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CHECK report for chromstaR on tokay1

This page was generated on 2018-04-12 13:28:18 -0400 (Thu, 12 Apr 2018).

Package 231/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.4.0
Aaron Taudt
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/chromstaR
Branch: RELEASE_3_6
Last Commit: b76d634
Last Changed Date: 2017-10-30 12:41:19 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromstaR
Version: 1.4.0
Command: rm -rf chromstaR.buildbin-libdir chromstaR.Rcheck && mkdir chromstaR.buildbin-libdir chromstaR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chromstaR.buildbin-libdir chromstaR_1.4.0.tar.gz >chromstaR.Rcheck\00install.out 2>&1 && cp chromstaR.Rcheck\00install.out chromstaR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chromstaR.buildbin-libdir --install="check:chromstaR-install.out" --force-multiarch --no-vignettes --timings chromstaR_1.4.0.tar.gz
StartedAt: 2018-04-11 22:55:00 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:08:28 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 807.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: chromstaR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf chromstaR.buildbin-libdir chromstaR.Rcheck && mkdir chromstaR.buildbin-libdir chromstaR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chromstaR.buildbin-libdir chromstaR_1.4.0.tar.gz >chromstaR.Rcheck\00install.out 2>&1 && cp chromstaR.Rcheck\00install.out chromstaR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chromstaR.buildbin-libdir --install="check:chromstaR-install.out" --force-multiarch --no-vignettes --timings chromstaR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chromstaR.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 'chromstaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chromstaR' version '1.4.0'
* 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 'chromstaR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/binReads.Rd:59: missing file link 'countOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/binReads.Rd:59: missing file link 'bamProfile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/binned.data.Rd:7: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/combinedMultiHMM.Rd:9: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/enrichment_analysis.Rd:52: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/getCombinations.Rd:16: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/getCombinations.Rd:10: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/multiHMM.Rd:10: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/multivariateSegmentation.Rd:10: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/multivariateSegmentation.Rd:15: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/plotGenomeBrowser.Rd:12: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/plotGenomeBrowser.Rd:14: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/readBamFileAsGRanges.Rd:28: missing file link 'scanBamWhat'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/simulateMultivariate.Rd:11: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/simulateReadsFromCounts.Rd:10: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/simulateReadsFromCounts.Rd:15: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/simulateUnivariate.Rd:10: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/uniHMM.Rd:10: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chromstaR.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.8Mb
    libs   1.2Mb
* 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 ... NOTE
Chromstar: multiple local function definitions for 'parallel.helper'
  with different formal arguments
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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/chromstaR.buildbin-libdir/chromstaR/libs/i386/chromstaR.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
combineMultivariates  22.38   0.25   26.58
enrichment_analysis   15.44   0.33   19.09
Chromstar             12.33   0.47   54.31
callPeaksMultivariate 11.43   0.14   14.27
readCustomBedFile      9.21   0.09    9.30
callPeaksReplicates    8.07   0.10    9.77
transitionFrequencies  7.64   0.28   70.20
combinatorialStates    6.72   0.07    6.80
unis2pseudomulti       6.36   0.11    6.47
plotExpression         1.77   0.13    5.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
combineMultivariates  24.17   0.22   24.39
enrichment_analysis   15.83   0.18   19.33
callPeaksMultivariate 10.38   0.31   10.69
Chromstar              9.56   0.22   48.86
readCustomBedFile      8.97   0.15    9.12
callPeaksReplicates    8.28   0.12    8.41
unis2pseudomulti       7.87   0.03    7.90
transitionFrequencies  7.30   0.20   70.48
combinatorialStates    6.58   0.14    6.72
plotExpression         2.10   0.02    5.12
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/chromstaR.Rcheck/00check.log'
for details.



