scran

Package: scran
Version: 1.0.3
Date: 2016-05-20
Title: Methods for Single-Cell RNA-Seq Data Analysis
Authors@R: c(person("Aaron", "Lun", role = c("aut", "cre"), email =
"alun@wehi.edu.au"), person("Karsten", "Bach", role = "aut"),
person("Jong Kyoung", "Kim", role = "ctb"), person("Antonio",
"Scialdone", role="ctb"))
Maintainer: Aaron Lun <alun@wehi.edu.au>
Depends: R (>= 3.3.0), BiocParallel, scater
Imports: dynamicTreeCut, zoo, edgeR, limma, stats, BiocGenerics,
methods, Biobase, utils, Matrix
Suggests: limSolve, testthat, knitr, BiocStyle, org.Mm.eg.db, DESeq2,
monocle, S4Vectors
biocViews: Normalization, Sequencing, RNASeq, Software, GeneExpression,
Transcriptomics
Description: This package implements a variety of low-level analyses of
single-cell RNA-seq data. Methods are provided for
normalization of cell-specific biases, assignment of cell cycle
phase, and detection of highly variable and significantly
correlated genes.
License: GPL-3
NeedsCompilation: yes
VignetteBuilder: knitr
Author: Aaron Lun [aut, cre], Karsten Bach [aut], Jong Kyoung Kim [ctb],
Antonio Scialdone [ctb]
Packaged: 2016-05-22 06:08:34 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'scran' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c compute_rho.cpp -o compute_rho.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c forge_system.cpp -o forge_system.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.cpp -o init.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c shuffle_scores.cpp -o shuffle_scores.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o scran.so compute_rho.o forge_system.o init.o shuffle_scores.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/scran/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'scran'
    finding HTML links ... done
    DM                                      html  
    computeSpikeFactors                     html  
    finding level-2 HTML links ... done

    computeSumFactors                       html  
    convertTo                               html  
Rd warning: /tmp/Rtmpf2E7II/R.INSTALL323245b1a565/scran/man/convertTo.Rd:61: missing file link 'DESeqDataSetFromMatrix'
    correlatePairs                          html  
    cyclone                                 html  
    decomposeVar                            html  
    normalize                               html  
    quickCluster                            html  
    sandbag                                 html  
    spikes                                  html  
    testVar                                 html  
    trendVar                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scran)
Making 'packages.html' ... done