Package: runibic

Version: 1.4.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:runibic.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings runibic_1.4.0.tar.gz

StartedAt: 2019-04-16 02:49:59 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:53:43 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 223.6 seconds

RetCode: 0

Status:  OK

CheckDir: runibic.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:runibic.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings runibic_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/runibic.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘runibic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘runibic’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘runibic’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
runibic 707.244   2.48  96.351
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/runibic.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL runibic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘runibic’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -Wall -c GlobalDefs.cpp -o GlobalDefs.o
GlobalDefs.cpp: In function ‘bool check_seed(int, int, int, const std::vector<BicBlock*>&, int, int)’:
GlobalDefs.cpp:69:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i=0; i<vecBlk[ind]->genes.size(); i++){
                ^
GlobalDefs.cpp:76:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i=0; i<vecBlk[ind]->genes.size(); i++){
                ^
GlobalDefs.cpp: In function ‘void block_init(int, int, int, BicBlock*, std::vector<int>&, std::vector<int>&, std::vector<bool>&, int, int*, std::vector<long double>&, Params*, std::vector<std::vector<int> >&, std::vector<std::vector<int> >*)’:
GlobalDefs.cpp:138:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i < (*inputData)[t0].size() ;i++){
                      ^
GlobalDefs.cpp:152:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(auto i=0;i<(*inputData)[j].size();i++)
                   ^
GlobalDefs.cpp:117:7: warning: unused variable ‘colNum’ [-Wunused-variable]
   int colNum = gParameters.ColNumber;
       ^
GlobalDefs.cpp: In function ‘std::vector<int> getGenesFullLCS(const std::vector<int>&, const std::vector<int>&)’:
GlobalDefs.cpp:240:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i=0;i<s1.size()+1;i++) {
                 ^
GlobalDefs.cpp:246:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i=0; i<s1.size()+1; i++) {
                  ^
GlobalDefs.cpp:250:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto j=0; j<s2.size()+1; j++) {
                  ^
GlobalDefs.cpp:255:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(auto i=1; i<s1.size()+1; i++) {
                    ^
GlobalDefs.cpp:256:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(auto j=1; j<s2.size()+1; j++) {
                    ^
GlobalDefs.cpp:273:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto j=1;j<s2.size()+1;j++) {
                  ^
GlobalDefs.cpp:284:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i=1;i<s1.size()+1;i++) {
                    ^
GlobalDefs.cpp:285:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto j=1;j<s2.size()+1;j++) {
                      ^
GlobalDefs.cpp:294:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i=0;i<s1.size()+1;i++) {
                 ^
GlobalDefs.cpp:232:16: warning: unused variable ‘rank’ [-Wunused-variable]
   int maxvalue,rank;
                ^
GlobalDefs.cpp: In function ‘void internalPairwiseLCS(std::vector<int>&, std::vector<int>&, std::vector<std::vector<int> >&)’:
GlobalDefs.cpp:336:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i=0; i<x.size()+1; i++) {
                   ^
GlobalDefs.cpp:341:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto j=0; j<y.size()+1; j++) {
                   ^
GlobalDefs.cpp:344:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i=1; i<x.size()+1; i++) {
                  ^
GlobalDefs.cpp:345:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(auto j=1; j<y.size()+1; j++) {
                      ^
GlobalDefs.cpp: In function ‘void block_init(int, int, int, BicBlock*, std::vector<int>&, std::vector<int>&, std::vector<bool>&, int, int*, std::vector<long double>&, Params*, std::vector<std::vector<int> >&, std::vector<std::vector<int> >*)’:
GlobalDefs.cpp:192:30: warning: ‘pvalue’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         pvalue=pvalue+poisson;
                              ^
In file included from GlobalDefs.cpp:34:0:
fibpriv.h: At global scope:
fibpriv.h:54:13: warning: ‘void fh_initheap(fibheap*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_initheap(struct fibheap *);
             ^
fibpriv.h:55:13: warning: ‘void fh_insertrootlist(fibheap*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_insertrootlist(struct fibheap *, struct fibheap_el *);
             ^
fibpriv.h:56:13: warning: ‘void fh_removerootlist(fibheap*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_removerootlist(struct fibheap *, struct fibheap_el *);
             ^
fibpriv.h:57:13: warning: ‘void fh_consolidate(fibheap*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_consolidate(struct fibheap *);
             ^
fibpriv.h:58:13: warning: ‘void fh_heaplink(fibheap*, fibheap_el*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_heaplink(struct fibheap *h, struct fibheap_el *y,
             ^
