[R] h5r package: cannot find hdf5

[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:

>
>
> > 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*
>
> >
>
> >       [[alternative HTML version deleted]]
>
> >
>
> > ______________________________________________
>
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>
> > https://stat.ethz.ch/mailman/listinfo/r-help
>
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
>
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> David Winsemius
>
> Alameda, CA, USA
>
>
>
> ______________________________________________
>
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>
> https://stat.ethz.ch/mailman/listinfo/r-help
>
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
>
> and provide commented, minimal, self-contained, reproducible code.

	[[alternative HTML version deleted]]