Installation output

chromstaR.Rcheck/00install.out


install for i386

* installing *source* package 'chromstaR' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c R_interface.cpp -o R_interface.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c densities.cpp -o densities.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c scalehmm.cpp -o scalehmm.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c utility.cpp -o utility.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o chromstaR.dll tmp.def R_interface.o densities.o init.o scalehmm.o utility.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/chromstaR.buildbin-libdir/chromstaR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'chromstaR'
    finding HTML links ... done
    Chromstar                               html  
    binReads                                html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/binReads.Rd:59: missing file link 'countOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/binReads.Rd:59: missing file link 'bamProfile'
    binned.data                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/binned.data.Rd:7: missing file link 'GRanges'
    callPeaksMultivariate                   html  
    callPeaksReplicates                     html  
    callPeaksUnivariate                     html  
    callPeaksUnivariateAllChr               html  
    changeFDR                               html  
    changePostCutoff                        html  
    chromstaR-objects                       html  
    chromstaR-package                       html  
    collapseBins                            html  
    combinatorialStates                     html  
    combineMultivariates                    html  
    combinedMultiHMM                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/combinedMultiHMM.Rd:9: missing file link 'GRanges'
    combined_model                          html  
    conversion                              html  
    enrichmentAtAnnotation                  html  
    enrichment_analysis                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/enrichment_analysis.Rd:52: missing file link 'GRanges'
    experiment.table                        html  
    exportFiles                             html  
    exportGRangesAsBedFile                  html  
    fixedWidthBins                          html  
    genes_rn4                               html  
    genomicFrequencies                      html  
    getCombinations                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/getCombinations.Rd:16: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/getCombinations.Rd:10: missing file link 'GRanges'
    getDistinctColors                       html  
    getStateColors                          html  
    heatmapCombinations                     html  
    heatmapCountCorrelation                 html  
    heatmapTransitionProbs                  html  
    loadHmmsFromFiles                       html  
    mergeChroms                             html  
    multiHMM                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/multiHMM.Rd:10: missing file link 'GRanges'
    multivariateSegmentation                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/multivariateSegmentation.Rd:10: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/multivariateSegmentation.Rd:15: missing file link 'GRanges'
    multivariate_model                      html  
    plotExpression                          html  
    plotGenomeBrowser                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/plotGenomeBrowser.Rd:12: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/plotGenomeBrowser.Rd:14: missing file link 'GRanges'
    plotHistogram                           html  
    plotHistograms                          html  
    plotKaryogram                           html  
    plotting                                html  
    print.combinedMultiHMM                  html  
    print.multiHMM                          html  
    print.uniHMM                            html  
    readBamFileAsGRanges                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/readBamFileAsGRanges.Rd:28: missing file link 'scanBamWhat'
    readBedFileAsGRanges                    html  
    readConfig                              html  
    readCustomBedFile                       html  
    removeCondition                         html  
    scanBinsizes                            html  
    scores                                  html  
    simulateMultivariate                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/simulateMultivariate.Rd:11: missing file link 'GRanges'
    simulateReadsFromCounts                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/simulateReadsFromCounts.Rd:10: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/simulateReadsFromCounts.Rd:15: missing file link 'GRanges'
    simulateUnivariate                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/simulateUnivariate.Rd:10: missing file link 'GRanges'
    state.brewer                            html  
    stateBrewer                             html  
    subsample                               html  
    transitionFrequencies                   html  
    uniHMM                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpg3lCKl/R.INSTALL11c425675e4d/chromstaR/man/uniHMM.Rd:10: missing file link 'GRanges'
    unis2pseudomulti                        html  
    variableWidthBins                       html  
    writeConfig                             html  
    zinbinom                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'chromstaR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c R_interface.cpp -o R_interface.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c densities.cpp -o densities.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c scalehmm.cpp -o scalehmm.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c utility.cpp -o utility.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o chromstaR.dll tmp.def R_interface.o densities.o init.o scalehmm.o utility.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/chromstaR.buildbin-libdir/chromstaR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chromstaR' as chromstaR_1.4.0.zip
* DONE (chromstaR)
In R CMD INSTALL
In R CMD INSTALL

Tests output

chromstaR.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(chromstaR)
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: ggplot2
Loading required package: chromstaRData

Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features.

