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Last data update: 2014.03.03
TSSi

Package: TSSi
Type: Package
Title: Transcription Start Site Identification
Version: 1.18.0
Author: Julian Gehring, Clemens Kreutz
Maintainer: Julian Gehring <jg-bioc@gmx.com>
Depends: R (>= 2.13.2)
Imports: methods, BiocGenerics (>= 0.3.2), S4Vectors, Hmisc, minqa,
stats, Biobase (>= 0.3.2), plyr, IRanges
Suggests: rtracklayer
Enhances: parallel
Description: Identify and normalize transcription start sites in high-throughput sequencing data.
License: GPL-3
LazyLoad: yes
biocViews: Sequencing, RNASeq, Genetics, Preprocessing
NeedsCompilation: yes
Packaged: 2016-05-04 04:09:45 UTC; biocbuild
● BiocViews: Genetics, Preprocessing, RNASeq, Sequencing
● 3 images, 11 functions, 1 datasets
● Reverse Depends: 0
Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'TSSi' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c assess.c -o assess.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o TSSi.so assess.o init.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/TSSi/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'segments' in package 'TSSi'
Creating a generic function for 'plot' from package 'graphics' in package 'TSSi'
** help
*** installing help indices
  converting help for package 'TSSi'
    finding HTML links ... done
    TSSi-package                            html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TSSi-package.Rd:54: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TSSi-package.Rd:54: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TSSi-package.Rd:55: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TSSi-package.Rd:66: missing file link 'physcoCounts'
    TssData-class                           html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssData-class.Rd:144: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssData-class.Rd:144: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssData-class.Rd:145: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssData-class.Rd:152: missing file link 'physcoCounts'
    TssNorm-class                           html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssNorm-class.Rd:74: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssNorm-class.Rd:74: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssNorm-class.Rd:75: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssNorm-class.Rd:82: missing file link 'physcoCounts'
    TssResult-class                         html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssResult-class.Rd:86: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssResult-class.Rd:86: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssResult-class.Rd:87: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/TssResult-class.Rd:94: missing file link 'physcoCounts'
    asRangedData-methods                    html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/asRangedData-methods.Rd:89: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/asRangedData-methods.Rd:89: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/asRangedData-methods.Rd:90: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/asRangedData-methods.Rd:97: missing file link 'physcoCounts'
    get-methods                             html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/get-methods.Rd:160: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/get-methods.Rd:160: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/get-methods.Rd:161: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/get-methods.Rd:168: missing file link 'physcoCounts'
    identify-methods                        html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/identify-methods.Rd:101: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/identify-methods.Rd:101: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/identify-methods.Rd:102: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/identify-methods.Rd:109: missing file link 'physcoCounts'
    normalize-methods                       html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/normalize-methods.Rd:112: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/normalize-methods.Rd:112: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/normalize-methods.Rd:113: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/normalize-methods.Rd:120: missing file link 'physcoCounts'
    physcoCounts-data                       html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/physcoCounts-data.Rd:49: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/physcoCounts-data.Rd:49: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/physcoCounts-data.Rd:50: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/physcoCounts-data.Rd:57: missing file link 'physcoCounts'
    plot-methods                            html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/plot-methods.Rd:154: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/plot-methods.Rd:154: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/plot-methods.Rd:155: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/plot-methods.Rd:162: missing file link 'physcoCounts'
    segmentize-methods                      html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/segmentize-methods.Rd:91: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/segmentize-methods.Rd:91: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/segmentize-methods.Rd:92: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/segmentize-methods.Rd:99: missing file link 'physcoCounts'
    subtract-functions                      html  
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/subtract-functions.Rd:50: missing file link 'segmentizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/subtract-functions.Rd:50: missing file link 'normalizeCounts'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/subtract-functions.Rd:51: missing file link 'identifyStartSites'
Rd warning: /tmp/RtmpW71MbM/R.INSTALL75fa36354dcf/TSSi/man/subtract-functions.Rd:58: missing file link 'physcoCounts'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TSSi)
Making 'packages.html' ... done