h5r package: cannot find hdf5

On 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") :

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.



--

David.

 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,type='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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