CHECK report for runibic on malbec2
This page was generated on 2019-04-09 11:49:32 -0400 (Tue, 09 Apr 2019).
runibic 1.5.0 Patryk Orzechowski
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
URL: https://git.bioconductor.org/packages/runibic |
Branch: master |
Last Commit: 1117470 |
Last Changed Date: 2018-10-30 11:54:38 -0400 (Tue, 30 Oct 2018) |
| 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 | |
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
Summary
Command output
Installation output
runibic.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL runibic
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘runibic’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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 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:255:20: 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:345:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto j=1; j<y.size()+1; j++) {
˜^˜˜˜˜˜˜˜˜˜˜
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);
^˜˜˜˜˜˜˜
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;
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/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 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<arrBlocks.size(); ind++)
˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o runibic.so GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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)
Tests output
runibic.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, 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
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("runibic")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 11 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
11.035 0.349 8.003
Example timings
runibic.Rcheck/runibic-Ex.timings