Skip to content

h5r package: cannot find hdf5

5 messages · Pedro Montenegro, David Winsemius, Dominik Schneider

Original
Pedro Montenegro
# 
I'm new to R and Linux, and I have an issue I didn't see solved on the
internet.

I'm using Ubuntu Mate and installed R version 2.11 since the current
version does not support R-kinetics.
What happens is that I have hdf5 headers and libraries installed

$ whereis hdf5
hdf5: /usr/include/hdf5

But when I'm installing the package inside R (install.packages) or outside
R (R CMD INSTALL) the program reports the following error:
Warning in install.packages("h5r") :
  argument 'lib' is missing: using
'/home/pedro/R/x86_64-unknown-linux-gnu-library/2.11'
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ?h5r? is not available
Warning in install.packages("/home/pedro/h5r_1.4.7.tar.gz", repos = NULL,  :
  argument 'lib' is missing: using
'/home/pedro/R/x86_64-unknown-linux-gnu-library/2.11'
* installing *source* package ?h5r? ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed


checking for library containing inflate... -lz
checking for library containing H5open... no
configure: error: Can't find HDF5
ERROR: configuration failed for package ?h5r?
* removing ?/home/pedro/R/x86_64-unknown-linux-gnu-library/2.11/h5r?
Warning message:
In install.packages("/home/pedro/h5r_1.4.7.tar.gz", repos = NULL,  :
  installation of package '/home/pedro/h5r_1.4.7.tar.gz' had non-zero exit
status.

I tried to reinstall HDF5, R and even the whole OS and do it all over
again. Also tried to add the library to the environment table, do it from
the library's directory and nothing works.

Is there someone who had the same error and was able to solve it?
Is there someone who as a clue how to solve?

I'm sorry if there is a similar post around, I've seen some but I don't
find one where the problem is solved.
Best regards!

*Pedro*
Dominik Schneider
# 
Pedro,
I've only worked with netcdf4 but I imagine your issue is similar to one's
I've had:
I think you can:
1. add your hdf5 lib directory to the LD_LIBRARY_PATH
http://grokbase.com/t/r/r-help/10at4wcjfq/r-ncdf4-package-installation-in-r
2. you can specify the direct path to lib and include directories for the
hdf5 library:

e.g.

install.packages("/home/user/Downloads/RNetCDF_1.6.1-2.tar.gz",
repos = NULL,
type="source",
dependencies=FALSE,
configure.args="--with-netcdf-include=/usr/local/netcdf-4.2.1-build/include
--with-netcdf-lib=/usr/local/netcdf-4.2.1-build/lib")

http://stackoverflow.com/questions/11319698/how-to-install-r-packages-rnetcdf-and-ncdf-on-ubuntu
On Sat, Dec 17, 2016 at 5:09 PM, Pedro Montenegro <a67355 at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Pedro Montenegro
    

    

      
      #
    

  


  

      
Hello!

It worked! Thank you!
Now I have another issue, when I try to input a cmp.h5 it reports the
following error:

            

      
      
      
    

        
PacBioCmpH5("/home/user/Documents/MFG-share/pacbio/GI.usequality.cmp.h5")
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 140365256419200:
  #000: ../../../src/H5F.c line 1514 in H5Fopen(): unable to open file
    major: File accessability
    minor: Unable to open file
  #001: ../../../src/H5F.c line 1309 in H5F_open(): unable to read
superblock
    major: File accessability
    minor: Read failed
  #002: ../../../src/H5Fsuper.c line 305 in H5F_super_read(): unable to
find file signature
    major: File accessability
    minor: Not an HDF5 file
  #003: ../../../src/H5Fsuper.c line 153 in H5F_locate_signature(): unable
to find a valid file signature
    major: Low-level I/O
    minor: Unable to initialize object
Error in .local(.Object, ...) :
  Problem opening file:
/home/user/Documents/MFG-share/pacbio/GI.usequality.cmp.h5

Any idea what can be happening? It must be about the libraries since the
file appears to be OK.

Best regards



*Pedro*
2016-12-18 19:06 GMT+00:00 Dominik Schneider <dosc3612 at colorado.edu>:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
      #
    

  


  

          

      
      
      
    

        
There is also a bioconductor package that provides an HDF5 interface:

http://bioconductor.org/packages/release/bioc/html/rhdf5.html

I have no idea whether it's config files might include a more extensive search for installed versions of HDF5. Unlike h5r it is available for all three major forks of R.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dominik Schneider
    

    

      
      #
    

  


  

      
Sorry I'm not sure what that error means.
Dominik

On Sun, Dec 18, 2016 at 17:21 David Winsemius <dwinsemius at comcast.net>
wrote: