usr/local/hdf5
/usr/local/hdf5/lib

2. Add LD_LIBRARY_PATH to .Renviron

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/hdf5/lib

Verify in R through Sys.getenv() that this variable is loaded.

  
**3. Install **
> install.packages("hdf5r", configure.args="--with-hdf5=/usr/local/hdf5/bin/h5cc")
...
* DONE (hdf5r)

Issue 2 - Package loading

This occurs post installation even though .Renviron worked previously.

> library("Seurat")
Attaching SeuratObject
Attaching sp
> Read10X_h5()
Error in Read10X_h5() : Please install hdf5r to read HDF5 files
> library("hdf5r")
Error: package or namespace load failed for ‘hdf5r’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/opt/R/4.2.0/lib/R/library/hdf5r/libs/hdf5r.so':
  libhdf5_hl.so.200: cannot open shared object file: No such file or directory

Workaround for Issue 2

> dyn.load("/usr/local/hdf5/lib/libhdf5_hl.so.200")
> library("hdf5r")
> library("Seurat")
Attaching SeuratObject
Attaching sp
> Read10X_h5()
Error in file.exists(filename) :
  argument "filename" is missing, with no default

Things that did not work for both Issues 1 and 2

1. Adding LD_LIBRARY_PATH to .bashrc and then source .bashrc
2. Creating /etc/ld.so.conf.d/custom.conf with hdf5 lib path and then ldconfig

[andrew-w-schroeder]

Hi @SuhasSrinivasan , did you ever find a working solution to this issue? I'm experiencing the same error on my CentOS system.

[SuhasSrinivasan]

Hi @andrew-w-schroeder, please see above. I have identified two issues and provided workarounds for both.

[mmokrejs]

Hi,
I have same issue here but the cause is that Rhdf5lib provides static libs, not dymanic-ones.

The command

x86_64-pc-linux-gnu-gcc -shared -L/usr/lib64/R/lib -Wl,-O1 -Wl,--as-needed -Wl,-rpath=/usr/lib64/R/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.o Wrapper_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/storage/vestec1-elixir/projects/biocev/mmokrejs/apps/anaconda3/lib -lhdf5_hl -lhdf5 -L/storage/vestec1-elixir/projects/biocev/mmokrejs/apps/anaconda3/lib -L/storage/vestec1-elixir/projects/biocev/mmokrejs/apps/anaconda3/lib -L/storage/vestec1-elixir/projects/biocev/mmokrejs/apps/anaconda3/lib -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm -L. -lhdf5_hl -lhdf5 -lz -lm -L/usr/lib64/R/lib -lR
installing to /auto/vestec1-elixir/projects/biocev/gentoo/usr/lib64/R/library/00LOCK-hdf5r/00new/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 from temporary location
Error: package or namespace load failed for 'hdf5r' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/lib64/R/library/00LOCK-hdf5r/00new/hdf5r/libs/hdf5r.so':
  libhdf5_hl.so.310: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/usr/lib64/R/library/hdf5r'
* restoring previous '/usr/lib64/R/library/hdf5r'

seems to work but during import R cannot find static library and fails to load it.

How can I force hdf5r to pick the static library during linking? Why didn't x86_64-pc-linux-gnu-gcc do it in the above command?

$ R CMD INSTALL --configure-args='--enable-static=yes' hdf5r_1.3.11.tar.gz 
* installing to library '/usr/lib64/R/library'
* installing *source* package 'hdf5r' ...
** package 'hdf5r' successfully unpacked and MD5 sums checked
** using staged installation
configure: WARNING: unrecognized options: --enable-static

$ R CMD INSTALL --configure-args='--enable-static' hdf5r_1.3.11.tar.gz 
* installing to library '/usr/lib64/R/library'
* installing *source* package 'hdf5r' ...
** package 'hdf5r' successfully unpacked and MD5 sums checked
** using staged installation
configure: WARNING: unrecognized options: --enable-static

I solved it by disabling conda env and installing hdf5-1.14.3 libs and headers on the system. Then, h5cc was picked by configure and the R package could be linked and loaded properly. See #100 (comment)