Patryk Orzechowski
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/runibic |
| Branch: RELEASE_3_6 |
| Last Commit: 3c10f82 |
| Last Changed Date: 2017-11-06 11:45:46 -0400 (Mon, 06 Nov 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:30:52 -0400 (Thu, 12 Apr 2018).
| Package 1233/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| runibic 1.0.2 Patryk Orzechowski
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: runibic |
| Version: 1.0.2 |
| Command: rm -rf runibic.buildbin-libdir runibic.Rcheck && mkdir runibic.buildbin-libdir runibic.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=runibic.buildbin-libdir runibic_1.0.2.tar.gz >runibic.Rcheck\00install.out 2>&1 && cp runibic.Rcheck\00install.out runibic-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=runibic.buildbin-libdir --install="check:runibic-install.out" --force-multiarch --no-vignettes --timings runibic_1.0.2.tar.gz |
| StartedAt: 2018-04-12 02:55:33 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:59:47 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 254.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: runibic.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf runibic.buildbin-libdir runibic.Rcheck && mkdir runibic.buildbin-libdir runibic.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=runibic.buildbin-libdir runibic_1.0.2.tar.gz >runibic.Rcheck\00install.out 2>&1 && cp runibic.Rcheck\00install.out runibic-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=runibic.buildbin-libdir --install="check:runibic-install.out" --force-multiarch --no-vignettes --timings runibic_1.0.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/runibic.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'runibic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'runibic' version '1.0.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'runibic' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpw3phSs/R.INSTALL1a2c669279af/runibic/man/runibic.Rd:69: missing file link 'biclust'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpw3phSs/R.INSTALL1a2c669279af/runibic/man/runibic.Rd:72: missing file link 'biclust'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/runibic.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/runibic.buildbin-libdir/runibic/libs/i386/runibic.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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. 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runibic 31.05 4.19 8.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runibic 26.37 4.39 7.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/runibic.Rcheck/00check.log'
for details.
runibic.Rcheck/00install.out
install for i386
* installing *source* package 'runibic' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -I. -fopenmp -O2 -Wall -mtune=generic -c GlobalDefs.cpp -o GlobalDefs.o
In file included from GlobalDefs.cpp:32:0:
GlobalDefs.h: In constructor 'Params::Params()':
GlobalDefs.h:60:7: warning: 'Params::Divided' will be initialized after [-Wreorder]
int Divided;
^
GlobalDefs.h:47:7: warning: 'int Params::RowNumber' [-Wreorder]
int RowNumber;
^
GlobalDefs.h:34:3: warning: when initialized here [-Wreorder]
Params()
^
GlobalDefs.cpp: In function 'bool check_seed(int, int, int, const std::vector<BicBlock*>&, int, int)':
GlobalDefs.cpp:69:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; i<vecBlk[ind]->genes.size(); i++){
^
GlobalDefs.cpp:76:16: warning: comparison between signed and unsigned integer expressions [-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 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<int> getGenesFullLCS(const std::vector<int>&, const std::vector<int>&)':
GlobalDefs.cpp:240:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=0;i<s1.size()+1;i++) {
^
GlobalDefs.cpp:246:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=0; i<s1.size()+1; i++) {
^
GlobalDefs.cpp:250:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto j=0; j<s2.size()+1; j++) {
^
GlobalDefs.cpp:255:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=1; i<s1.size()+1; i++) {
^
GlobalDefs.cpp:256:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto j=1; j<s2.size()+1; j++) {
^
GlobalDefs.cpp:273:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto j=1;j<s2.size()+1;j++) {
^
GlobalDefs.cpp:284:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i=1;i<s1.size()+1;i++) {
^
GlobalDefs.cpp:285:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto j=1;j<s2.size()+1;j++) {
^
GlobalDefs.cpp:294:17: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i=0; i<x.size()+1; i++) {
^
GlobalDefs.cpp:341:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto j=0; j<y.size()+1; j++) {
^
GlobalDefs.cpp:344:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=1; i<x.size()+1; i++) {
^
GlobalDefs.cpp:345:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto j=1; j<y.size()+1; j++) {
^
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:192:30: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -I. -fopenmp -O2 -Wall -mtune=generic -c runibic.cpp -o runibic.o
In file included from runibic.cpp:34:0:
GlobalDefs.h: In constructor 'Params::Params()':
GlobalDefs.h:60:7: warning: 'Params::Divided' will be initialized after [-Wreorder]
int Divided;
^
GlobalDefs.h:47:7: warning: 'int Params::RowNumber' [-Wreorder]
int RowNumber;
^
GlobalDefs.h:34:3: warning: when initialized here [-Wreorder]
Params()
^
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:499:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(k = 0; k < components; k++) {
^
runibic.cpp:508:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(components > vecGenes.size())
^
runibic.cpp:514:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto ki=0; ki < vecGenes.size() ; ki++) {
^
