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CHECK report for runibic on malbec2

This page was generated on 2019-10-16 12:12:42 -0400 (Wed, 16 Oct 2019).

Package 1439/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: runibic
Version: 1.6.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:runibic.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings runibic_1.6.0.tar.gz
StartedAt: 2019-10-16 04:44:28 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:48:14 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 225.7 seconds
RetCode: 0
Status:  OK 
CheckDir: runibic.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:runibic.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings runibic_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/runibic.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘runibic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘runibic’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘runibic’ can be installed ... OK
* 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
* 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
runibic 622.08  3.009  78.579
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/runibic.Rcheck/00check.log’
for details.

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&, 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:192:15: 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

Tests output

runibic.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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, 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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.920   0.314   7.842

Example timings

runibic.Rcheck/runibic-Ex.timings

nameusersystemelapsed
backtrackLCS000
calculateLCS0.1260.0000.019
cluster0.1580.0000.024
pairwiseLCS0.0000.0000.001
runiDiscretize0.0190.0000.004
runibic622.080 3.009 78.579
set_runibic_params0.0040.0000.000
unisort0.0710.0000.009