OncoSimulR

Package: OncoSimulR
Type: Package
Title: Forward Genetic Simulation of Cancer Progresion with Epistasis
Version: 2.2.2
Date: 2016-04-14
Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
email = "rdiaz02@gmail.com"),
person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))
Author: Ramon Diaz-Uriarte [aut, cre],
Mark Taylor [ctb]
Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
Description: Functions for forward population genetic simulation in
asexual populations, with special focus on cancer progression.
Fitness can be an arbitrary function of genetic interactions between
multiple genes or modules of genes, including epistasis, order
restrictions in mutation accumulation, and order effects. Simulations
use continuous-time models and can include driver and passenger genes
and modules. Also included are functions for simulating random DAGs
of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks,
and other tumor progression models, and for plotting and sampling from
single or multiple realizations of the simulations, including
single-cell sampling, as well as functions for plotting the true
phylogenetic relationships of the clones.
biocViews: BiologicalQuestion, SomaticMutation
License: GPL (>= 3)
URL: https://github.com/rdiaz02/OncoSimul,
https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
BugReports: https://github.com/rdiaz02/OncoSimul/issues
Depends: R (>= 3.1.0)
Imports: Rcpp (>= 0.11.1), parallel, data.table, graph, Rgraphviz,
gtools, igraph, methods, RColorBrewer, grDevices
Suggests: BiocStyle, knitr, Oncotree, testthat
LinkingTo: Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-05-16 04:43:01 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'OncoSimulR' ...
** 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 BNB_nr.cpp -o BNB_nr.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 BNB_v1.cpp -o BNB_v1.o
gcc -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 OncoSimulR_init.c -o OncoSimulR_init.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 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 bnb_common.cpp -o bnb_common.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 new_restrict.cpp -o new_restrict.o
g++ -std=c++11 -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o OncoSimulR.so BNB_nr.o BNB_v1.o OncoSimulR_init.o RcppExports.o bnb_common.o new_restrict.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/OncoSimulR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'OncoSimulR'
    finding HTML links ... done
    OncoSimulWide2Long                      html  
    allFitnessEffects                       html  
    evalAllGenotypes                        html  
    example-missing-drivers                 html  
    examplePosets                           html  
    examplesFitnessEffects                  html  
    mcfLs                                   html  
    oncoSimulIndiv                          html  
    plot.fitnessEffects                     html  
    plot.oncosimul                          html  
    finding level-2 HTML links ... done

    plotClonePhylog                         html  
    plotPoset                               html  
    poset                                   html  
    samplePop                               html  
    simOGraph                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OncoSimulR)
Making 'packages.html' ... done