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CHECK report for chromVAR on tokay1

This page was generated on 2018-04-12 13:30:38 -0400 (Thu, 12 Apr 2018).

Package 233/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromVAR 1.0.2
Alicia Schep
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/chromVAR
Branch: RELEASE_3_6
Last Commit: bb0722d
Last Changed Date: 2018-04-02 13:48:25 -0400 (Mon, 02 Apr 2018)
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: chromVAR
Version: 1.0.2
Command: rm -rf chromVAR.buildbin-libdir chromVAR.Rcheck && mkdir chromVAR.buildbin-libdir chromVAR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chromVAR.buildbin-libdir chromVAR_1.0.2.tar.gz >chromVAR.Rcheck\00install.out 2>&1 && cp chromVAR.Rcheck\00install.out chromVAR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chromVAR.buildbin-libdir --install="check:chromVAR-install.out" --force-multiarch --no-vignettes --timings chromVAR_1.0.2.tar.gz
StartedAt: 2018-04-11 22:56:06 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:05:44 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 577.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: chromVAR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf chromVAR.buildbin-libdir chromVAR.Rcheck && mkdir chromVAR.buildbin-libdir chromVAR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chromVAR.buildbin-libdir chromVAR_1.0.2.tar.gz >chromVAR.Rcheck\00install.out 2>&1 && cp chromVAR.Rcheck\00install.out chromVAR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chromVAR.buildbin-libdir --install="check:chromVAR-install.out" --force-multiarch --no-vignettes --timings chromVAR_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chromVAR.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 'chromVAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chromVAR' version '1.0.2'
* 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 'chromVAR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/chromVARDeviations-class.Rd:12: missing file link 'SummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/example_counts.Rd:11: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getJasparMotifs.Rd:16: missing file link 'getMatrixSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getJasparMotifs.Rd:25: missing file link 'getMatrixSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getJasparMotifs.Rd:26: missing file link 'JASPAR2016'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getJasparMotifs.Rd:19: missing file link 'PFMatrixList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getPeaks.Rd:17: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/matchKmers.Rd:41: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/matchKmers.Rd:42: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/matchKmers.Rd:42: missing file link 'DNAString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/matchKmers.Rd:53: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/mini_counts.Rd:11: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/mini_ix.Rd:11: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/pwmDistance.Rd:27: missing file link 'PWMatrixList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/pwmDistance.Rd:28: missing file link 'PFMatrixList'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chromVAR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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/chromVAR.buildbin-libdir/chromVAR/libs/i386/chromVAR.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
deviationsCovariability 20.2   1.56   21.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
deviationsCovariability 18.81   0.87   19.73
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/chromVAR.Rcheck/00check.log'
for details.



Installation output

chromVAR.Rcheck/00install.out


install for i386

* installing *source* package 'chromVAR' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c pwm_similarity.cpp -o pwm_similarity.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::NumericVector row_sds(arma::mat&, bool)':
utils.cpp:12:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int j=0; j < X.n_rows; j++ ) {
                     ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o chromVAR.dll tmp.def RcppExports.o pwm_similarity.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/chromVAR.buildbin-libdir/chromVAR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'chromVAR'
    finding HTML links ... done
    addGCBias                               html  
    annotationMatches                       html  
    assembleKmers                           html  
    cbind-chromVARDeviations-method         html  
    chromVAR                                html  
    chromVARDeviations-class                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/chromVARDeviations-class.Rd:12: missing file link 'SummarizedExperiment'
    chromVAR_theme                          html  
    computeDeviations                       html  
    computeExpectations                     html  
    computeVariability                      html  
    counts                                  html  
    deviationScores                         html  
    deviations                              html  
    deviationsCovariability                 html  
    deviationsTsne                          html  
    differentialDeviations                  html  
    differentialVariability                 html  
    example_counts                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/example_counts.Rd:11: missing file link 'RangedSummarizedExperiment'
    filterPeaks                             html  
    filterSamples                           html  
    filterSamplesPlot                       html  
    getAnnotationCorrelation                html  
    getAnnotationSynergy                    html  
    getAnnotations                          html  
    getBackgroundPeaks                      html  
    getCisGroups                            html  
    getCounts                               html  
    getFragmentsPerPeak                     html  
    getFragmentsPerSample                   html  
    getJasparMotifs                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getJasparMotifs.Rd:16: missing file link 'getMatrixSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getJasparMotifs.Rd:25: missing file link 'getMatrixSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getJasparMotifs.Rd:26: missing file link 'JASPAR2016'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getJasparMotifs.Rd:19: missing file link 'PFMatrixList'
    getPeaks                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/getPeaks.Rd:17: missing file link 'GenomicRanges'
    getPermutedData                         html  
    getSampleCorrelation                    html  
    getSampleDepths                         html  
    getSampleDistance                       html  
    getTotalFragments                       html  
    makeBiasBins                            html  
    makePermutedSets                        html  
    matchKmers                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/matchKmers.Rd:41: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/matchKmers.Rd:42: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/matchKmers.Rd:42: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/matchKmers.Rd:53: missing file link 'GenomicRanges'
    mini_counts                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/mini_counts.Rd:11: missing file link 'RangedSummarizedExperiment'
    mini_dev                                html  
    mini_ix                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/mini_ix.Rd:11: missing file link 'RangedSummarizedExperiment'
    plotDeviationsTsne                      html  
    plotKmerMismatch                        html  
    plotVariability                         html  
    pwmDistance                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/pwmDistance.Rd:27: missing file link 'PWMatrixList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwXFLxA/R.INSTALLbb87da85a6f/chromVAR/man/pwmDistance.Rd:28: missing file link 'PFMatrixList'
    rbind-chromVARDeviations-method         html  
    readNarrowpeaks                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'chromVAR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c pwm_similarity.cpp -o pwm_similarity.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::NumericVector row_sds(arma::mat&, bool)':
utils.cpp:12:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int j=0; j < X.n_rows; j++ ) {
                     ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o chromVAR.dll tmp.def RcppExports.o pwm_similarity.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/chromVAR.buildbin-libdir/chromVAR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chromVAR' as chromVAR_1.0.2.zip
* DONE (chromVAR)
In R CMD INSTALL
In R CMD INSTALL

