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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL runibic
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'runibic' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c fib.c -o fib.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-runibic/00new/runibic/libs/x64
** 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
* DONE (runibic)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MetNet' is missing or broken
done