> 
> test_check("chromstaR")
HMM: number of states = 3
HMM: number of bins = 125194
HMM: maximum number of iterations = 5000
HMM: maximum running time = none
HMM: epsilon = 1
HMM: data mean = 4.06434, data variance = 10.7002
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
         0                -inf                   -                   -              0
         1      -221107.608192                 inf                4898              0
         2      -202927.094167        18180.514025               17717              0
         3      -200120.881709         2806.212458                5825              0
         4      -199468.394347          652.487362                 888              0
         5      -199127.131702          341.262646                1058              0
         6      -198860.279250          266.852451                 603              1
         7      -198629.337990          230.941260                 795              1
         8      -198419.546135          209.791855                 735              1
         9      -198220.599452          198.946683                 705              1
        10      -198025.863024          194.736428                 601              1
        11      -197831.634581          194.228443                 629              1
        12      -197636.953896          194.680685                 605              1
        13      -197443.159115          193.794781                 551              1
        14      -197253.226838          189.932277                 526              1
        15      -197070.870496          182.356342                 462              1
        16      -196899.581897          171.288599                 504              1
        17      -196741.879226          157.702671                 518              1
        18      -196598.968651          142.910575                 455              1
        19      -196470.829967          128.138683                 414              1
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
        20      -196356.547470          114.282498                 478              1
        21      -196254.666304          101.881166                 436              1
        22      -196163.460342           91.205962                 408              1
        23      -196081.121315           82.339027                 403              2
        24      -196005.917090           75.204225                 380              2
        25      -195936.332041           69.585049                 347              2
        26      -195871.165174           65.166867                 353              2
        27      -195809.562263           61.602912                 366              2
        28      -195750.988447           58.573815                 382              2
        29      -195695.169980           55.818467                 418              2
        30      -195642.025316           53.144664                 382              2
        31      -195591.590246           50.435070                 358              2
        32      -195543.944190           47.646056                 358              2
        33      -195499.151606           44.792584                 307              2
        34      -195457.227470           41.924136                 285              2
        35      -195418.125988           39.101483                 257              2
        36      -195381.745667           36.380321                 216              2
        37      -195347.942282           33.803385                 244              2
        38      -195316.543289           31.398993                 165              2
        39      -195287.360604           29.182684                 168              2
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
        40      -195260.200914           27.159691                 142              2
        41      -195234.873581           25.327333                 163              2
        42      -195211.196441           23.677140                 134              2
        43      -195188.999774           22.196666                  94              2
        44      -195168.128759           20.871016                  84              3
        45      -195148.444676           19.684082                 121              3
        46      -195129.825149           18.619528                 115              3
        47      -195112.163631           17.661518                 104              3
        48      -195095.368371           16.795260                  82              3
        49      -195079.361021           16.007349                  79              3
        50      -195064.075048           15.285974                  65              3
        51      -195049.454066           14.620982                 101              3
        52      -195035.450211           14.003855                  64              3
        53      -195022.022611           13.427600                  54              3
        54      -195009.136022           12.886589                  73              3
        55      -194996.759650           12.376372                  66              3
        56      -194984.866167           11.893483                  56              3
        57      -194973.430930           11.435238                  54              3
        58      -194962.431364           10.999566                  53              3
        59      -194951.846510           10.584854                  33              3
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
        60      -194941.656694           10.189816                  50              4
        61      -194931.843299            9.813395                  48              4
        62      -194922.388613            9.454686                  35              4
        63      -194913.275737            9.112876                  32              4
        64      -194904.488524            8.787213                  31              4
        65      -194896.011551            8.476973                  38              4
        66      -194887.830099            8.181453                  23              4
        67      -194879.930141            7.899958                  26              4
        68      -194872.298334            7.631807                  28              4
        69      -194864.922010            7.376324                  22              4
        70      -194857.789160            7.132850                  25              4
        71      -194850.888420            6.900740                  28              4
        72      -194844.209049            6.679371                  28              4
        73      -194837.740907            6.468142                  28              4
        74      -194831.474431            6.266476                  37              4
        75      -194825.400605            6.073826                  25              4
        76      -194819.510934            5.889672                  30              4
        77      -194813.797412            5.713521                  20              4
        78      -194808.252500            5.544913                  17              4
