tcR

Package: tcR
Type: Package
Title: Advanced Data Analysis of Immune Receptor Repertoires
Version: 2.2.1.11
Date: 2016-04-22
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>
Description: Platform for the advanced analysis of T cell receptor and
Immunoglobulin repertoires data and visualisation of the analysis results.
License: Apache License 2.0
Depends: R (>= 2.15.1), ggplot2 (>= 1.0.0), dplyr (>= 0.4.0), gridExtra
(>= 0.9.0), reshape2 (>= 1.2.0), igraph (>= 0.7.1)
Imports: utils (>= 3.1.0), Rcpp (>= 0.11.1), grid (>= 3.0.0),
data.table (>= 1.9.0), gtable (>= 0.1.2), stringdist (>=
0.7.3), scales (>= 0.3.0)
Suggests: knitr (>= 1.8), roxygen2 (>= 3.0.0)
LinkingTo: Rcpp
URL: http://imminfo.github.io/tcr/
BugReports: https://github.com/imminfo/tcr/issues
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-04-22 09:23:06 UTC; vdn
Repository: CRAN
Date/Publication: 2016-04-22 13:10:15

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'tcR' ...
** package 'tcR' successfully unpacked and MD5 sums checked
** libs
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2 -c neighbour.search.cpp -o neighbour.search.o
g++ -std=c++11 -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o tcR.so RcppExports.o neighbour.search.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/tcR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'tcR'
    finding HTML links ... done
    AA_TABLE                                html  
    apply.symm                              html  
    assymetry                               html  
    barcodes.to.reads                       html  
    beta.prob                               html  
    bootstrap.tcr                           html  
    check.distribution                      html  
    clonal.space.homeostasis                html  
    cloneset.stats                          html  
    codon.variants                          html  
    column.summary                          html  
    contamination.stats                     html  
    convergence.index                       html  
    cosine.sharing                          html  
    cosine.similarity                       html  
    entropy                                 html  
    entropy.seg                             html  
    find.clonotypes                         html  
    find.similar.sequences                  html  
    fix.alleles                             html  
    gc.content                              html  
    geneUsage                               html  
    generate.kmers                          html  
    generate.tcr                            html  
    get.all.substrings                      html  
    get.deletions.alpha                     html  
    get.inframes                            html  
    get.kmers                               html  
    gibbs.sampler                           html  
    group.clonotypes                        html  
    has.class                               html  
    intersectClonesets                      html  
    inverse.simpson                         html  
    kmer.profile                            html  
    kmer.table                              html  
    loglikelihood                           html  
    matrixSubgroups                         html  
    matrixdiagcopy                          html  
    mutated.neighbours                      html  
    mutation.network                        html  
    ozScore                                 html  
    parse.cloneset                          html  
    parse.folder                            html  
    pca.segments                            html  
    pca2euclid                              html  
    permutDistTest                          html  
    permutedf                               html  
    rarefaction                             html  
    repDiversity                            html  
    repLoad                                 html  
    repOverlap                              html  
    repSave                                 html  
    resample                                html  
    revcomp                                 html  
    reverse.string                          html  
    sample.clones                           html  
    sample2D                                html  
    segments.alphabets                      html  
    segments.list                           html  
    set.group.vector                        html  
    set.pb                                  html  
    set.people.vector                       html  
    set.rank                                html  
    shared.repertoire                       html  
    spectratyping                           html  
    startmitcr                              html  
    tailbound.proportion                    html  
    top.cross                               html  
    top.fun                                 html  
    twinsdata                               html  
    vis.clonal.dynamics                     html  
    vis.clonal.space                        html  
    vis.count.len                           html  
    vis.gene.usage                          html  
    vis.group.boxplot                       html  
    vis.heatmap                             html  
    vis.kmer.histogram                      html  
    vis.logo                                html  
    vis.number.count                        html  
    vis.pca                                 html  
    vis.radarlike                           html  
    vis.rarefaction                         html  
    vis.shared.clonotypes                   html  
    vis.top.proportions                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tcR)
Making 'packages.html' ... done