How can I install topicmodels package in R?

Question

I am trying to install the package called topicmodels in R and I have not had success. Here's what I have tried...

Action: Install the package using install.packages("topicmodels")

Result:

package ‘topicmodels’ is available as a source package but not as a binary

Warning in install.packages :
  package ‘topicmodels’ is not available (for R version 3.1.0)

So there I said okay let's install from source

Action: install.packages("/Users/my_name/Downloads/topicmodels_0.2-1.tar.gz",repos=NULL,type="source")

Result:

* installing *source* package ‘topicmodels’ ...
** package ‘topicmodels’ successfully unpacked and MD5 sums checked
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c cokus.c -o cokus.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c common.c -o common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c ctm.c -o ctm.o
ctm.c:29:10: fatal error: 'gsl/gsl_rng.h' file not found

include gsl/gsl_rng.h

1 error generated.
make: *** [ctm.o] Error 1
ERROR: compilation failed for package ‘topicmodels’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/topicmodels’
Warning in install.packages :
  installation of package ‘/Users/me/Downloads/topicmodels_0.2-1.tar.gz’ had non-zero exit status

So then I researched this gsl thing and came upon this link. And for the moment I thought all of my problems were gone and when I finally follow these directions. I get the following error (in the terminal)...

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  using pax extended headers
ERROR: cannot extract package from ‘topicmodels.tar.gz’

Answer 1

First of all you have to install gsl. Once you have that installed you can try to install the R package. You can download gsl from here (there you can pick the latest version gsl-latest.tar.gz). Once it's been downloaded, install it by doing the following:

1. Decompress the downloaded file (in my case the "latest" file contained this version: gsl-1.16)
2. Open the "Terminal"

3. Then (using the Terminal), move inside the folder that you created on step 1. In my case I had the file on the folder called "Downloads", so I moved to the newly created folder by doing:

   cd Downloads/gsl-1.16
   

4. Once you are within that folder run the following commands (in order):

   ./configure
   make
   sudo make install
   

5. After doing it you won't get the previous error saying fatal error: 'gsl/gsl_rng.h' file not found, so you can try again the installation.

6. Now go back to your R environment (e.g., RStudio) to try again to install the package by doing:

   install.packages("PATH_TO_TOPIC_MODELS.tar.gz", repos=NULL, type="source").
   

I had the same problem, and after doing this I got the R package correctly installed, I hope it also works in your case.

Answer 2

If you already using homebrew. It is better and faster to fix with variables than installing gsl manually from source.

1. Install gsl with homebrew brew install gsl

2. Edit ~/.R/Makevars and add.

   PKG_LIBS=-L/usr/local/opt/gettext/lib
   CFLAGS=-I/usr/local/opt/gsl/include
   LDFLAGS=-L/usr/local/opt/gsl/lib -lgsl -lgslcblas