Problems Installing rgeos and rgdal on Mac OS X High Sierra - r

Question

I have looked at the multiple sources to figure out how to install rgeos and rgdal on Mac OS X High Sierra in a way that works with Anaconda Navigator. I mention Anaconda because I want to be able to build static project-specific, package environments to ensure that my projects work 6 months from now when the dependent packages change. I have successfully installed and used both rgeos and rgdal on a couple other computers but seem to be having issues on a new computer. I want to launch Shiny apps from Anaconda Navigator's RStudio. None of the solutions I found, listed below, worked:
https://dyerlab.ces.vcu.edu/2015/03/31/install-rgeos-on-osx/
https://cran.rstudio.com/web/packages/rgeos/rgeos.pdf
http://tlocoh.r-forge.r-project.org/mac_rgeos_rgdal.html
https://anaconda.org/conda-forge/r-rgdal
Based on the above sources and my slow progression through a series of error messages, I tried the following:
Install GDAL 2.2 Complete [30.0 MiB] 2018-3-10 from http://www.kyngchaos.com/software/frameworks. This installs GDAL, GEOS, PROJ, SQLite and UnixImageIO frameworks.
The above installed without an error message. But attempting to install rgeos gave an error message:
configure: error: geos-config not found or not executable.
Consequently, either the install failed and didn't notify me, or there is some type of $PATH issue (?). On a blog, someone suggested to do the following in response to the aforementioned issue:
brew install geos
The above completed successfully. So I went into RStudio and tried the following, which resolved the former error but produced a new one:
install.packages("~/Downloads/rgeos_0.3-28.tar.gz", repos = NULL, type = "source")
installing source package ‘rgeos’ ...
configure: CC: x86_64-apple-darwin13.4.0-clang
configure: CXX: x86_64-apple-darwin13.4.0-clang++
configure: rgeos: 0.3-28
checking for /usr/bin/svnversion... yes
cat: inst/SVN_VERSION: No such file or directory
configure: svn revision:
checking for geos-config... /usr/local/bin/geos-config
checking geos-config usability... yes
configure: GEOS version: 3.6.2
checking geos version at least 3.2.0... yes
checking geos-config clibs... yes
checking geos_c.h presence and usability... no
configure: error: geos_c.h not found in standard or given locations.
ERROR: configuration failed for package ‘rgeos’
removing ‘/Users/aloha2018/anaconda2/lib/R/library/rgeos’
Warning in install.packages :
installation of package ‘/Users/aloha2018/Downloads/rgeos_0.3-28.tar.gz’ had non-zero exit status
Any ideas on what to try next?
Naturally, I already tried in an RStudio application launched from Anaconda Navigator:
install.packages("rgeos")
install.packages("rgdal")
both from CRAN and from tar.gz. But it seems like it is unable to find a file called geos_c.h, which does indeed exist on my computer at:
/Library/Frameworks/GEOS.framework/Versions/3B/Headers/geos_c.h
Is there a way to tell RStudio to look in the directory containing that file so my rgeos and rgdal installations work? Are there other errors I should expect to encounter and if so, how do I avoid/resolve them?
I also tried in a Terminal window:
conda install -c conda-forge r-rgdal
but that fails after spending a long time attempting to "solve environment":
Andrews-MacBook-Pro:~ aloha2018$ conda install -c conda-forge r-rgdal
Solving environment: failed
UnsatisfiableError: The following specifications were found to be in conflict:
- r-rgdal
- rstudio==1.1.423
Use "conda info <package>" to see the dependencies for each package.
So I try:
conda r-rgdal
But there is no output:
Andrews-MacBook-Pro:~ aloha2018$ conda info r-rgdal
Andrews-MacBook-Pro:~ aloha2018$

Answer 1

I've had a similar issue. I first solved it by installing everything using conda using the following environment.yml configuration
name: london-crime-r
channels:
- conda-forge
- conda
dependencies:
- gdal
- geos
- r-base
- r-rcpp
- r-irkernel
- r-mass
- r-dplyr
- r-rgdal
- r-rgeos
- r-raster
- rstudio
However, after updating conda, resolving dependencies did not finish within the 10 hours so I went the traditional route:
Use brew to install geos and gdal. It takes 40 minutes to build on my machine.
brew install geos gdal
Once that has been achieved, install R packages in this sequence.
install.packages('sp', type='source')
install.packages("rgeos", repos="http://R-Forge.R-project.org", type="source")
require(rgeos)
install.packages("rgdal", repos="http://R-Forge.R-project.org", type="source")
require(rgdal)
Subsequently, the packages below are ok with the plain install.
libraries <- c("rgdal",
"rgeos",
"raster",
"spdep",
"spatstat")
install.packages(libraries)