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carlos-alberto-silva / rGEDI

rGEDI: An R Package for NASA's Global Ecosystem Dynamics Investigation (GEDI) Data Visualization and Processing.
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System dependencies for rGEDI? #10

Closed serbinsh closed 4 years ago

serbinsh commented 4 years ago

I have bumped into an issue installing rGEDI on my mac

trying URL 'https://cloud.r-project.org/src/contrib/rGEDI_0.1.6.tar.gz'
Content type 'application/x-gzip' length 3665792 bytes (3.5 MB)
==================================================
downloaded 3.5 MB

* installing *source* package ‘rGEDI’ ...
** package ‘rGEDI’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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 gsl-config... /usr/local/bin/gsl-config
checking for GSL - version >= 0.1... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking for grep that handles long lines and -e... /usr/bin/grep
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for h5cc... /usr/local/bin/h5cc
checking for HDF5 type... serial
checking for HDF5 libraries... yes (version 1.10.5)
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for H5Fcreate in -lhdf5... yes
checking for main in -lhdf5_hl... yes
checking for matching HDF5 Fortran wrapper... no
checking geotiff.h usability... no
checking geotiff.h presence... no
checking for geotiff.h... no
configure: error: cannot find geotiff.h
ERROR: configuration failed for package ‘rGEDI’
* removing ‘/Users/sserbin/R/library/rGEDI’
Warning in install.packages :
  installation of package ‘rGEDI’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T/RtmpE92gjD/downloaded_packages’
Error in library(rGEDI) : there is no package called ‘rGEDI’

I see its looking for HDF5 and geotiff. Are these depends listed somewhere? I was looking for this info. Thanks!

serbinsh commented 4 years ago

FYI - I solved this with Homebrew

brew install libgeotiff
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rGEDI)

The downloaded source packages are in
    ‘/private/var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T/RtmpDjxY7j/downloaded_packages’