Tests output

chromVAR.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(chromVAR)

> BiocParallel::register(BiocParallel::SerialParam())
> test_check("chromVAR")
== testthat results  ===========================================================
OK: 65 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  17.21    1.15   18.36 

chromVAR.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(chromVAR)

> BiocParallel::register(BiocParallel::SerialParam())
> test_check("chromVAR")
== testthat results  ===========================================================
OK: 65 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  23.42    0.64   24.04 

Example timings

chromVAR.Rcheck/examples_i386/chromVAR-Ex.timings

nameusersystemelapsed
addGCBias1.980.112.09
annotationMatches0.010.000.01
chromVAR_theme0.060.000.06
computeDeviations3.580.073.78
computeExpectations000
computeVariability0.400.050.45
counts0.020.000.02
deviationScores000
deviations0.020.000.01
deviationsCovariability20.20 1.5621.94
deviationsTsne0.200.000.73
differentialDeviations000
differentialVariability0.030.000.03
example_counts000
filterPeaks0.30.00.3
filterSamples0.060.000.06
filterSamplesPlot0.150.000.16
getAnnotations0.410.030.43
getBackgroundPeaks1.940.112.05
getCisGroups0.080.000.08
getCounts3.120.323.45
getFragmentsPerPeak0.020.000.02
getFragmentsPerSample000
getJasparMotifs2.370.152.53
getPeaks0.160.020.17
getPermutedData4.080.144.22
getSampleCorrelation0.010.000.01
getSampleDepths0.140.010.16
getSampleDistance000
getTotalFragments0.020.000.02
makeBiasBins0.030.000.03
makePermutedSets0.860.050.92
matchKmers2.300.102.39
mini_counts000
mini_dev000
mini_ix000
plotVariability1.020.011.03
pwmDistance2.560.202.76
rbind-chromVARDeviations-method0.030.000.03

chromVAR.Rcheck/examples_x64/chromVAR-Ex.timings

nameusersystemelapsed
addGCBias2.000.012.01
annotationMatches0.010.000.01
chromVAR_theme0.150.000.15
computeDeviations4.280.084.36
computeExpectations000
computeVariability0.440.000.43
counts0.010.000.02
deviationScores000
deviations0.020.000.02
deviationsCovariability18.81 0.8719.73
deviationsTsne0.110.000.11
differentialDeviations0.010.000.02
differentialVariability0.040.000.03
example_counts000
filterPeaks0.310.000.31
filterSamples0.080.000.08
filterSamplesPlot0.170.000.17
getAnnotations0.420.000.42
getBackgroundPeaks1.800.071.86
getCisGroups0.110.000.11
getCounts4.450.434.89
getFragmentsPerPeak0.020.000.02
getFragmentsPerSample000
getJasparMotifs2.780.082.86
getPeaks0.180.000.18
getPermutedData2.750.192.94
getSampleCorrelation0.020.000.02
getSampleDepths0.330.020.34
getSampleDistance0.010.000.02
getTotalFragments0.020.000.01
makeBiasBins0.050.000.05
makePermutedSets1.290.031.33
matchKmers2.210.032.23
mini_counts000
mini_dev000
mini_ix000
plotVariability0.440.000.43
pwmDistance3.730.203.94
rbind-chromVARDeviations-method0.050.000.05