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This page was generated on 2022-04-13 12:07:16 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for runibic on tokay2


To the developers/maintainers of the runibic package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/runibic.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1679/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
runibic 1.16.0  (landing page)
Patryk Orzechowski
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/runibic
git_branch: RELEASE_3_14
git_last_commit: 4507cce
git_last_commit_date: 2021-10-26 12:39:56 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: runibic
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:runibic.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings runibic_1.16.0.tar.gz
StartedAt: 2022-04-13 02:10:14 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 02:14:28 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 253.2 seconds
RetCode: 0
Status:   OK  
CheckDir: runibic.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:runibic.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings runibic_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/runibic.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'runibic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'runibic' version '1.16.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/runibic/libs/i386/runibic.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/runibic/libs/x64/runibic.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/runibic.Rcheck/00check.log'
for details.



Installation output

runibic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/runibic_1.16.0.tar.gz && rm -rf runibic.buildbin-libdir && mkdir runibic.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=runibic.buildbin-libdir runibic_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL runibic_1.16.0.zip && rm runibic_1.16.0.tar.gz runibic_1.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 34363  100 34363    0     0   289k      0 --:--:-- --:--:-- --:--:--  291k

install for i386

* installing *source* package 'runibic' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (i=0; i<vecBlk[ind]->genes.size(); i++){
               ~^~~~~~~~~~~~~~~~~~~~~~~~~~
GlobalDefs.cpp:76:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < (*inputData)[t0].size() ;i++){
                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~
GlobalDefs.cpp:152:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(auto i=0;i<s1.size()+1;i++) {
                ~^~~~~~~~~~~~
GlobalDefs.cpp:246:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(auto i=0; i<s1.size()+1; i++) {
                 ~^~~~~~~~~~~~
GlobalDefs.cpp:250:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(auto j=0; j<s2.size()+1; j++) {
                 ~^~~~~~~~~~~~
GlobalDefs.cpp:255:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(auto i=1; i<s1.size()+1; i++) {
                   ~^~~~~~~~~~~~
GlobalDefs.cpp:256:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(auto j=1; j<s2.size()+1; j++) {
                   ~^~~~~~~~~~~~
GlobalDefs.cpp:273:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto j=1;j<s2.size()+1;j++) {
                 ~^~~~~~~~~~~~
GlobalDefs.cpp:284:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (auto i=1;i<s1.size()+1;i++) {
                   ~^~~~~~~~~~~~
GlobalDefs.cpp:285:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for (auto j=1;j<s2.size()+1;j++) {
                     ~^~~~~~~~~~~~
GlobalDefs.cpp:294:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i=0; i<x.size()+1; i++) {
                  ~^~~~~~~~~~~
GlobalDefs.cpp:341:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto j=0; j<y.size()+1; j++) {
                  ~^~~~~~~~~~~
GlobalDefs.cpp:344:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(auto i=1; i<x.size()+1; i++) {
                 ~^~~~~~~~~~~
GlobalDefs.cpp:345:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(auto j=1; j<y.size()+1; j++) {
                     ~^~~~~~~~~~~
In file included from GlobalDefs.cpp:34:
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);
                   ^~~~~~~~
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:192:15: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized]
         pvalue=pvalue+poisson;
         ~~~~~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fib.c -o fib.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c runibic.cpp -o runibic.o
runibic.cpp: In function 'Rcpp::List calculateLCS(Rcpp::IntegerMatrix, bool)':
runibic.cpp:329:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < discreteInputData.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<triple>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < discreteInputData.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:498:18: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
     for(k = 0; k < components; k++) {
                ~~^~~~~~~~~~~~
runibic.cpp:507:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(components > vecGenes.size())
        ~~~~~~~~~~~^~~~~~~~~~~~~~~~~
runibic.cpp:513:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (auto i = 0; i < discreteInputData[vecGenes[0]].size() ;i++){
                      ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:621:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for (auto i = 0; i < discreteInputData[ki].size() ;i++){
                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:700:26: warning: comparison of integer expressions of different signedness: 'std::vector<BicBlock*>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
     if (arrBlocks.size() == gParameters.SchBlock)
         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:719:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<BicBlock*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   while (i < arrBlocks.size() && j < n) {
          ~~^~~~~~~~~~~~~~~~~~
runibic.cpp:755:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<BicBlock*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(auto ind =0; ind<arrBlocks.size(); ind++)
