cn.farms

Package: cn.farms
Title: cn.FARMS - factor analysis for copy number estimation
Version: 1.20.0
Date: 2014-05-19
Type: Package
License: LGPL (>= 2.0)
Author: Andreas Mitterecker, Djork-Arne Clevert
Maintainer: Andreas Mitterecker <mitterecker@bioinf.jku.at>
Description: This package implements the cn.FARMS algorithm for copy
number variation (CNV) analysis. cn.FARMS allows to analyze the
most common Affymetrix (250K-SNP6.0) array types, supports
high-performance computing using snow and ff.
URL: http://www.bioinf.jku.at/software/cnfarms/cnfarms.html
Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow
Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5,
pd.genomewidesnp.6
Collate: 'callSummarize.R' 'combineData.R' 'correctPkgname.R'
'cnFarms.R' 'createAnnotation.R' 'createMatrix.R'
'determineBaselineArray.R' 'distributionDistance.R'
'dnaCopySf.R' 'doCnFarms.R' 'fragLengthCorr.R' 'normAdd.R'
'normalizeAverage.R' 'normalizeCels.R' 'normalizeNpData.R'
'normalizeQuantiles.R' 'normalizeSor.R' 'plotDendrogram.R'
'plotDensity.R' 'plotEvalIc.R' 'plotSmoothScatter.R'
'plotsRegions.R' 'plotViolines.R' 'sparseFarmsC.R'
'summarizationMl.R' 'summarizationSl.R'
'summarizeFarmsGaussian.R' 'summarizeFarmsLaplaceExact.R'
'summarizeFarmsLaplaceVar.R' 'summarizeFarmsMethods.R'
'summarizeStatistics.R' 'windowFunctions.R' 'windowMethods.R'
'normalizeProbeSequence.R' 'snowfallExt.R'
'summarizeFarmsLaplaceExact2.R' 'summarizeFarmsLaplaceExact3.R'
'normalizeNone.R' 'utils-lds.R' 'zzz.R' 'sFclusterFunctions.R'
'sFinit.R' 'sFsnowfall-internal.R' 'sFsnowWrappers.R'
'sFsocketRequest.R' 'vanillaIce.R'
biocViews: Microarray, CopyNumberVariation
Roxygen: list(wrap = FALSE)
NeedsCompilation: yes
Packaged: 2016-05-04 03:59:42 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'cn.farms' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c laplace.cpp -o laplace.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sparse_farms.c -o sparse_farms.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'cn.farms'
    finding HTML links ... done
    callSummarize                           html  
    cn.farms                                html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/cn.farms.Rd:16: missing file link 'ExpressionSet-class'
    cnLibrary                               html  
    combineData                             html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/combineData.Rd:10: missing file link 'ExpressionSet-class'
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/combineData.Rd:13: missing file link 'ExpressionSet-class'
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/combineData.Rd:29: missing file link 'ExpressionSet-class'
    createAnnotation                        html  
    createMatrix                            html  
    distributionDistance                    html  
    dnaCopySf                               html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/dnaCopySf.Rd:22: missing file link 'ExpressionSet-class'
    doCnFarmsSingle                         html  
    flcSnp6Std                              html  
    flcStd                                  html  
    fragLengCorr                            html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/fragLengCorr.Rd:10: missing file link 'ExpressionSet-class'
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/fragLengCorr.Rd:20: missing file link 'ExpressionSet-class'
    getFragmentSet                          html  
    getSingleProbeSetSize                   html  
    mlSummarization                         html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/mlSummarization.Rd:10: missing file link 'ExpressionSet-class'
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/mlSummarization.Rd:36: missing file link 'ExpressionSet-class'
    normAdd                                 html  
    normalizeAverage                        html  
    normalizeCels                           html  
    normalizeNone                           html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/normalizeNone.Rd:29: missing file link 'ExpressionSet-class'
    normalizeNpData                         html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/normalizeNpData.Rd:25: missing file link 'ExpressionSet-class'
    normalizeQuantiles                      html  
    normalizeSequenceEffect                 html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/normalizeSequenceEffect.Rd:11: missing file link 'ExpressionSet-class'
    normalizeSor                            html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/normalizeSor.Rd:29: missing file link 'ExpressionSet-class'
    plotDendrogram                          html  
    plotDensity                             html  
    plotEvalIc                              html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/plotEvalIc.Rd:12: missing file link 'ExpressionSet-class'
    plotRegions                             html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/plotRegions.Rd:10: missing file link 'ExpressionSet-class'
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/plotRegions.Rd:12: missing file link 'ExpressionSet-class'
    plotSmoothScatter                       html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/plotSmoothScatter.Rd:9: missing file link 'ExpressionSet-class'
    plotViolines                            html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/plotViolines.Rd:10: missing file link 'ExpressionSet-class'
    slSummarization                         html  
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/slSummarization.Rd:12: missing file link 'ExpressionSet-class'
Rd warning: /tmp/RtmpH03Y06/R.INSTALL13aadc4286c/cn.farms/man/slSummarization.Rd:35: missing file link 'ExpressionSet-class'
    sparseFarmsC                            html  
    summarizeFarmsExact                     html  
    summarizeFarmsExact2                    html  
    summarizeFarmsExact3                    html  
    summarizeFarmsGaussian                  html  
    summarizeFarmsMethods                   html  
    summarizeFarmsStatistics                html  
    summarizeFarmsVariational               html  
    summarizeWindowBps                      html  
    summarizeWindowMethods                  html  
    summarizeWindowStd                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.farms)
Making 'packages.html' ... done