runibic 1.6.0
Patryk Orzechowski
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/runibic |
| Branch: RELEASE_3_9 |
| Last Commit: a3c898e |
| Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/runibic_1.6.0.tar.gz && rm -rf runibic.buildbin-libdir && mkdir runibic.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=runibic.buildbin-libdir runibic_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL runibic_1.6.0.zip && rm runibic_1.6.0.tar.gz runibic_1.6.0.zip
###
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% 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 35408 100 35408 0 0 558k 0 --:--:-- --:--:-- --:--:-- 617k
install for i386
* installing *source* package 'runibic' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I. -fopenmp -O2 -Wall -mtune=generic -c GlobalDefs.cpp -o GlobalDefs.o
GlobalDefs.cpp: In function 'bool check_seed(int, int, int, const std::vector&, int, int)':
GlobalDefs.cpp:69:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; igenes.size(); i++){
^
GlobalDefs.cpp:76:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; igenes.size(); i++){
^
GlobalDefs.cpp: In function 'void block_init(int, int, int, BicBlock*, std::vector&, std::vector&, std::vector&, int, int*, std::vector&, Params*, std::vector >&, std::vector >*)':
GlobalDefs.cpp:138:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < (*inputData)[t0].size() ;i++){
^
GlobalDefs.cpp:152:19: warning: comparison between signed and unsigned integer expressions [-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 getGenesFullLCS(const std::vector&, const std::vector&)':
GlobalDefs.cpp:240:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=0;i&, std::vector&, std::vector >&)':
GlobalDefs.cpp:336:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i=0; i&, std::vector&, std::vector&, int, int*, std::vector&, Params*, std::vector >&, std::vector >*)':
GlobalDefs.cpp:192:30: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized]
pvalue=pvalue+poisson;
^
In file included from GlobalDefs.cpp:34:0:
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);
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I. -fopenmp -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c fib.c -o fib.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I. -fopenmp -O2 -Wall -mtune=generic -c runibic.cpp -o runibic.o
runibic.cpp: In function 'Rcpp::List calculateLCS(Rcpp::IntegerMatrix, bool)':
runibic.cpp:329:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData.size(); i++) {
^
runibic.cpp:358:21: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData.size(); i++) {
^
runibic.cpp:498:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(k = 0; k < components; k++) {
^
runibic.cpp:507:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(components > vecGenes.size())
^
runibic.cpp:513:24: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData[vecGenes[0]].size() ;i++){
^
runibic.cpp:621:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData[ki].size() ;i++){
^
runibic.cpp:700:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (arrBlocks.size() == gParameters.SchBlock)
^
runibic.cpp:719:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (i < arrBlocks.size() && j < n) {
^
runibic.cpp:755:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto ind =0; ind&, int, int)':
GlobalDefs.cpp:69:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; igenes.size(); i++){
^
GlobalDefs.cpp:76:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; igenes.size(); i++){
^
GlobalDefs.cpp: In function 'void block_init(int, int, int, BicBlock*, std::vector&, std::vector&, std::vector&, int, int*, std::vector&, Params*, std::vector >&, std::vector >*)':
GlobalDefs.cpp:138:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < (*inputData)[t0].size() ;i++){
^
GlobalDefs.cpp:152:19: warning: comparison between signed and unsigned integer expressions [-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 getGenesFullLCS(const std::vector&, const std::vector&)':
GlobalDefs.cpp:240:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=0;i&, std::vector&, std::vector >&)':
GlobalDefs.cpp:336:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i=0; i&, std::vector&, std::vector&, int, int*, std::vector&, Params*, std::vector >&, std::vector >*)':
GlobalDefs.cpp:192:30: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized]
pvalue=pvalue+poisson;
^
In file included from GlobalDefs.cpp:34:0:
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);
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I. -fopenmp -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c fib.c -o fib.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I. -fopenmp -O2 -Wall -mtune=generic -c runibic.cpp -o runibic.o
runibic.cpp: In function 'Rcpp::List calculateLCS(Rcpp::IntegerMatrix, bool)':
runibic.cpp:329:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData.size(); i++) {
^
runibic.cpp:358:21: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData.size(); i++) {
^
runibic.cpp:498:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(k = 0; k < components; k++) {
^
runibic.cpp:507:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(components > vecGenes.size())
^
runibic.cpp:513:24: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData[vecGenes[0]].size() ;i++){
^
runibic.cpp:621:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData[ki].size() ;i++){
^
runibic.cpp:700:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (arrBlocks.size() == gParameters.SchBlock)
^
runibic.cpp:719:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (i < arrBlocks.size() && j < n) {
^
runibic.cpp:755:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto ind =0; ind