> On Dec 17, 2016, at 5:09 PM, Pedro Montenegro <[email protected]> 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]] > > ______________________________________________ > [email protected] 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 ______________________________________________ [email protected] 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.