        79      -194802.869088            5.383412                  13              4
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
        80      -194797.640477            5.228611                  16              4
        81      -194792.560346            5.080131                  12              4
        82      -194787.622729            4.937617                  11              5
        83      -194782.821992            4.800737                  17              5
        84      -194778.152810            4.669182                  15              5
        85      -194773.610144            4.542666                  17              5
        86      -194769.189224            4.420919                  21              5
        87      -194764.885531            4.303693                  19              5
        88      -194760.694777            4.190754                  17              5
        89      -194756.612893            4.081885                  13              5
        90      -194752.636009            3.976883                  12              5
        91      -194748.760450            3.875560                  16              5
        92      -194744.982713            3.777737                  12              5
        93      -194741.299463            3.683250                  12              5
        94      -194737.707521            3.591943                   9              5
        95      -194734.203851            3.503670                   9              5
        96      -194730.785554            3.418296                  15              5
        97      -194727.449862            3.335692                   9              5
        98      -194724.194125            3.255737                   9              5
        99      -194721.015807            3.178318                  14              6
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
       100      -194717.912479            3.103328                   5              6
       101      -194714.881814            3.030665                  14              6
       102      -194711.921579            2.960234                  12              6
       103      -194709.029634            2.891945                  11              6
       104      -194706.203921            2.825713                  12              6
       105      -194703.442465            2.761456                   8              6
       106      -194700.743366            2.699098                  10              6
       107      -194698.104800            2.638567                   9              6
       108      -194695.525008            2.579792                  10              6
       109      -194693.002300            2.522708                   9              6
       110      -194690.535048            2.467253                   8              6
       111      -194688.121681            2.413366                  10              6
       112      -194685.760689            2.360993                  19              6
       113      -194683.450612            2.310077                   7              6
       114      -194681.190044            2.260568                   5              6
       115      -194678.977628            2.212416                  12              7
       116      -194676.812054            2.165574                  14              7
       117      -194674.692057            2.119998                  10              7
       118      -194672.616414            2.075643                   9              7
       119      -194670.583945            2.032469                  15              7
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
       120      -194668.593508            1.990437                   8              7
       121      -194666.644000            1.949508                  12              7
       122      -194664.734354            1.909646                   8              7
       123      -194662.863537            1.870817                  14              7
       124      -194661.030550            1.832987                  11              7
       125      -194659.234427            1.796124                  14              7
       126      -194657.474230            1.760197                  12              7
       127      -194655.749053            1.725177                  13              7
       128      -194654.058017            1.691035                  12              7
       129      -194652.400273            1.657745                   9              8
       130      -194650.774994            1.625279                  13              8
       131      -194649.181381            1.593613                  16              8
       132      -194647.618659            1.562722                   4              8
       133      -194646.086077            1.532582                  11              8
       134      -194644.582905            1.503172                  10              8
       135      -194643.108436            1.474469                   9              8
       136      -194641.661983            1.446453                   6              8
       137      -194640.242879            1.419103                   8              8
       138      -194638.850479            1.392400                   7              8
       139      -194637.484154            1.366325                  12              8
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
       140      -194636.143294            1.340860                   7              8
       141      -194634.827307            1.315987                   8              8
       142      -194633.535617            1.291690                   7              8
       143      -194632.267664            1.267952                   2              8
       144      -194631.022907            1.244758                   6              8
       145      -194629.800816            1.222091                  10              8
       146      -194628.600877            1.199939                   7              8
       147      -194627.422592            1.178285                   9              9
       148      -194626.265475            1.157117                   6              9
       149      -194625.129053            1.136422                   5              9
       150      -194624.012868            1.116185                   8              9
       151      -194622.916472            1.096396                   4              9
       152      -194621.839430            1.077042                   7              9
       153      -194620.781320            1.058111                  10              9
       154      -194619.741728            1.039592                  10              9
       155      -194618.720255            1.021474                   8              9
       156      -194617.716509            1.003746                   9              9
       157      -194616.730110            0.986399                  12              9
HMM: Convergence reached!
HMM: Recoding posteriors ...
== testthat results  ===========================================================
OK: 44 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  23.50    0.57   24.06 