runibic.cpp:562:13: warning: unused variable 'temp' [-Wunused-variable]
int temp;
^
runibic.cpp:592:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData[vecGenes[0]].size() ;i++){
^
runibic.cpp:616:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData[ki].size() ;i++){
^
runibic.cpp:695:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (arrBlocks.size() == gParameters.SchBlock)
^
runibic.cpp:714:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (i < arrBlocks.size() && j < n) {
^
runibic.cpp:750:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto ind =0; ind<arrBlocks.size(); ind++)
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o runibic.dll tmp.def GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/runibic.buildbin-libdir/runibic/libs/i386
** R
** inst
** preparing 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
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpw3phSs/R.INSTALL1a2c669279af/runibic/man/runibic.Rd:69: missing file link 'biclust'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpw3phSs/R.INSTALL1a2c669279af/runibic/man/runibic.Rd:72: missing file link 'biclust'
set_runibic_params html
unisort html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'runibic' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -I. -fopenmp -O2 -Wall -mtune=generic -c GlobalDefs.cpp -o GlobalDefs.o
In file included from GlobalDefs.cpp:32:0:
GlobalDefs.h: In constructor 'Params::Params()':
GlobalDefs.h:60:7: warning: 'Params::Divided' will be initialized after [-Wreorder]
int Divided;
^
GlobalDefs.h:47:7: warning: 'int Params::RowNumber' [-Wreorder]
int RowNumber;
^
GlobalDefs.h:34:3: warning: when initialized here [-Wreorder]
Params()
^
GlobalDefs.cpp: In function 'bool check_seed(int, int, int, const std::vector<BicBlock*>&, int, int)':
GlobalDefs.cpp:69:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; i<vecBlk[ind]->genes.size(); i++){
^
GlobalDefs.cpp:76:16: warning: comparison between signed and unsigned integer expressions [-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 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<int> getGenesFullLCS(const std::vector<int>&, const std::vector<int>&)':
GlobalDefs.cpp:240:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=0;i<s1.size()+1;i++) {
^
GlobalDefs.cpp:246:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=0; i<s1.size()+1; i++) {
^
GlobalDefs.cpp:250:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto j=0; j<s2.size()+1; j++) {
^
GlobalDefs.cpp:255:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=1; i<s1.size()+1; i++) {
^
GlobalDefs.cpp:256:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto j=1; j<s2.size()+1; j++) {
^
GlobalDefs.cpp:273:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto j=1;j<s2.size()+1;j++) {
^
GlobalDefs.cpp:284:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i=1;i<s1.size()+1;i++) {
^
GlobalDefs.cpp:285:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto j=1;j<s2.size()+1;j++) {
^
GlobalDefs.cpp:294:17: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i=0; i<x.size()+1; i++) {
^
GlobalDefs.cpp:341:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto j=0; j<y.size()+1; j++) {
^
GlobalDefs.cpp:344:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i=1; i<x.size()+1; i++) {
^
GlobalDefs.cpp:345:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto j=1; j<y.size()+1; j++) {
^
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:192:30: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -I. -fopenmp -O2 -Wall -mtune=generic -c runibic.cpp -o runibic.o
In file included from runibic.cpp:34:0:
GlobalDefs.h: In constructor 'Params::Params()':
GlobalDefs.h:60:7: warning: 'Params::Divided' will be initialized after [-Wreorder]
int Divided;
^
GlobalDefs.h:47:7: warning: 'int Params::RowNumber' [-Wreorder]
int RowNumber;
^
GlobalDefs.h:34:3: warning: when initialized here [-Wreorder]
Params()
^
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:499:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(k = 0; k < components; k++) {
^
runibic.cpp:508:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(components > vecGenes.size())
^
runibic.cpp:514:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto ki=0; ki < vecGenes.size() ; ki++) {
^
runibic.cpp:562:13: warning: unused variable 'temp' [-Wunused-variable]
int temp;
^
runibic.cpp:592:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData[vecGenes[0]].size() ;i++){
^
runibic.cpp:616:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < discreteInputData[ki].size() ;i++){
^
runibic.cpp:695:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (arrBlocks.size() == gParameters.SchBlock)
^
runibic.cpp:714:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (i < arrBlocks.size() && j < n) {
^
runibic.cpp:750:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto ind =0; ind<arrBlocks.size(); ind++)
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o runibic.dll tmp.def GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/runibic.buildbin-libdir/runibic/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'runibic' as runibic_1.0.2.zip
* DONE (runibic)
In R CMD INSTALL
In R CMD INSTALL
|
runibic.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
>
> test_check("runibic")
== testthat results ===========================================================
OK: 11 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.87 0.20 5.06
|
runibic.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
>
> test_check("runibic")
== testthat results ===========================================================
OK: 11 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
6.62 0.26 6.84
|
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runibic.Rcheck/examples_i386/runibic-Ex.timings
|
runibic.Rcheck/examples_x64/runibic-Ex.timings
|