tilingArray

Package: tilingArray
Version: 1.50.0
Title: Transcript mapping with high-density oligonucleotide tiling
arrays
Author: Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie
Maintainer: Zhenyu Xu <zxu@embl.de>
Depends: R (>= 2.11.0), Biobase, methods, pixmap
Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
Suggests:
Description: The package provides functionality that can be
useful for the analysis of high-density tiling microarray data (such
as from Affymetrix genechips) for measuring transcript abundance and
architecture. The main functionalities of the package are: 1. the class
'segmentation' for representing partitionings of a linear series of
data; 2. the function 'segment' for fitting piecewise constant models
using a dynamic programming algorithm that is both fast and exact; 3.
the function 'confint' for calculating confidence intervals using the
strucchange package; 4. the function 'plotAlongChrom' for generating
pretty plots; 5. the function 'normalizeByReference' for probe-sequence
dependent response adjustment from a (set of) reference
hybridizations.
Reference: Huber W, Toedling J, Steinmetz, L. Transcript mapping with
high-density oligonucleotide tiling arrays. Bioinformatics 22,
1963-1970 (2006).
License: Artistic-2.0
Collate: AllClasses.R AllGenerics.R normalizeByReference.R posMin.R
otherStrand.R qcPlots.R comparisonPlot.R plotAlongChromLegend.R
readCel2eSet.R confint.segmentation.R plotAlongChrom.R
sampleStep.R costMatrix.R plotPenLL.R segChrom.R findsegments.R
grid.image.R raster.image.R plotSegmentationDots.R
plotSegmentationHeatmap.R PMindex.R methods-segmentation.R
zzz.R
LazyLoad: Yes
biocViews: Microarray, OneChannel, Preprocessing, Visualization
NeedsCompilation: yes
Packaged: 2016-05-04 02:44:24 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'tilingArray' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c findsegments.c -o findsegments.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sampleStep.c -o sampleStep.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o tilingArray.so findsegments.o sampleStep.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/tilingArray/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'tilingArray'
    finding HTML links ... done
    PMindex                                 html  
    breakpointsPretend                      html  
    class-segmentation                      html  
    comparisonPlot                          html  
    costMatrix                              html  
    findsegments                            html  
    gffSub                                  html  
    normalizeByReference                    html  
    otherStrand                             html  
    plotAlongChrom                          html  
    plotAlongChromLegend                    html  
    plotFeatures                            html  
    plotSegmentationDots                    html  
    plotSegmentationHeatmap                 html  
    plotpenLL                               html  
    posMin                                  html  
    qcPlots                                 html  
    readCel2eSet                            html  
    sampleStep                              html  
    segChrom                                html  
    segment                                 html  
    segnf                                   html  
    tilingArray-package                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tilingArray)
Making 'packages.html' ... done