chromstaR.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(chromstaR)
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: ggplot2
Loading required package: chromstaRData

Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features.

> 
> test_check("chromstaR")
HMM: number of states = 3
HMM: number of bins = 125194
HMM: maximum number of iterations = 5000
HMM: maximum running time = none
HMM: epsilon = 1
HMM: data mean = 4.06434, data variance = 10.7002
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
         0                -inf                   -                   -              0
         1      -221107.608192                 inf                4898              0
         2      -202927.094167        18180.514025               17717              0
         3      -200120.881709         2806.212458                5825              0
         4      -199468.394347          652.487362                 888              0
         5      -199127.131702          341.262646                1058              0
         6      -198860.279250          266.852451                 603              0
         7      -198629.337990          230.941260                 795              0
         8      -198419.546135          209.791855                 735              0
         9      -198220.599452          198.946683                 705              1
        10      -198025.863024          194.736428                 601              1
        11      -197831.634581          194.228443                 629              1
        12      -197636.953896          194.680685                 605              1
        13      -197443.159115          193.794781                 551              1
        14      -197253.226838          189.932277                 526              1
        15      -197070.870496          182.356342                 462              1
        16      -196899.581897          171.288599                 504              1
        17      -196741.879226          157.702671                 518              1
        18      -196598.968651          142.910575                 455              1
        19      -196470.829967          128.138683                 414              1
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
        20      -196356.547470          114.282498                 478              1
        21      -196254.666304          101.881166                 436              1
        22      -196163.460342           91.205962                 408              1
        23      -196081.121315           82.339027                 403              1
        24      -196005.917090           75.204225                 380              1
        25      -195936.332041           69.585049                 347              1
        26      -195871.165174           65.166867                 353              1
        27      -195809.562263           61.602912                 366              1
        28      -195750.988447           58.573815                 382              1
        29      -195695.169980           55.818467                 418              1
        30      -195642.025316           53.144664                 382              1
        31      -195591.590246           50.435070                 358              1
        32      -195543.944190           47.646056                 358              1
        33      -195499.151606           44.792584                 307              1
        34      -195457.227470           41.924136                 285              1
        35      -195418.125988           39.101483                 257              1
        36      -195381.745667           36.380321                 216              1
        37      -195347.942282           33.803385                 244              1
        38      -195316.543289           31.398993                 165              1
        39      -195287.360604           29.182684                 168              1
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
        40      -195260.200914           27.159691                 142              1
        41      -195234.873581           25.327333                 163              1
        42      -195211.196441           23.677140                 134              1
        43      -195188.999774           22.196666                  94              2
        44      -195168.128759           20.871016                  84              2
        45      -195148.444676           19.684082                 121              2
        46      -195129.825149           18.619528                 115              2
        47      -195112.163631           17.661518                 104              2
        48      -195095.368371           16.795260                  82              2
        49      -195079.361021           16.007349                  79              2
        50      -195064.075048           15.285974                  65              2
        51      -195049.454066           14.620982                 101              2
        52      -195035.450211           14.003855                  64              2
        53      -195022.022611           13.427600                  54              2
        54      -195009.136022           12.886589                  73              2
        55      -194996.759650           12.376372                  66              2
        56      -194984.866167           11.893483                  56              2
        57      -194973.430930           11.435238                  54              2
        58      -194962.431364           10.999566                  53              2
        59      -194951.846510           10.584854                  33              2
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
        60      -194941.656694           10.189816                  50              2
        61      -194931.843299            9.813395                  48              2
        62      -194922.388613            9.454686                  35              2
        63      -194913.275737            9.112876                  32              2
        64      -194904.488524            8.787213                  31              2
        65      -194896.011551            8.476973                  38              2
        66      -194887.830099            8.181453                  23              2
        67      -194879.930141            7.899958                  26              2
        68      -194872.298334            7.631807                  28              2
        69      -194864.922010            7.376324                  22              2
        70      -194857.789160            7.132850                  25              2
        71      -194850.888420            6.900740                  28              2
        72      -194844.209049            6.679371                  28              2
        73      -194837.740907            6.468142                  28              2
        74      -194831.474431            6.266476                  37              2
        75      -194825.400605            6.073826                  25              2
        76      -194819.510934            5.889672                  30              2
        77      -194813.797412            5.713521                  20              2
