girafe

Package: girafe
Type: Package
Title: Genome Intervals and Read Alignments for Functional Exploration
Version: 1.24.0
Date: 2016-01-13
Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors
(>= 0.7.21), Rsamtools, intervals (>= 0.13.1), ShortRead (>=
1.3.21), genomeIntervals (>= 1.25.1), grid
Imports: methods, Biobase, Biostrings, graphics, grDevices, stats,
utils, IRanges (>= 2.3.23)
Suggests: MASS, org.Mm.eg.db, RColorBrewer
Enhances: genomeIntervals
Author: Joern Toedling, with contributions from Constance Ciaudo,
Olivier Voinnet, Edith Heard, Emmanuel Barillot, and Wolfgang
Huber
Maintainer: J. Toedling <jtoedling@yahoo.de>
Description: The package 'girafe' deals with the genome-level
representation of aligned reads from next-generation sequencing
data. It contains an object class for enabling a detailed
description of genome intervals with aligned reads and
functions for comparing, visualising, exporting and working
with such intervals and the aligned reads. As such, the package
interacts with and provides a link between the packages
ShortRead, IRanges and genomeIntervals.
License: Artistic-2.0
LazyLoad: yes
biocViews: Sequencing
NeedsCompilation: yes
Packaged: 2016-05-04 03:31:05 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'girafe' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coverage.cpp -o coverage.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c girafe_init.c -o girafe_init.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o girafe.so coverage.o girafe_init.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/girafe/libs
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: sort
Creating a generic function for 'hist' from package 'graphics' in package 'girafe'
Creating a generic function for 'sample' from package 'base' in package 'girafe'
** help
*** installing help indices
  converting help for package 'girafe'
    finding HTML links ... done
    AlignedGenomeIntervals-class            html  
    agiFromBam                              html  
    countReadsAnnotated                     html  
    fracOverlap                             html  
Rd warning: /tmp/RtmpcolHZx/R.INSTALL3285300f09c4/girafe/man/fracOverlap.Rd:38: missing file link 'interval_overlap'
    getFeatureCounts                        html  
    girafe-internal                         html  
    intPhred                                html  
    medianByPosition                        html  
    negbinomsig                             html  
    perWindow                               html  
    plotAligned                             html  
    plotReads                               html  
    plotnegbinomfit                         html  
    reduce-extras                           html  
    trimAdapter                             html  
Rd warning: /tmp/RtmpcolHZx/R.INSTALL3285300f09c4/girafe/man/trimAdapter.Rd:39: missing file link 'narrow'
Rd warning: /tmp/RtmpcolHZx/R.INSTALL3285300f09c4/girafe/man/trimAdapter.Rd:41: missing file link 'writeFastq'
    weightedConsensusMatrix                 html  
Rd warning: /tmp/RtmpcolHZx/R.INSTALL3285300f09c4/girafe/man/weightedConsensusMatrix.Rd:23: missing file link 'consensusMatrix'
    whichNearestMethods                     html  
Rd warning: /tmp/RtmpcolHZx/R.INSTALL3285300f09c4/girafe/man/whichNearestMethods.Rd:44: missing file link 'which_nearest'
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: sort
* DONE (girafe)
Making 'packages.html' ... done