messina

Package: messina
Type: Package
Title: Single-gene classifiers and outlier-resistant detection of
differential expression for two-group and survival problems.
Version: 1.8.2
Date: 2014-03-20
Authors@R: c(person(given = "Mark", family = "Pinese", role = c("aut",
"cre", "cph"), email = "m.pinese@garvan.org.au"))
Description: Messina is a collection of algorithms for constructing
optimally robust single-gene classifiers, and for identifying
differential expression in the presence of outliers or unknown
sample subgroups. The methods have application in identifying
lead features to develop into clinical tests (both diagnostic
and prognostic), and in identifying differential expression
when a fraction of samples show unusual patterns of expression.
biocViews: GeneExpression, DifferentialExpression,
BiomedicalInformatics, Classification, Survival
License: EPL (>= 1.0)
Depends: R (>= 3.1.0), survival (>= 2.37-4), methods
Imports: Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid
(>= 3.1.0), foreach (>= 1.4.1), graphics
Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
Enhances: doMC (>= 1.3.3)
LinkingTo: Rcpp
BuildDepends: roxygen2 (>= 3.1.0)
VignetteBuilder: knitr
Roxygen: list(wrap = TRUE)
Author: Mark Pinese [aut], Mark Pinese [cre], Mark Pinese [cph]
Maintainer: Mark Pinese <m.pinese@garvan.org.au>
NeedsCompilation: yes
Packaged: 2016-05-16 04:23:42 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'messina' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c Classifier.cpp -o Classifier.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c Data.cpp -o Data.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c crossval.cpp -o crossval.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c errors.cpp -o errors.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c init.cpp -o init.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c messinaExtern.cpp -o messinaExtern.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o messina.so Classifier.o Data.o RcppExports.o crossval.o errors.o init.o messinaExtern.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/messina/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'messina'
** help
*** installing help indices
  converting help for package 'messina'
    finding HTML links ... done
    MessinaFits-class                       html  
    MessinaParameters-class                 html  
    MessinaResult-class                     html  
    messina-package                         html  
    messina                                 html  
Rd warning: /tmp/Rtmp8n53HM/R.INSTALL4f08226366c6/messina/man/messina.Rd:125: missing file link 'ExpressionSet'
    messinaDE                               html  
Rd warning: /tmp/Rtmp8n53HM/R.INSTALL4f08226366c6/messina/man/messinaDE.Rd:130: missing file link 'ExpressionSet'
    messinaSurv                             html  
Rd warning: /tmp/Rtmp8n53HM/R.INSTALL4f08226366c6/messina/man/messinaSurv.Rd:166: missing file link 'ExpressionSet'
    messinaTopResults                       html  
    plot-MessinaClassResult-missing-method
                                            html  
    plot-MessinaSurvResult-missing-method   html  
    show-methods                            html  
    tcga_kirc_example                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (messina)
Making 'packages.html' ... done