        78      -194808.252500            5.544913                  17              3
        79      -194802.869088            5.383412                  13              3
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
        80      -194797.640477            5.228611                  16              3
        81      -194792.560346            5.080131                  12              3
        82      -194787.622729            4.937617                  11              3
        83      -194782.821992            4.800737                  17              3
        84      -194778.152810            4.669182                  15              3
        85      -194773.610144            4.542666                  17              3
        86      -194769.189224            4.420919                  21              3
        87      -194764.885531            4.303693                  19              3
        88      -194760.694777            4.190754                  17              3
        89      -194756.612893            4.081885                  13              3
        90      -194752.636009            3.976883                  12              3
        91      -194748.760450            3.875560                  16              3
        92      -194744.982713            3.777737                  12              3
        93      -194741.299463            3.683250                  12              3
        94      -194737.707521            3.591943                   9              3
        95      -194734.203851            3.503670                   9              3
        96      -194730.785554            3.418296                  15              3
        97      -194727.449862            3.335692                   9              3
        98      -194724.194125            3.255737                   9              3
        99      -194721.015807            3.178318                  14              3
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
       100      -194717.912479            3.103328                   5              3
       101      -194714.881814            3.030665                  14              3
       102      -194711.921579            2.960234                  12              3
       103      -194709.029634            2.891945                  11              3
       104      -194706.203921            2.825713                  12              3
       105      -194703.442465            2.761456                   8              3
       106      -194700.743366            2.699098                  10              3
       107      -194698.104800            2.638567                   9              3
       108      -194695.525008            2.579792                  10              3
       109      -194693.002300            2.522708                   9              4
       110      -194690.535048            2.467253                   8              4
       111      -194688.121681            2.413366                  10              4
       112      -194685.760689            2.360993                  19              4
       113      -194683.450612            2.310077                   7              4
       114      -194681.190044            2.260568                   5              4
       115      -194678.977628            2.212416                  12              4
       116      -194676.812054            2.165574                  14              4
       117      -194674.692057            2.119998                  10              4
       118      -194672.616414            2.075643                   9              4
       119      -194670.583945            2.032469                  15              4
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
       120      -194668.593508            1.990437                   8              4
       121      -194666.644000            1.949508                  12              4
       122      -194664.734354            1.909646                   8              4
       123      -194662.863537            1.870817                  14              4
       124      -194661.030550            1.832987                  11              4
       125      -194659.234427            1.796124                  14              4
       126      -194657.474230            1.760197                  12              4
       127      -194655.749053            1.725177                  13              4
       128      -194654.058017            1.691035                  12              4
       129      -194652.400273            1.657745                   9              4
       130      -194650.774994            1.625279                  13              4
       131      -194649.181381            1.593613                  16              4
       132      -194647.618659            1.562722                   4              4
       133      -194646.086077            1.532582                  11              4
       134      -194644.582905            1.503172                  10              4
       135      -194643.108436            1.474469                   9              4
       136      -194641.661983            1.446453                   6              4
       137      -194640.242879            1.419103                   8              4
       138      -194638.850479            1.392400                   7              4
       139      -194637.484154            1.366325                  12              4
 Iteration              log(P)             dlog(P)     Diff in state 2    Time in sec
       140      -194636.143294            1.340860                   7              4
       141      -194634.827307            1.315987                   8              5
       142      -194633.535617            1.291690                   7              5
       143      -194632.267664            1.267952                   2              5
       144      -194631.022907            1.244758                   6              5
       145      -194629.800816            1.222091                  10              5
       146      -194628.600877            1.199939                   7              5
       147      -194627.422592            1.178285                   9              5
       148      -194626.265475            1.157117                   6              5
       149      -194625.129053            1.136421                   5              5
       150      -194624.012868            1.116185                   8              5
       151      -194622.916472            1.096396                   4              5
       152      -194621.839430            1.077042                   7              5
       153      -194620.781320            1.058111                  10              5
       154      -194619.741728            1.039592                  10              5
       155      -194618.720255            1.021474                   8              5
       156      -194617.716509            1.003746                   9              5
       157      -194616.730110            0.986399                  12              5
HMM: Convergence reached!
HMM: Recoding posteriors ...
== testthat results  ===========================================================
OK: 44 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  17.42    0.37   17.79 