                    ~~~^~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o runibic.dll tmp.def GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/runibic.buildbin-libdir/00LOCK-runibic/00new/runibic/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'runibic'
    finding HTML links ... done
    BCUnibic-class                          html  
    BCUnibicD-class                         html  
    backtrackLCS                            html  
    calculateLCS                            html  
    cluster                                 html  
    pairwiseLCS                             html  
    runiDiscretize                          html  
    runibic                                 html  
    set_runibic_params                      html  
    unisort                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'runibic' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (i=0; i<vecBlk[ind]->genes.size(); i++){
               ~^~~~~~~~~~~~~~~~~~~~~~~~~~
GlobalDefs.cpp:76:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < (*inputData)[t0].size() ;i++){
                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~
GlobalDefs.cpp:152:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto i=0;i<s1.size()+1;i++) {
                ~^~~~~~~~~~~~
GlobalDefs.cpp:246:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto i=0; i<s1.size()+1; i++) {
                 ~^~~~~~~~~~~~
GlobalDefs.cpp:250:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto j=0; j<s2.size()+1; j++) {
                 ~^~~~~~~~~~~~
GlobalDefs.cpp:255:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(auto i=1; i<s1.size()+1; i++) {
                   ~^~~~~~~~~~~~
GlobalDefs.cpp:256:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(auto j=1; j<s2.size()+1; j++) {
                   ~^~~~~~~~~~~~
GlobalDefs.cpp:273:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto j=1;j<s2.size()+1;j++) {
                 ~^~~~~~~~~~~~
GlobalDefs.cpp:284:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (auto i=1;i<s1.size()+1;i++) {
                   ~^~~~~~~~~~~~
GlobalDefs.cpp:285:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       for (auto j=1;j<s2.size()+1;j++) {
                     ~^~~~~~~~~~~~
GlobalDefs.cpp:294:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i=0; i<x.size()+1; i++) {
                  ~^~~~~~~~~~~
GlobalDefs.cpp:341:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto j=0; j<y.size()+1; j++) {
                  ~^~~~~~~~~~~
GlobalDefs.cpp:344:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto i=1; i<x.size()+1; i++) {
                 ~^~~~~~~~~~~
GlobalDefs.cpp:345:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       for(auto j=1; j<y.size()+1; j++) {
                     ~^~~~~~~~~~~
In file included from GlobalDefs.cpp:34:
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);
                   ^~~~~~~~
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:192:15: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized]
         pvalue=pvalue+poisson;
         ~~~~~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fib.c -o fib.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I. -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c runibic.cpp -o runibic.o
runibic.cpp: In function 'Rcpp::List calculateLCS(Rcpp::IntegerMatrix, bool)':
runibic.cpp:329:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < discreteInputData.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<triple>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < discreteInputData.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:498:18: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
     for(k = 0; k < components; k++) {
                ~~^~~~~~~~~~~~
runibic.cpp:507:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     if(components > vecGenes.size())
        ~~~~~~~~~~~^~~~~~~~~~~~~~~~~
runibic.cpp:513:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (auto i = 0; i < discreteInputData[vecGenes[0]].size() ;i++){
                      ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:621:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       for (auto i = 0; i < discreteInputData[ki].size() ;i++){
                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:700:26: warning: comparison of integer expressions of different signedness: 'std::vector<BicBlock*>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
     if (arrBlocks.size() == gParameters.SchBlock)
         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
runibic.cpp:719:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<BicBlock*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   while (i < arrBlocks.size() && j < n) {
          ~~^~~~~~~~~~~~~~~~~~
runibic.cpp:755:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<BicBlock*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto ind =0; ind<arrBlocks.size(); ind++)
                    ~~~^~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o runibic.dll tmp.def GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/runibic.buildbin-libdir/runibic/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'runibic' as runibic_1.16.0.zip
* DONE (runibic)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'runibic' successfully unpacked and MD5 sums checked

Tests output

runibic.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> test_check("runibic")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
   7.15    0.53    7.67 

runibic.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> test_check("runibic")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
   7.53    0.26    7.76 

Example timings

runibic.Rcheck/examples_i386/runibic-Ex.timings

nameusersystemelapsed
backtrackLCS000
calculateLCS000
cluster000
pairwiseLCS000
runiDiscretize000
runibic2.730.142.00
set_runibic_params000
unisort000

runibic.Rcheck/examples_x64/runibic-Ex.timings

nameusersystemelapsed
backtrackLCS0.000.000.08
calculateLCS0.000.000.03
cluster000
pairwiseLCS000
runiDiscretize0.000.020.02
runibic3.060.172.28
set_runibic_params000
unisort000