##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:runibic.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings runibic_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/runibic.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'runibic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'runibic' version '1.27.0'
* 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
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in 'NEWS':
  Cannot process chunk/lines:
    Fixing warnings.
  Cannot process chunk/lines:
    Removing warnings.
  Cannot process chunk/lines:
    Updating references.
  Cannot process chunk/lines:
    Improvement of results for sets with a small number of columns.
  Cannot process chunk/lines:
    Fixing build warning/errors on Windows/OSX.
  Cannot process chunk/lines:
    Synchronizing the last change with Bioconductor 3.7
  Cannot process chunk/lines:
    Applying previous releases in the dev branch.
  Cannot process chunk/lines:
    Fix: modification of default parameters for small datasets in order to keep consistency between different sizes of the input.
  Cannot process chunk/lines:
    Updating tutorial, adding citation.
  Cannot process chunk/lines:
    Documentation to the package was updated. 
  Cannot process chunk/lines:
    Including required biocViews. Refactoring R code.
  Cannot process chunk/lines:
    Code optimizations.
  Cannot process chunk/lines:
    Parallel version using OpenMP.
  Cannot process chunk/lines:
    Fixing discretize() function bug.
  Cannot process chunk/lines:
    Improved performance of functions in package.
  Cannot process chunk/lines:
    Removing some errors and warnings.
  Cannot process chunk/lines:
    Compatibility with SummarizedExperiment.
  Cannot process chunk/lines:
    Providing documentation and examples.
  Cannot process chunk/lines:
    Development of the runibic package prototype completed.
  Cannot process chunk/lines:
    First upload to Bioconductor.
  Cannot process chunk/lines:
    Working version of UniBic algorithm.
* checking code 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/runibic/libs/x64/runibic.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/runibic.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL runibic
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'runibic' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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]
   69 |     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]
   76 |     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]
  138 |   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]
  152 |     for(auto i=0;i<(*inputData)[j].size();i++)
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
GlobalDefs.cpp:117:7: warning: unused variable 'colNum' [-Wunused-variable]
  117 |   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]
  240 |   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]
  246 |   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]
  250 |   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]
  255 |     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]
  256 |     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]
  273 |   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]
  284 |     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]
  285 |       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]
  294 |   for(auto i=0;i<s1.size()+1;i++) {
      |                ~^~~~~~~~~~~~
GlobalDefs.cpp:232:16: warning: unused variable 'rank' [-Wunused-variable]
  232 |   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]
  336 |   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]
  341 |   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]
  344 |   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]
  345 |       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]
   54 | static void fh_initheap(struct fibheap *);
      |             ^~~~~~~~~~~
fibpriv.h:55:13: warning: 'void fh_insertrootlist(fibheap*, fibheap_el*)' declared 'static' but never defined [-Wunused-function]
   55 | 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]
   56 | 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]
   57 | 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]
   58 | 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]
   60 | 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]
   61 | 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]
   62 | static struct fibheap_el *fh_extractminel(struct fibheap *);
      |                           ^~~~~~~~~~~~~~~
fibpriv.h:63:13: warning: 'void fh_checkcons(fibheap*)' declared 'static' but never defined [-Wunused-function]
   63 | static void fh_checkcons(struct fibheap *h);
      |             ^~~~~~~~~~~~
fibpriv.h:64:13: warning: 'void fh_destroyheap(fibheap*)' declared 'static' but never defined [-Wunused-function]
   64 | 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]
   65 | 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]
   67 | 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]
   69 | 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]
   70 | 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]
   86 | static struct fibheap_el *fhe_newelem(void);
      |                           ^~~~~~~~~~~
fibpriv.h:87:13: warning: 'void fhe_initelem(fibheap_el*)' declared 'static' but never defined [-Wunused-function]
   87 | 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]
   88 | 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]
   89 | 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]
   90 | 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]
   96 | 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:211:5: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized]
  211 |     if (pvalue < block->pvalue)
      |     ^~
GlobalDefs.cpp:120:15: note: 'pvalue' was declared here
  120 |   long double pvalue;
      |               ^~~~~~
In function 'int edge_cmpr(void*, void*)',
    inlined from 'void internalCalulateLCS(std::vector<std::vector<int> >&, std::vector<triple>&, bool)' at GlobalDefs.cpp:412:22:
GlobalDefs.cpp:44:28: warning: array subscript 'triple[0]' is partly outside array bounds of 'triple [0]' [-Warray-bounds=]
   44 |   score_a = ((triple *)a)->lcslen;
      |             ~~~~~~~~~~~~~~~^~~~~~
GlobalDefs.cpp: In function 'void internalCalulateLCS(std::vector<std::vector<int> >&, std::vector<triple>&, bool)':
GlobalDefs.cpp:378:11: note: object '_cur_min' of size 8
  378 |   triple *_cur_min = &__cur_min;
      |           ^~~~~~~~
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I. -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fib.c -o fib.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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]
  329 |   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]
  358 |   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]
  417 |   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]
  498 |     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]
  507 |     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]
  513 |     for (auto ki=0; ki < vecGenes.size() ; ki++) {
      |                     ~~~^~~~~~~~~~~~~~~~~
runibic.cpp:567:13: warning: unused variable 'temp' [-Wunused-variable]
  567 |         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]
  597 |     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]
  621 |       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]
  700 |     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]
  719 |   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]
  755 |   for(auto ind =0; ind<arrBlocks.size(); ind++)
      |                    ~~~^~~~~~~~~~~~~~~~~
g++ -shared -s -static-libgcc -o runibic.dll tmp.def GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-runibic/00new/runibic/libs/x64
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (runibic)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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'

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    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

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Attaching package: 'S4Vectors'

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Loading required package: IRanges

Attaching package: 'IRanges'

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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'

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> 
> test_check("runibic")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
   8.87    0.67    9.76