[R] h5r package: cannot find hdf5

[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:

> cmpH5 <-
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>:

> 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-in
> stallation-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:
>
>> 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:
>>
>> > install.packages('h5r')
>> 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
>> > install.packages('/home/pedro/h5r_1.4.7.tar.gz',repos=NULL,t
>> ype='source')
>> 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*
>>
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>>
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>
>
>

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