carlos-alberto-silva/rGEDI

Downloading on MacOS: HDF5 compilation error

Closed this issue · 3 comments

sarahsmithtripp commented

I am trying to download rGEDI on MacOS 10.11.6. I was originally getting an error for not having 'gsl' installed. I installed gsl using homebrew via terminal and downloaded the 'gsl' package successfully. Now I am getting an error the h5pcc and the h5pcc is not compiling.

I've tried both:

devtools::install_github("carlos-alberto-silva/rGEDI", dependencies = TRUE)
devtools::install_git("https://github.com/carlos-alberto-silva/rGEDI", dependencies = TRUE)

And get out:

configure: WARNING:
Unable to locate HDF5 compilation helper scripts 'h5cc' or 'h5pcc'.
Please specify --with-hdf5=<LOCATION> as the full path to h5cc or h5pcc.
HDF5 support is being disabled (equivalent to --with-hdf5=no).

Where would hdf5 be located here?

Thanks!

caiohamamura commented
sarahsmithtripp commented

Hi Caio,

I tried brew install hdf5 in terminal, but am getting an invalid certificate warning. It suggests visiting this site: https://curl.haxx.se/docs/sslcerts.html

Following this I tried installing hdf5 without the certificate verification (pretense here I have little clue what I am doing bumbling around in terminal...) using:

brew install hdf5 -k

and now get the following:
Warning: hdf5 1.12.0_1 is already installed and up-to-date

So it appears I now have hdf5, but now I am running into not having geotiff.h when I go back to attempt to download rGEDI. I ran:
brew install geotiff.h

but it cannot find an install for this part. Do you have any thoughts on where geotiff.h would be?

Thank you so much for your help!

caiohamamura commented