installing R gsl package on Mac
gsl, macos, r
Solution
I was able to get things working (OS X Yosemite 10.10, R 3.1.1, gsl 1.16, gsl R package 1.9-10) with standard brew-installed R and gsl by manually prefixing `CFLAGS` and `LDFLAGS` with the output from `gsl-config --cflags` and `gsl-config --libs` respectively.
The following:
CFLAGS="-I/usr/local/opt/gsl/include" LDFLAGS="-L/usr/local/opt/gsl/lib -lgsl -lgslcblas" R
...
> install.packages("gsl")
worked for me.
Note that `gsl-config` lists the direct path to my Cellar, the paths above are brew symlinks.
Problem
I'm trying to install the `gsl` package for R, which I understand is simply a wrapper around the GSL, under OSX Mavericks. I've tried the obvious: ``` > install.packages('gsl') Installing package into ‘/Users/myusername/Library/R/3.1/library’ (as ‘lib’ is unspecified) package ‘gsl’ is available as a source package but not as a binary Warning in install.packages : package ‘gsl’ is not available (for R version 3.1.0) ``` So I ran ``` > install.packages('gsl',type = 'source') Installing package into ‘/Users/myusername/Library/R/3.1/library’ (as ‘lib’ is unspecified) trying URL 'http://cran.rstudio.com/src/contrib/gsl_1.9-10.tar.gz' Content type 'application/x-gzip' length 342803 bytes (334 Kb) opened URL ================================================== downloaded 334 Kb * installing *source* package ‘gsl’ ... ** package ‘gsl’ successfully unpacked and MD5 sums checked checking for gsl-config... no configure: error: gsl-config not found, is GSL installed? ERROR: configuration failed for package ‘gsl’ * removing ‘/Users/myusername/Library/R/3.1/library/gsl’ Warning in install.packages : installation of package ‘gsl’ had non-zero exit status ``` No GSL install. D'oh! So I install GSL via Homebrew: ``` ~ brew install gsl ==> Downloading http://ftpmirror.gnu.org/gsl/gsl-1.15.tar.gz ######################################################################## 100.0% ==> ./configure --prefix=/usr/local/Cellar/gsl/1.15 ==> make ==> make install /usr/local/Cellar/gsl/1.15: 239 files, 6.7M, built in 101 seconds ``` Try to install the R package again: ``` > install.packages('gsl',type = 'source') Installing package into ‘/Users/myusername/Library/R/3.1/library’ (as ‘lib’ is unspecified) trying URL 'http://cran.rstudio.com/src/contrib/gsl_1.9-10.tar.gz' Content type 'application/x-gzip' length 342803 bytes (334 Kb) opened URL ================================================== downloaded 334 Kb * installing *source* package ‘gsl’ ... ** package ‘gsl’ successfully unpacked and MD5 sums checked checking for gsl-config... /usr/local/bin/gsl-config checking if GSL version >= 1.12... 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 configure: error: Need GSL version >= 1.12 ERROR: configuration failed for package ‘gsl’ * removing ‘/Users/myusername/Library/R/3.1/library/gsl’ Warning in install.packages : installation of package ‘gsl’ had non-zero exit status ``` I'm obviously going about this the wrong way but am unsure about where exactly the problem lies.