QUBIC

Package: QUBIC
Type: Package
Title: An R package for qualitative biclustering in support of gene
co-expression analyses
Description: The core function of this R package is to provide the
implementation of the well-cited and well-reviewed QUBIC algorithm, aiming to
deliver an effective and efficient biclustering capability. This package also
includes the following related functions: (i) a qualitative representation
of the input gene expression data, through a well-designed discretization way
considering the underlying data property, which can be directly used in other
biclustering programs; (ii) visualization of identified biclusters using heatmap
in support of overall expression pattern analysis; (iii) bicluster-based
co-expression network elucidation and visualization, where different correlation
coefficient scores between a pair of genes are provided; and (iv) a generalize
output format of biclusters and corresponding network can be freely downloaded
so that a user can easily do following comprehensive functional enrichment
analysis (e.g. DAVID) and advanced network visualization (e.g. Cytoscape).
Authors@R: c(person("Yu", "Zhang", role = c("aut", "cre"), email = "zy26@jlu.edu.cn"),
person("Qin", "Ma", role = "aut", email = "qin.ma@sdstate.edu"))
VignetteBuilder: knitr
biocViews: StatisticalMethod, Microarray, DifferentialExpression,
MultipleComparison, Clustering, Visualization, GeneExpression,
Network
Version: 1.0.2
License: CC BY-NC-ND 4.0 + file LICENSE
Depends: R (>= 3.1), biclust
Imports: Rcpp (>= 0.11.0)
LinkingTo: Rcpp
Suggests: knitr, rmarkdown
SystemRequirements: C++11, Rtools (>= 3.1)
Enhances: QUBICdata, RColorBrewer, qgraph, methods, fields
URL: http://github.com/zy26/QUBIC
BugReports: http://github.com/zy26/QUBIC/issues
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-16 06:05:56 UTC; biocbuild
Author: Yu Zhang [aut, cre],
Qin Ma [aut]
Maintainer: Yu Zhang <zy26@jlu.edu.cn>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'QUBIC' ...
** 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 charset.cc -o charset.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 discretize.cc -o discretize.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 edge_list.cc -o edge_list.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 fib.c -o fib.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 fopen_matrix.cc -o fopen_matrix.o
fopen_matrix.cc: In function 'void FopenMatrix::internal::fscanf2(FILE*, short int*)':
fopen_matrix.cc:5:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(file, "%hd", x);
                         ^
fopen_matrix.cc: In function 'void FopenMatrix::internal::fscanf2(FILE*, double*)':
fopen_matrix.cc:10:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(file, "%lf", x);
                         ^
fopen_matrix.cc: In function 'void FopenMatrix::internal::fscanf2(FILE*, float*)':
fopen_matrix.cc:15:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(file, "%f", x);
                        ^
fopen_matrix.cc: In function 'void FopenMatrix::internal::fscanf2(FILE*, int*)':
fopen_matrix.cc:20:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(file, "%d", x);
                        ^
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 qubic.cc -o qubic.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 rcpp_qubic.cpp -o rcpp_qubic.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 run_qubic.cc -o run_qubic.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 struct.cc -o struct.o
g++ -std=c++11 -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o QUBIC.so RcppExports.o charset.o discretize.o edge_list.o fib.o fopen_matrix.o qubic.o rcpp_qubic.o run_qubic.o struct.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/QUBIC/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'QUBIC'
    finding HTML links ... done
    BCQU-class                              html  
    finding level-2 HTML links ... done

    QUBIC                                   html  
    qudiscretize                            html  
    quheatmap                               html  
    qunet2xml                               html  
    qunetwork                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (QUBIC)
Making 'packages.html' ... done