yCrypticRNAs

Package: yCrypticRNAs
Type: Package
Title: Cryptic Transcription Analysis in Yeast
Version: 0.99.2
Author: Nicole Uwimana, Benjamin Haibe-Kains, Francois Robert
Maintainer: Nicole Uwimana <nicole.uwimana@gmail.com>
Description: Calculates cryptic scores for genes using the ratio
(Cheung et al., 2008), the 3' enrichment method
(DeGennaro et al., 2013) and the probabilistic
method. It also provide methods to estimates
cryptic transcription start sites.
Depends: R (>= 3.2.0)
URL: https://bitbucket.org/nuwimana/ycrypticrnas
BugReports: https://bitbucket.org/nuwimana/ycrypticrnas/issues
License: GPL-2
LazyData: true
Imports: biomaRt (>= 2.24.1), data.table (>= 1.9.6), IRanges (>=
2.2.9), mclust (>= 5.1), MESS (>= 0.3-2), parallel (>= 3.2.2),
Rcpp (>= 0.12.1), Rsamtools (>= 1.20.5)
Suggests: knitr, testthat, rmarkdown
VignetteBuilder: knitr
LinkingTo: Rcpp
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-02-08 18:37:38 UTC; nicoleuwimana
Repository: CRAN
Date/Publication: 2016-02-08 23:43:06

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'yCrypticRNAs' ...
** package 'yCrypticRNAs' successfully unpacked and MD5 sums checked
** libs
g++ -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 BlockedIntervals.cpp -o BlockedIntervals.o
g++ -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++ -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 bedFile.cpp -o bedFile.o
g++ -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 my_coverage.cpp -o my_coverage.o
g++ -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 my_coverageMain.cpp -o my_coverageMain.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o yCrypticRNAs.so BlockedIntervals.o RcppExports.o bedFile.o my_coverage.o my_coverageMain.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/yCrypticRNAs/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'yCrypticRNAs'
    finding HTML links ... done
    annotations                             html  
    annotationsSet                          html  
    as.annotationsSet                       html  
    bam_to_reads                            html  
    coverage                                html  
    coverageDataSet                         html  
    enrichment_score                        html  
    gene_coverage                           html  
    genome_wide_scores                      html  
    initiation_sites                        html  
    introns                                 html  
    ratio_score                             html  
    rna_seq_signals                         html  
    yCrypticRNAs                            html  
    yer109c                                 html  
    zscore_score                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (yCrypticRNAs)
Making 'packages.html' ... done