qpgraph

Package: qpgraph
Title: Estimation of genetic and molecular regulatory networks from
high-throughput genomics data
Version: 2.6.1
Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="robert.castelo@upf.edu"),
person("Alberto", "Roverato", role="aut", email="alberto.roverato@unibo.it"))
Description: Estimate gene and eQTL networks from high-throughput expression and genotyping assays.
License: GPL (>= 2)
Depends: R (>= 3.0.0)
Imports: methods, parallel, Matrix (>= 1.0), grid, annotate, graph (>=
1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi,
IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm,
qtl, Rgraphviz
Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db,
rlecuyer, snow, Category, GOstats
LazyData: yes
URL: http://functionalgenomics.upf.edu/qpgraph
biocViews: Microarray, GeneExpression, Transcription, Pathways,
NetworkInference, GraphAndNetwork, GeneRegulation, Genetics,
GeneticVariability, SNP, Software
NeedsCompilation: yes
Packaged: 2016-05-18 02:04:09 UTC; biocbuild
Author: Robert Castelo [aut, cre],
Alberto Roverato [aut]
Maintainer: Robert Castelo <robert.castelo@upf.edu>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'qpgraph' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2  -c cliquer.c -o cliquer.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2  -c graph.c -o graph.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2  -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'qp_fast_path_weight':
qpgraph.c:5849:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int i = edges[k, 0];
                    ^
qpgraph.c:5850:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int j = edges[k, 1];
                    ^
qpgraph.c: In function 'ssd_A':
qpgraph.c:8157:17: warning: unused variable 'm' [-Wunused-variable]
   int     i,j,k,m;
                 ^
qpgraph.c:8157:15: warning: unused variable 'k' [-Wunused-variable]
   int     i,j,k,m;
               ^
qpgraph.c: In function 'qp_fast_rnd_graph':
qpgraph.c:8286:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   G = LOGICAL(GR);
     ^
In file included from qpgraph.c:27:0:
qpgraph.c: In function 'qp_edge_nrr':
/home/ddbj/local/lib64/R/include/Rmath.h:302:13: warning: 'Rf_df' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define pt  Rf_pt
             ^
/home/ddbj/local/lib64/R/include/Rmath.h:236:13: note: 'Rf_df' was declared here
 #define df  Rf_df
             ^
qpgraph.c:5082:16: note: in expansion of macro 'df'
   int    k, l, df, n_upper_tri;
                ^
qpgraph.c: In function 'qp_fast_edge_nrr':
qpgraph.c:5534:12: warning: 'pcorR' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return pcorR;
            ^
qpgraph.c: In function 'qp_ci_test_hmgm.isra.9':
qpgraph.c:3976:36: warning: 'rss1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       *partial_eta_squared = (rss1 - rss2) / rss0;
                                    ^
qpgraph.c:3703:11: note: 'rss1' was declared here
   double  rss1, rss2;
           ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2  -c reorder.c -o reorder.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/ddbj/local/lib64/R/lib -lRblas -L/home/ddbj/local/lib64/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'det' from package 'Matrix' in package 'qpgraph'
Creating a generic function from function 'rmvnorm' in package 'qpgraph'
Creating a generic function from function 'sim.cross' in package 'qpgraph'
** help
*** installing help indices
  converting help for package 'qpgraph'
    finding HTML links ... done
    EcoliOxygen                             html  
    HMgmm-class                             html  
Rd warning: /tmp/RtmpnLXxy5/R.INSTALL76e8639915ba/qpgraph/man/HMgmm-class.Rd:65: missing file link 'dspMatrix-class'
    SsdMatrix-class                         html  
Rd warning: /tmp/RtmpnLXxy5/R.INSTALL76e8639915ba/qpgraph/man/SsdMatrix-class.Rd:14: missing file link 'dspMatrix-class'
Rd warning: /tmp/RtmpnLXxy5/R.INSTALL76e8639915ba/qpgraph/man/SsdMatrix-class.Rd:27: missing file link 'dspMatrix-class'
    UGgmm-class                             html  
Rd warning: /tmp/RtmpnLXxy5/R.INSTALL76e8639915ba/qpgraph/man/UGgmm-class.Rd:56: missing file link 'dspMatrix-class'
    eQTLcross-class                         html  
    eQTLnetwork-class                       html  
    eQTLnetworkEstimate                     html  
    eQTLnetworkEstimationParam-class        html  
    graphParam-class                        html  
    qpAllCItests                            html  
    qpAnyGraph                              html  
    qpAvgNrr                                html  
    qpBoundary                              html  
    qpCItest                                html  
    qpClique                                html  
    qpCliqueNumber                          html  
    qpCov                                   html  
    qpEdgeNrr                               html  
    qpFunctionalCoherence                   html  
    qpG2Sigma                               html  
Rd warning: /tmp/RtmpnLXxy5/R.INSTALL76e8639915ba/qpgraph/man/qpG2Sigma.Rd:51: missing file link 'rmvnorm'
    qpGenNrr                                html  
    qpGetCliques                            html  
    qpGraph-class                           html  
    qpGraphDensity                          html  
    qpHTF                                   html  
    qpHist                                  html  
    qpIPF                                   html  
    qpImportNrr                             html  
    qpK2ParCor                              html  
Rd warning: /tmp/RtmpnLXxy5/R.INSTALL76e8639915ba/qpgraph/man/qpK2ParCor.Rd:17: missing file link 'cov2cor'
    qpNrr                                   html  
    qpPAC                                   html  
    qpPCC                                   html  
    qpPRscoreThreshold                      html  
    qpPathWeight                            html  
    qpPlotMap                               html  
    qpPlotNetwork                           html  
    qpPrecisionRecall                       html  
    qpRndGraph                              html  
    qpRndWishart                            html  
    qpTopPairs                              html  
    qpUnifRndAssociation                    html  
    qpUpdateCliquesRemoving                 html  
    qpgraph-package                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qpgraph)
Making 'packages.html' ... done