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CHECK report for runibic on merida1

This page was generated on 2019-04-16 12:03:32 -0400 (Tue, 16 Apr 2019).

Package 1370/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
runibic 1.4.0
Patryk Orzechowski
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/runibic
Branch: RELEASE_3_8
Last Commit: fa38dc2
Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: runibic
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:runibic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings runibic_1.4.0.tar.gz
StartedAt: 2019-04-16 02:33:50 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:36:31 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 160.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: runibic.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:runibic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings runibic_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/runibic.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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 ... WARNING
Found the following significant warnings:
  GlobalDefs.cpp:280:37: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/Users/biocbuild/bbs-3.8-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
* 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 17.206 11.586   3.519
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/runibic.Rcheck/00check.log’
for details.



Installation output

runibic.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL runibic
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘runibic’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c GlobalDefs.cpp -o GlobalDefs.o
GlobalDefs.cpp:117:7: warning: unused variable 'colNum' [-Wunused-variable]
  int colNum = gParameters.ColNumber;
      ^
GlobalDefs.cpp:280:37: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
    for (auto i=maxRecord.size()-1;i>=0;i--) {
                                   ˜^ ˜
GlobalDefs.cpp:232:16: warning: unused variable 'rank' [-Wunused-variable]
  int maxvalue,rank;
               ^
In file included from GlobalDefs.cpp:34:
./fibpriv.h:54:13: warning: unused function 'fh_initheap' [-Wunused-function]
static void fh_initheap(struct fibheap *);
            ^
./fibpriv.h:55:13: warning: unused function 'fh_insertrootlist' [-Wunused-function]
static void fh_insertrootlist(struct fibheap *, struct fibheap_el *);
            ^
./fibpriv.h:56:13: warning: unused function 'fh_removerootlist' [-Wunused-function]
static void fh_removerootlist(struct fibheap *, struct fibheap_el *);
            ^
./fibpriv.h:57:13: warning: unused function 'fh_consolidate' [-Wunused-function]
static void fh_consolidate(struct fibheap *);
            ^
./fibpriv.h:58:13: warning: unused function 'fh_heaplink' [-Wunused-function]
static void fh_heaplink(struct fibheap *h, struct fibheap_el *y,
            ^
./fibpriv.h:60:13: warning: unused function 'fh_cut' [-Wunused-function]
static void fh_cut(struct fibheap *, struct fibheap_el *, struct fibheap_el *);
            ^
./fibpriv.h:61:13: warning: unused function 'fh_cascading_cut' [-Wunused-function]
static void fh_cascading_cut(struct fibheap *, struct fibheap_el *);
            ^
./fibpriv.h:62:27: warning: unused function 'fh_extractminel' [-Wunused-function]
static struct fibheap_el *fh_extractminel(struct fibheap *);
                          ^
./fibpriv.h:63:13: warning: unused function 'fh_checkcons' [-Wunused-function]
static void fh_checkcons(struct fibheap *h);
            ^
./fibpriv.h:64:13: warning: unused function 'fh_destroyheap' [-Wunused-function]
static void fh_destroyheap(struct fibheap *h);
            ^
./fibpriv.h:65:12: warning: unused function 'fh_compare' [-Wunused-function]
static int fh_compare(struct fibheap *h, struct fibheap_el *a,
           ^
./fibpriv.h:67:12: warning: unused function 'fh_comparedata' [-Wunused-function]
static int fh_comparedata(struct fibheap *h, int key, void *data,
           ^
./fibpriv.h:69:13: warning: unused function 'fh_insertel' [-Wunused-function]
static void fh_insertel(struct fibheap *h, struct fibheap_el *x);
            ^
./fibpriv.h:70:13: warning: unused function 'fh_deleteel' [-Wunused-function]
static void fh_deleteel(struct fibheap *h, struct fibheap_el *x);
            ^
./fibpriv.h:86:27: warning: unused function 'fhe_newelem' [-Wunused-function]
static struct fibheap_el *fhe_newelem(void);
                          ^
./fibpriv.h:87:13: warning: unused function 'fhe_initelem' [-Wunused-function]
static void fhe_initelem(struct fibheap_el *);
            ^
./fibpriv.h:88:13: warning: unused function 'fhe_insertafter' [-Wunused-function]
static void fhe_insertafter(struct fibheap_el *a, struct fibheap_el *b);
            ^
./fibpriv.h:90:27: warning: unused function 'fhe_remove' [-Wunused-function]
static struct fibheap_el *fhe_remove(struct fibheap_el *a);
                          ^
21 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c fib.c -o fib.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c runibic.cpp -o runibic.o
runibic.cpp:567:13: warning: unused variable 'temp' [-Wunused-variable]
        int temp;
            ^
1 warning generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o runibic.so GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
* DONE (runibic)

Tests output

runibic.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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

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

> 
> test_check("runibic")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 11 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  8.005   1.687   7.995 

Example timings

runibic.Rcheck/runibic-Ex.timings

nameusersystemelapsed
backtrackLCS0.0010.0000.001
calculateLCS0.6320.0020.081
cluster0.0110.0120.004
pairwiseLCS0.0020.0030.001
runiDiscretize0.0170.0250.006
runibic17.20611.586 3.519
set_runibic_params0.0010.0020.000
unisort0.0020.0050.001