Last data update: 2014.03.03
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XDE
Package: XDE
Title: XDE: a Bayesian hierarchical model for cross-study analysis of
differential gene expression
Version: 2.18.0
Date: 2011-05-10
Author: R.B. Scharpf, G. Parmigiani, A.B. Nobel, and H. Tjelmeland
Description: Multi-level model for cross-study detection of
differential gene expression.
Depends: R (>= 2.10.0), Biobase (>= 2.5.5), methods, graphics
Imports: Biobase, BiocGenerics, genefilter, graphics, grDevices,
gtools, MergeMaid, methods, stats, utils, mvtnorm
Suggests: siggenes, genefilter, MASS, RColorBrewer, GeneMeta, RUnit
Maintainer: Robert Scharpf <rscharpf@jhsph.edu>
Enhances: coda
License: LGPL-2
Collate: functions.R AllClasses.R AllGenerics.R RUpdates.R
methods-XdeParameter.R methods-matrix.R methods-data.frame.R
methods-ExpressionSet.R methods-ExpressionSetList.R
methods-mergeExpressionSet.R methods-Parameters.R
methods-XdeMcmc.R xde.R zzz.R
LazyLoad: yes
biocViews: Microarray, DifferentialExpression
NeedsCompilation: yes
Packaged: 2016-05-04 03:06:36 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'XDE' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Cholesky.cpp -o Cholesky.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Matrix_v2.cpp -o Matrix_v2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Potential_v2.cpp -o Potential_v2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Random_v2.cpp -o Random_v2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Update_v2.h:8:0,
from Rinterface_v2.cpp:2:
Random.h:19:0: warning: "PI" redefined
#define PI 3.14159265
^
In file included from /home/ddbj/local/lib64/R/include/R.h:69:0,
from Rinterface_v2.cpp:1:
/home/ddbj/local/lib64/R/include/R_ext/Constants.h:32:0: note: this is the location of the previous definition
#define PI M_PI
^
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Structure.cpp -o Structure.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Update_v2.cpp -o Update_v2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Utility_v2.cpp -o Utility_v2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:16:0:
Random.h:19:0: warning: "PI" redefined
#define PI 3.14159265
^
In file included from /home/ddbj/local/lib64/R/include/R.h:69:0,
from diffExpressed_main.cpp:4:
/home/ddbj/local/lib64/R/include/R_ext/Constants.h:32:0: note: this is the location of the previous definition
#define PI M_PI
^
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o -lm -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/XDE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'pairs' from package 'graphics' in package 'XDE'
Creating a generic function for 'plot' from package 'graphics' in package 'XDE'
** help
*** installing help indices
converting help for package 'XDE'
finding HTML links ... done
ExpressionSetList-class html
ExpressionSetList-methods html
Parameters-class html
XdeMcmc-class html
XdeParameter-class html
burnin html
calculatePosteriorAvg html
empiricalStart html
expressionSetList html
firstMcmc html
geneCenter html
hyperparameters html
iterations html
lastMcmc html
output html
pairs html
posteriorAvg html
seed html
ssStatistic html
standardizeSamples html
studyCenter html
symbolsInteresting html
thin html
tuning html
updates html
xde html
xmcmc html
xsScores html
zeroNu html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (XDE)
Making 'packages.html' ... done
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