RTextTools, now 100% rJava-free

[Tim Jurka]

Hi team,

Due to the rJava problems we've been having, I've replaced all Java components with R or C/C++ equivalents. You may try installing again and should not encounter and rJava-related problems.

Loren and Wouter, I replaced AdaBoost with LogitBoost in caTools ( http://cran.r-project.org/web/packages/caTools/caTools.pdf ) and bagging with the implementation in ipred ( http://cran.r-project.org/web/packages/ipred/ipred.pdf ). Neither support SparseM matrices, but I've contacted the developer of the LogitBoost implementation to see if he'll consider since the algorithm is very impressive.

Best,
Tim

--
Timothy P. Jurka
Graduate Student
Department of Political Science
University of California, Davis
www.timjurka.com

[Paul Wolfgang]

No luck, now I get the following error message:

* installing *source* package 'slam' ...
** libs

*** arch - i386

*** arch - x64
ERROR: compilation failed for package 'slam'
* removing 'C:/Users/Paul/Documents/R/win-library/2.12/slam'
*

I tired it with and without Rtools in the path.

It would be nice if there was some way to get the error log from R's
install script.

Paul Wolfgang

[Loren Collingwood]

You probably just need to type install.packages('slam') in the R console and then run the RTextTools install lines. This happened to me when installing with respect to some of the other packages. Also, if you bump up to R-2.13 then that might solve the problems. I've noticed this happens sometimes with different R versions and some packages...not exactly sure why.
-Loren

Loren Collingwood
Ph.D. Candidate
Department of Political Science
University of Washington
http://staff.washington.edu/lorenc2
lor...@uw.edu

[Tim Jurka]

I don't think the version # is the problem. For example, Ana wasn't able to install any of the dependencies on her computer and she's running R-2.13.0. Both Paul and Ana are using Windows, so I think that's the source of the problem. Ana is getting an error: Warning in install.packages("RTextTools", repos = repositories, type = "source") : 'lib = "C:/Program Files/R/R-2.13.0/library"' is not writable, which sounds like she doesn't have administrative privileges on the computer she's using.

Paul, can you type traceback() after the error and see if any useful information pops up? I'm unable to recreate this on my machine, but am working to do so.

Tim

[Paul Wolfgang]

The only thing traceback() gives is:

1: install.packages("RTextTools", repos = repository, type = "source")

After manually installing slam
the install of RTextTools fails on
mlbench

I am not getting the message that lib is not writable. Instead I get the
message:

Installing package(s) into ‘C:\Users\Paul\Documents/R/win-library/2.12’
(as ‘lib’ is unspecified)
also installing the dependencies ‘mlbench’, ‘bitops’, ‘SparseM’,
‘randomForest’, ‘glmnet’, ‘tree’, ‘tm’, ‘e1071’, ‘Rstem’, ‘ipred’, ‘caTools’

Paul Wolfgang

[Tim Jurka]

That should be fine... it's just installing it to the 2.12 library instead of globally on the system. When I uninstall Rtools I get the same error you're getting ( ERROR: compilation failed for package 'slam' ) which leads me to believe something isn't right with the Rtools installation.

Tim

[Loren Collingwood]

I have had problems with the initial installation of late and have had to manually install a few packages each time (which isn't anything I'm not used to). This is on both Windows, Mac, and Ubuntu server. Perhaps it's a bug in the install script? For Rtools are you putting C:\Rtools\bin; C:\Rtools\MinGW\bin on your path, not just Rtools?

-Loren

--
Loren Collingwood
loren.co...@gmail.com

[Tim Jurka]

I only experience problems on Windows, not on Mac or Ubuntu. What issues are your running into on Linux/OS X? Still investigating the Windows issue... it's tough without the error log.

Best,

Tim

[Loren Collingwood]

Just random install problems (this was with the last version) with respect to installing some of the packages. I'd just get an error message saying RTextTools won't load because such and such package couldn't install.  I just installed the new version and had this problem:

ERROR: dependencies ‘ipred’, ‘caTools’ are not available for package ‘RTextTools’

* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RTextTools’

So I just went install.packages('ipred','caTools')

and then 

install.packages("RTextTools", repos=repositories, type="source")

[Paul Wolfgang]

I reinstalled RTools.  And after double checking the PATH I got it to work.

Paul Wolfgang

[Tim Jurka]

Hi Paul,

I think I noticed you have to check a box for the installer to update the path. We need to make note of this step somewhere.

Glad to hear it worked! Ana's problems seem to be that she doesn't have write privileges for where the R libraries are being installed.

Tim

[Tim Jurka]

Loren,

You need to specify the CRAN repository in addition to the RTextTools repository:

repositories <- c("http://install.rtexttools.com/","http://cran.r-project.org","http://www.omegahat.org/R")

install.packages("RTextTools", repos=repositories, type="source")

Otherwise it can't find ipred and caTools in the install.rtexttools.com repository by itself.

Best,

Tim

[Loren Collingwood]

Right, I do that each time: 

> repositories <- c("http://install.rtexttools.com/","http://cran.r-project.org","http://www.omegahat.org/R")

> install.packages("RTextTools", repos=repositories, type="source")

trying URL 'http://install.rtexttools.com/src/contrib/RTextTools_1.0.tar.gz'

Content type 'application/x-tar' length 15410 bytes (15 Kb)

opened URL

==================================================

downloaded 15 Kb

ERROR: dependencies ‘ipred’, ‘caTools’ are not available for package ‘RTextTools’

* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RTextTools’

[Amber Boydstun]

Yea!  Let us know how it works Paul.

Cheers,
Amber

~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Amber E. Boydstun
Assistant Professor

Department of Political Science
University of California, Davis

One Shields Ave
Davis, CA 95616

http://psfaculty.ucdavis.edu/boydstun/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[Tim Jurka]

Strange... that error indicates it's not looking in the CRAN repository for ipred and caTools, only in http://install.rtexttools.com/ .

Tim