installing R gsl package on Mac

问题:

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.

回答1:

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.

回答2:

I finally got this to work though I'm not sure which parts of the following are absolutely essential. Here's a step-by-step list of instructions:

(steps in parentheses may be optional. Perhaps the whole thing works with homebrew)

1. (download the latest version of the GSL from http://ftp.gnu.org/gnu/gsl/ (as of this writing the file to get is gsl-1.16.tar.gz))
2. (open up a terminal window, untar the file, cd into the directory and then run ./configure, make and make install)
3. download the sources to the R package from http://cran.r-project.org/web/packages/gsl/index.html
4. open up a terminal window and run launchctl setenv PATH "/usr/local/bin:$PATH"
5. in the same terminal window, build the R package (I couldn't get this to work from within R) by untar'ing the file just downloaded, cding into the directory and then running R CMD build ./gsl and R CMD INSTALL gsl_1.9-10.tar.gz

回答3:

I believe that others will find your steps successful and I think they do need to be done in that order. The build of gsl from source does need to be done after adding the homebrew default directory to the path. If you had used the binary, it was built on a CRAN machine that was able to find the (external) GSL package in the expected directy (which is not the default for homebreww installations. You might have succeeded with `install.packages('gsl_1.9-10.tar.gz', repo=NULL, type="source") if the source package were in your working directory (or add the full path/name as the first argument.) Just as with using Terminal, if you click-hold-drag a file to the R console, you will get a text entry of the full path/name.

回答4:

For Mac, just run:

brew install gsl

then install the package in r

回答5:

gsl-config in included with the gsl-devel package, try installing that. After that it should work

回答6:

On OS X Mavericks at least, after installing gsl via brew install gsl, the gsl-config --prefix yields /usr/local/Cellar/gsl/1.16. However, many applications/libraries like gsll for Common Lisp (in my case) expect /usr/local/Cellar/gsl/1.16/lib instead. In my case, the super lazy (long-term unacceptable) solution was just to symlink the libs from /usr/local/Cellar/gsl/1.16/lib into /usr/local/Cellar/gsl/1.16 and all was well. Hope this helps.

回答7:

Note to self: On Debian, to fix

checking for gsl-config... no
configure: error: gsl-config not found, is GSL installed?

I needed to

sudo apt-get install libgsl-dev

Note that the package name on Debian is not gsl-devel as elsewhere. Sigh.