h5vc

Package: h5vc
Type: Package
Title: Managing alignment tallies using a hdf5 backend
Version: 2.6.3
Author: Paul Theodor Pyl
Maintainer: Paul Theodor Pyl <paul.theodor.pyl@gmail.com>
Description: This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files. For detail see the webpage at http://www.ebi.ac.uk/~pyl/h5vc.
License: GPL (>= 3)
VignetteBuilder: knitr
Depends: grid, gridExtra, ggplot2
LinkingTo: Rsamtools
Imports: rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
1.19.38), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, bit64, biomaRt,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics
NeedsCompilation: yes
Packaged: 2016-05-16 04:14:52 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'h5vc' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c tallyBAM.cpp -o tallyBAM.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o h5vc.so tallyBAM.o /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbam.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbcf.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/h5vc/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'h5vc'
    finding HTML links ... done
    applyTallies                            html  
    batchTallies                            html  
    binGenome                               html  
    binnedAFs                               html  
    callVariants                            html  
    callVariantsFisher                      html  
    callVariantsSingle                      html  
    coverage                                html  
    geom_h5vc                               html  
Rd warning: /tmp/RtmpNMR3M7/R.INSTALL347025185273/h5vc/man/geom_h5vc.Rd:25: missing file link 'geom_rect'
    getSampleData                           html  
    h5dapply                                html  
    h5readBlock                             html  
    h5vc-package                            html  
    helpers                                 html  
    mergeTallies                            html  
    mergeTallyFiles                         html  
    mismatchPlot                            html  
    mutationSpectrum                        html  
    plotMutationSpectrum                    html  
    prepareForHDF5                          html  
    prepareTallyFile                        html  
    tallyBAM                                html  
    tallyRanges                             html  
    finding level-2 HTML links ... done

    writeReference                          html  
    writeToTallyFile                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (h5vc)
Making 'packages.html' ... done