Last data update: 2014.03.03
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VanillaICE
Package: VanillaICE
Version: 1.34.0
Title: A Hidden Markov Model for high throughput genotyping arrays
Author: Robert Scharpf <rscharpf@jhu.edu>, Kevin Scharpf, and Ingo Ruczinski
<ingo@jhsph.edu>
Maintainer: Robert Scharpf <rscharpf@jhsph.edu>
Description: Hidden Markov Models for characterizing chromosomal alterations in
high throughput SNP arrays.
Date: Sat Sep 27 11:46:03 EDT 2014
Depends: R (>= 3.0.0), BiocGenerics (>= 0.13.6), GenomicRanges (>=
1.19.47), SummarizedExperiment (>= 0.2.0)
Imports: Biobase, S4Vectors (>= 0.9.25), IRanges (>= 1.14.0),
oligoClasses (>= 1.31.1), foreach, matrixStats, data.table,
grid, lattice, methods, GenomeInfoDb, crlmm, tools, stats,
utils, BSgenome.Hsapiens.UCSC.hg18
Suggests: RUnit, SNPchip, human610quadv1bCrlmm, ArrayTV
Collate: 'AllClasses.R' 'AllGenerics.R' 'datasets.R' 'defunct.R'
'functions.R' 'help.R' 'hmm-methods.R' 'methods-ArrayViews.R'
'methods-CopyNumScanParams.R' 'methods-EmissionParam.R'
'methods-FilterParam.R' 'methods-HMM.R' 'methods-HMMList.R'
'methods-HmmGRanges.R' 'methods-HmmParam.R'
'methods-HmmTrellisParam.R' 'methods-IdiogramParams.R'
'methods-LogLik.R' 'methods-SnpArrayExperiment.R'
'methods-SnpDataFrame.R' 'methods-TransitionParam.R'
'methods-Viterbi.R' 'updates.R' 'zzz.R'
Enhances: doMC, doMPI, doSNOW, doParallel, doRedis
License: LGPL-2
LazyLoad: yes
biocViews: CopyNumberVariation
Roxygen: list(wrap=FALSE)
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-04 03:03:20 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'VanillaICE' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rinit.c -o rinit.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c viterbi.c -o viterbi.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o VanillaICE.so rinit.o viterbi.o -lm -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/VanillaICE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'distance' in package 'VanillaICE'
** help
*** installing help indices
converting help for package 'VanillaICE'
finding HTML links ... done
ArrayViews-class html
BeadStudioSet html
CopyNumScanParams html
finding level-2 HTML links ... done
Defunct html
Deprecated html
EmissionParam-methods html
FilterParam-class html
HMM html
HMMList-class html
HMMList html
HmmGRanges-methods html
HmmParam html
HmmTrellisParam html
IO html
IdiogramParam-class html
IdiogramParams-class html
LogLik-class html
LogLik html
LowLevelSummaries html
NA_filter html
SnpArrayExperiment-class html
SnpExperiment html
SnpGRanges html
TransitionParam html
VanillaICE html
Viterbi-methods html
acf2 html
baumWelchUpdate html
calculateEmission html
cnvFilter html
constraints html
doUpdate html
dropDuplicatedMapLocs html
dropSexChrom html
emission html
emissionParam html
filters html
getExampleSnpExperiment html
getHmmParams html
hmm2 html
hmmResults html
icePlatforms html
isHeterozygous html
matrixOrNULL-class html
numberFeatures html
oligoSetList html
parseSourceFile html
parsedPath html
plotting html
probability html
read.bsfiles html
rescale html
robust-statistics html
segs html
snpArrayAssays html
snp_exp html
sourcePaths html
start-oligoSnpSet-method html
state-methods html
sweepMode html
threshold html
updateHmmParams html
viewports html
viterbi2Wrapper html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VanillaICE)
Making 'packages.html' ... done
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