Example timings

chromstaR.Rcheck/examples_i386/chromstaR-Ex.timings

nameusersystemelapsed
Chromstar12.33 0.4754.31
binReads0.840.031.41
callPeaksMultivariate11.43 0.1414.27
callPeaksReplicates8.070.109.77
callPeaksUnivariate2.70.02.7
changeFDR3.060.043.11
changePostCutoff3.130.043.15
collapseBins0.930.000.94
combinatorialStates6.720.076.80
combineMultivariates22.38 0.2526.58
combined_model0.120.020.14
conversion000
enrichment_analysis15.44 0.3319.09
experiment.table0.020.000.02
exportFiles0.640.010.65
exportGRangesAsBedFile0.810.000.82
fixedWidthBins0.050.020.06
genes_rn40.120.000.12
genomicFrequencies0.140.000.14
getCombinations0.170.000.18
getDistinctColors0.030.000.03
getStateColors0.020.000.01
heatmapCombinations0.390.010.41
heatmapCountCorrelation0.30.00.3
heatmapTransitionProbs0.280.020.29
loadHmmsFromFiles1.950.052.00
multiHMM0.130.010.14
multivariate_model0.120.000.13
plotExpression1.770.135.08
plotHistogram2.420.032.45
readBamFileAsGRanges0.720.030.75
readBedFileAsGRanges4.510.084.70
readCustomBedFile9.210.099.30
removeCondition1.230.021.25
state.brewer000
stateBrewer0.020.010.03
transitionFrequencies 7.64 0.2870.20
unis2pseudomulti6.360.116.47
variableWidthBins3.230.193.44

chromstaR.Rcheck/examples_x64/chromstaR-Ex.timings

nameusersystemelapsed
Chromstar 9.56 0.2248.86
binReads0.730.020.75
callPeaksMultivariate10.38 0.3110.69
callPeaksReplicates8.280.128.41
callPeaksUnivariate2.310.052.36
changeFDR3.170.063.23
changePostCutoff2.880.022.89
collapseBins0.670.000.67
combinatorialStates6.580.146.72
combineMultivariates24.17 0.2224.39
combined_model0.090.010.11
conversion000
enrichment_analysis15.83 0.1819.33
experiment.table000
exportFiles0.630.000.63
exportGRangesAsBedFile0.780.030.81
fixedWidthBins0.040.010.06
genes_rn40.130.000.13
genomicFrequencies0.110.000.11
getCombinations0.150.000.15
getDistinctColors0.040.000.03
getStateColors0.020.000.01
heatmapCombinations0.420.020.44
heatmapCountCorrelation0.260.010.28
heatmapTransitionProbs0.30.00.3
loadHmmsFromFiles2.030.032.06
multiHMM0.110.000.11
multivariate_model0.110.000.11
plotExpression2.100.025.12
plotHistogram2.140.032.17
readBamFileAsGRanges0.730.060.80
readBedFileAsGRanges3.640.083.72
readCustomBedFile8.970.159.12
removeCondition1.170.071.24
state.brewer000
stateBrewer0.050.000.05
transitionFrequencies 7.30 0.2070.48
unis2pseudomulti7.870.037.90
variableWidthBins4.560.224.78