Sorry I'm not sure what that error means. Dominik On Sun, Dec 18, 2016 at 17:21 David Winsemius <[email protected]> wrote:
> > > > 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. [[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.
