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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL runibic
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘runibic’ ...
** this is package ‘runibic’ version ‘1.33.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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;
      |               ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c fib.c -o fib.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -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 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 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 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 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 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 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 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 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 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 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 unsigned int’} [-Wsign-compare]
  755 |   for(auto ind =0; ind<arrBlocks.size(); ind++)
      |                    ~~~^~~~~~~~~~~~~~~~~
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o runibic.so GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-runibic/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (runibic)