ruv

Package: ruv
Title: Detect and Remove Unwanted Variation using Negative Controls
Description: Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', and 'RUV-rinv', along with various supporting algorithms.
Version: 0.9.6
Date: 2015-07-17
Imports: stats
Author: Johann Gagnon-Bartsch <johanngb@umich.edu>
Maintainer: Johann Gagnon-Bartsch <johanngb@umich.edu>
License: GPL
URL: http://www.stat.berkeley.edu/~johann/ruv
LazyLoad: yes
Packaged: 2015-07-18 00:58:25 UTC; johann
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-07-18 17:00:34

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ruv' ...
** package 'ruv' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c getsizeratios.c -o getsizeratios.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c increasingreg.c -o increasingreg.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sigmashrink.c -o sigmashrink.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c wipeout.c -o wipeout.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o ruv.so getsizeratios.o increasingreg.o sigmashrink.o wipeout.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/ruv/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ruv'
    finding HTML links ... done
    RUV1                                    html  
    RUV2                                    html  
    RUV4                                    html  
    RUVinv                                  html  
    RUVrinv                                 html  
    getK                                    html  
    get_empirical_variances                 html  
    inputcheck1                             html  
    invvar                                  html  
    randinvvar                              html  
    residop                                 html  
    ruv-package                             html  
    sigmashrink                             html  
    variance_adjust                         html  
** building package indices
** testing if installed package can be loaded
* DONE (ruv)
Making 'packages.html' ... done