fibpriv.h:60:13: warning: ‘void fh_cut(fibheap*, fibheap_el*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_cut(struct fibheap *, struct fibheap_el *, struct fibheap_el *);
             ^
fibpriv.h:61:13: warning: ‘void fh_cascading_cut(fibheap*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_cascading_cut(struct fibheap *, struct fibheap_el *);
             ^
fibpriv.h:62:27: warning: ‘fibheap_el* fh_extractminel(fibheap*)’ declared ‘static’ but never defined [-Wunused-function]
 static struct fibheap_el *fh_extractminel(struct fibheap *);
                           ^
fibpriv.h:63:13: warning: ‘void fh_checkcons(fibheap*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_checkcons(struct fibheap *h);
             ^
fibpriv.h:64:13: warning: ‘void fh_destroyheap(fibheap*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_destroyheap(struct fibheap *h);
             ^
fibpriv.h:65:12: warning: ‘int fh_compare(fibheap*, fibheap_el*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static int fh_compare(struct fibheap *h, struct fibheap_el *a,
            ^
fibpriv.h:67:12: warning: ‘int fh_comparedata(fibheap*, int, void*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static int fh_comparedata(struct fibheap *h, int key, void *data,
            ^
fibpriv.h:69:13: warning: ‘void fh_insertel(fibheap*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_insertel(struct fibheap *h, struct fibheap_el *x);
             ^
fibpriv.h:70:13: warning: ‘void fh_deleteel(fibheap*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fh_deleteel(struct fibheap *h, struct fibheap_el *x);
             ^
fibpriv.h:86:27: warning: ‘fibheap_el* fhe_newelem()’ declared ‘static’ but never defined [-Wunused-function]
 static struct fibheap_el *fhe_newelem(void);
                           ^
fibpriv.h:87:13: warning: ‘void fhe_initelem(fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fhe_initelem(struct fibheap_el *);
             ^
fibpriv.h:88:13: warning: ‘void fhe_insertafter(fibheap_el*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static void fhe_insertafter(struct fibheap_el *a, struct fibheap_el *b);
             ^
fibpriv.h:89:20: warning: ‘void fhe_insertbefore(fibheap_el*, fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static inline void fhe_insertbefore(struct fibheap_el *a, struct fibheap_el *b);
                    ^
fibpriv.h:90:27: warning: ‘fibheap_el* fhe_remove(fibheap_el*)’ declared ‘static’ but never defined [-Wunused-function]
 static struct fibheap_el *fhe_remove(struct fibheap_el *a);
                           ^
fibpriv.h:96:19: warning: ‘int ceillog2(unsigned int)’ declared ‘static’ but never defined [-Wunused-function]
 static inline int ceillog2(unsigned int a);
                   ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c fib.c -o fib.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -Wall -c runibic.cpp -o runibic.o
runibic.cpp: In function ‘Rcpp::List calculateLCS(Rcpp::IntegerMatrix, bool)’:
runibic.cpp:329:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i < discreteInputData.size(); i++) {
                      ^
runibic.cpp:358:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < out.size(); i++)
                     ^
runibic.cpp: In function ‘Rcpp::List cluster(Rcpp::IntegerMatrix, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int)’:
runibic.cpp:417:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i < discreteInputData.size(); i++) {
                      ^
runibic.cpp:498:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(k = 0; k < components; k++) {
                  ^
runibic.cpp:507:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(components > vecGenes.size())
                   ^
runibic.cpp:513:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto ki=0; ki < vecGenes.size() ; ki++) {
                        ^
runibic.cpp:567:13: warning: unused variable ‘temp’ [-Wunused-variable]
         int temp;
             ^
runibic.cpp:597:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i < discreteInputData[vecGenes[0]].size() ;i++){
                        ^
runibic.cpp:621:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i < discreteInputData[ki].size() ;i++){
                          ^
runibic.cpp:700:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (arrBlocks.size() == gParameters.SchBlock) 
                          ^
runibic.cpp:719:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while (i < arrBlocks.size() && j < n) {
            ^
runibic.cpp:755:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto ind =0; ind<arrBlocks.size(); ind++)
                       ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o runibic.so GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/runibic/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (runibic)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(runibic)
Loading required package: biclust
Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
Loading required package: lattice
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

> 
> test_check("runibic")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 11 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.192   0.308   7.924 

name	user	system	elapsed
backtrackLCS	0.000	0.000	0.014
calculateLCS	0.156	0.008	0.047
cluster	0.232	0.000	0.034
pairwiseLCS	0.004	0.000	0.000
runiDiscretize	0.004	0.000	0.004
runibic	707.244	2.480	96.351
set_runibic_params	0.000	0.000	0.001
unisort	0.060	0.004	0.008