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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL runibic
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘runibic’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-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 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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-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 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++)
| ~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o runibic.so GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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)
