[rkward-devel] Installing new packages using RKWard on Mac OS X

Mon Sep 24 11:10:17 UTC 2012

Hi,

I'm using RKWard on my Mac and so far things have been working quite 
well. Since the latest easy-to-install Version of RKWard for Mac OS X 
I've been successfully advertising RKWard to my department and they are 
thinking about switching from SPSS to RKWard as primary statistics software.

In the process of demonstrating RKWard to our PI I had difficulties 
installing packages from CRAN. First, I installed "rk.ANOVA" and 
everything worked as expected. Trying to run the analysis RKWard tried 
to install the "ez" packages that "rk.ANOVA" depends on. After 
successfully downloading all package components I got an error message 
concerned with "make":

"R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin11.4.0/x86_64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

 > options (repos= c("http://ftp5.gwdg.de/pub/misc/cran", 
"http://rkward.sf.net/R/", "http://rkward.sf.net/R/"))
 > install.packages (pkgs=c ("ez"), 
lib="/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15", 
dependencies=TRUE)

also installing the dependencies 'colorspace', 'digest', 'munsell', 
'ggplot2', 'lme4', 'memoise', 'plyr', 'reshape2', 'scales', 'stringr'

trying URL 
'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/colorspace_1.1-1.tar.gz'
Content type 'application/x-gzip' length 336592 bytes (328 Kb)
opened URL
==================================================
downloaded 328 Kb

trying URL 
'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/digest_0.5.2.tar.gz'
Content type 'application/x-gzip' length 41787 bytes (40 Kb)
opened URL
==================================================
downloaded 40 Kb

trying URL 
'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/munsell_0.4.tar.gz'
Content type 'application/x-gzip' length 87713 bytes (85 Kb)
opened URL
==================================================
downloaded 85 Kb

trying URL 
'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/ggplot2_0.9.2.1.tar.gz'
Content type 'application/x-gzip' length 2310996 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb

trying URL 
'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/lme4_0.999999-0.tar.gz'
Content type 'application/x-gzip' length 1074142 bytes (1.0 Mb)
opened URL
==================================================
downloaded 1.0 Mb

trying URL 
'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/memoise_0.1.tar.gz'
Content type 'application/x-gzip' length 1373 bytes
opened URL
==================================================
downloaded 1373 bytes

trying URL 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/plyr_1.7.1.tar.gz'
Content type 'application/x-gzip' length 367683 bytes (359 Kb)
opened URL
==================================================
downloaded 359 Kb

trying URL 
'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/reshape2_1.2.1.tar.gz'
Content type 'application/x-gzip' length 1952562 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb

trying URL 
'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/scales_0.2.2.tar.gz'
Content type 'application/x-gzip' length 38485 bytes (37 Kb)
opened URL
==================================================
downloaded 37 Kb

trying URL 
'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/stringr_0.6.1.tar.gz'
Content type 'application/x-gzip' length 20657 bytes (20 Kb)
opened URL
==================================================
downloaded 20 Kb

trying URL 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/ez_4.1-1.tar.gz'
Content type 'application/x-gzip' length 139207 bytes (135 Kb)
opened URL
==================================================
downloaded 135 Kb

* installing *source* package 'colorspace' ...
** package 'colorspace' successfully unpacked and MD5 sums checked
** libs
*** arch - x86_64
sh: make: command not found
ERROR: compilation failed for package 'colorspace'
* removing 
'/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/colorspace'
* installing *source* package 'digest' ...
** package 'digest' successfully unpacked and MD5 sums checked
** libs
*** arch - x86_64
sh: make: command not found
ERROR: compilation failed for package 'digest'
* removing '/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/digest'
* installing *source* package 'lme4' ...
** package 'lme4' successfully unpacked and MD5 sums checked
** libs
*** arch - x86_64
sh: make: command not found
ERROR: compilation failed for package 'lme4'
* removing '/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/lme4'
* installing *source* package 'plyr' ...
** package 'plyr' successfully unpacked and MD5 sums checked
** libs
*** arch - x86_64
sh: make: command not found
ERROR: compilation failed for package 'plyr'
* removing '/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/plyr'
ERROR: dependency 'colorspace' is not available for package 'munsell'
* removing '/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/munsell'
ERROR: dependency 'digest' is not available for package 'memoise'
* removing '/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/memoise'
ERROR: dependency 'plyr' is not available for package 'stringr'
* removing '/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/stringr'
ERROR: dependencies 'plyr', 'stringr' are not available for package 
'reshape2'
* removing 
'/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/reshape2'
ERROR: dependencies 'stringr', 'munsell', 'plyr' are not available for 
package 'scales'
* removing '/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/scales'
ERROR: dependencies 'plyr', 'digest', 'reshape2', 'scales', 'memoise' 
are not available for package 'ggplot2'
* removing '/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/ggplot2'
ERROR: dependencies 'ggplot2', 'lme4', 'memoise', 'plyr', 'reshape2', 
'scales', 'stringr' are not available for package 'ez'
* removing '/Users/wascher/R/x86_64-apple-darwin11.4.0-library/2.15/ez'

The downloaded source packages are in
'/private/var/folders/j8/q18h8hks4nx5pyw287_p31y00000gr/T/RtmpezVOAe/downloaded_packages'

There were 11 warnings (use warnings() to see them)

 > q ()"

After installing Apple XCode, which provides among other things make, my 
PI was able to install "ez" without further difficulties. After some 
research I found that this problem is probably specific to RKWard 
because "R for Mac OS X recognizes packages in two forms: binary 
packages and source packages. [...] Unlike on other unix systems, R for 
Mac OS X installs binary packages by default, i.e. install.packages will 
look for binary repositories unless instructed otherwise." 
(<http://tinyurl.com/cusftyz>).

I'm not sure whether this problem is best solved by making installation 
of binaries a default setting in RKWard for Mac OS X or by providing 
"make" with the RKWard installer. Either way, it would be nice if RKWard 
did not depend on Apple XCode.

Cheers,
Frederik

-- 
Dipl.-Psych. Frederik Aust

Leibniz Research Center for Working Environment and Human Factors
Research Group: Perceptual cybernetics
Ardeystr. 67
44139 Dortmund
Germany

E-mail: austf at ifado.de
Tel.: +49 / 231 1084 382
Web: http://www.ifado.de/