Multiple platform build/check report for BioC 3.6 - CHECK report for genomation on tokay1

Package: genomation

Version: 1.11.3

Command: rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.11.3.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.11.3.tar.gz

StartedAt: 2018-04-12 00:16:44 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:25:21 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 517.4 seconds

RetCode: 0

Status: OK

CheckDir: genomation.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.11.3.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.11.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genomation.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 'genomation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomation' version '1.11.3'
* package encoding: latin1
* 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 'genomation' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   1.2Mb
    libs      1.6Mb
* 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
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'RUnit'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
  variable 'cvg'
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
  variable 'id'
ScoreMatrixBin,RleList-GRangesList: no visible global function
  definition for ':='
Undefined global functions or variables:
  := cvg id
* 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 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/genomation.buildbin-libdir/genomation/libs/i386/genomation.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' ... NOTE
The following directory looks like a leftover from 'knitr':
  'cache'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                                    user system elapsed
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 7.16   0.71   35.64
enrichmentMatrix-ScoreMatrixList-method             5.81   0.62    6.44
enrichmentMatrix-ScoreMatrix-method                 5.63   0.31   19.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                                    user system elapsed
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 5.17   0.62    5.79
enrichmentMatrix-ScoreMatrix-method                 5.11   0.28    5.39
enrichmentMatrix-ScoreMatrixList-method             4.70   0.61    5.32
ScoreMatrix-methods                                 4.89   0.27    5.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'genomation_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'genomation_unit_tests.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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/genomation.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'genomation' ...
** libs
C:/Rtools/mingw_32/bin/g++  -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:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -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:/local323/include"     -O2 -Wall  -mtune=generic -c binSum.cpp -o binSum.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o genomation.dll tmp.def RcppExports.o binSum.o -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/genomation.buildbin-libdir/genomation/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'genomation'
    finding HTML links ... done
    AnnotationByFeature-class               html  
    AnnotationByGeneParts-class             html  
    AnnotationByGeneParts-methods           html  
    Max_c                                   html  
    Mean_c                                  html  
    Median_c                                html  
    Min_c                                   html  
    Ops-ScoreMatrix-ScoreMatrix-method      html  
    Ops-ScoreMatrixList-ScoreMatrixList-method
                                            html  
    Ops-ScoreMatrixList-numeric-method      html  
    Ops-numeric-ScoreMatrixList-method      html  
    RandomEnrichment-class                  html  
    ScoreMatrix-class                       html  
    ScoreMatrix-methods                     html  
    ScoreMatrixBin-methods                  html  
    ScoreMatrixList-class                   html  
    ScoreMatrixList-methods                 html  
    Sum_c                                   html  
    annotatGrWithGeneParts                  html  
    annotateWithFeature-methods             html  
    annotateWithFeatureFlank-methods        html  
    annotateWithFeatures-methods            html  
    annotateWithGeneParts-methods           html  
    finding level-2 HTML links ... done

    bed12ToExons                            html  
    bed12ToIntrons                          html  
    binMatrix-methods                       html  
    binMax                                  html  
    binMean                                 html  
    binMedian                               html  
    binMin                                  html  
    binSum                                  html  
    binner                                  html  
    c.ScoreMatrix                           html  
    c.ScoreMatrixList                       html  
    cage                                    html  
    calculateOverlapSignificance-methods    html  
    checkBedValidity                        html  
    checkClass                              html  
    compressedAndUrl2temp                   html  
    constrainRanges                         html  
    convertBed2Exons-methods                html  
    convertBed2Introns-methods              html  
    convertBedDf-methods                    html  
    cpgi                                    html  
    detectUCSCheader                        html  
    distance2NearestFeature                 html  
    enrichmentMatrix-ScoreMatrix-method     html  
    enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method
                                            html  
    enrichmentMatrix-ScoreMatrixList-method
                                            html  
    file.ext                                html  
    findFeatureComb-methods                 html  
    galpTo2Ranges                           html  
    genes                                   html  
    getColors                               html  
    getFeatsWithTargetsStats-methods        html  
    getFlanks-methods                       html  
    getMembers-methods                      html  
    getRandomEnrichment-methods             html  
    getTargetAnnotationStats-methods        html  
    gffToGRanges                            html  
    heatMatrix                              html  
    heatMeta                                html  
    heatTargetAnnotation-methods            html  
    intersectScoreMatrixList-methods        html  
    listSliceMax                            html  
    listSliceMean                           html  
    listSliceMedian                         html  
    listSliceMin                            html  
    listSliceSum                            html  
    multiHeatMatrix                         html  
    orderBy-methods                         html  
    patternMatrix-methods                   html  
    plotMeta                                html  
    plotTargetAnnotation-methods            html  
    promoters                               html  
    randomizeFeature-methods                html  
    read.zip                                html  
    readBam                                 html  
    readBed                                 html  
    readBigWig                              html  
    readBroadPeak                           html  
    readFeatureFlank-methods                html  
    readGeneric                             html  
    readNarrowPeak                          html  
    readTableFast                           html  
    readTranscriptFeatures-methods          html  
    scaleScoreMatrix-methods                html  
    scaleScoreMatrixList                    html  
    show-methods                            html  
    sub-ScoreMatrix-ANY-ANY-ANY-method      html  
    sub-ScoreMatrixList-ANY-ANY-ANY-method
                                            html  
    target.type                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'genomation' ...
** libs
C:/Rtools/mingw_64/bin/g++  -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:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -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:/local323/include"     -O2 -Wall  -mtune=generic -c binSum.cpp -o binSum.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o genomation.dll tmp.def RcppExports.o binSum.o -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/genomation.buildbin-libdir/genomation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genomation' as genomation_1.11.3.zip
* DONE (genomation)
In R CMD INSTALL
In R CMD INSTALL


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.

> (require("genomation") & require("GenomicRanges") & require("GenomicAlignments") & require("rtracklayer") & require("readr") & require("Biostrings")) || stop("unable to load genomation package")
Loading required package: genomation
Loading required package: grid
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: GenomicAlignments
Loading required package: SummarizedExperiment
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


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
Loading required package: rtracklayer
Loading required package: readr
[1] TRUE
> genomation:::.test()
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
testing:min
testing:max
testing:median
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Parsed with column specification:
cols(
  X1 = col_character(),
  X2 = col_integer(),
  X3 = col_integer(),
  X4 = col_character(),
  X5 = col_integer(),
  X6 = col_character(),
  X7 = col_integer(),
  X8 = col_integer(),
  X9 = col_number()
)
Parsed with column specification:
cols(
  X1 = col_character(),
  X2 = col_integer(),
  X3 = col_integer(),
  X4 = col_character(),
  X5 = col_integer(),
  X6 = col_character(),
  X7 = col_integer(),
  X8 = col_integer(),
  X9 = col_number()
)


RUNIT TEST PROTOCOL -- Thu Apr 12 00:24:16 2018 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
genomation RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In .local(target, windows, strand.aware) :
  1 windows fall off the target
2: In .local(target, windows, strand.aware) :
  2 windows fall off the target
3: In .local(target, windows, strand.aware) :
  2 windows fall off the target
4: In .local(target, windows, strand.aware) :
  2 windows fall off the target
5: In .local(target, windows, strand.aware) :
  2 windows fall off the target
6: In .local(target, windows, strand.aware) :
  2 windows fall off the target
7: In .local(target, windows, bin.num, bin.op, strand.aware) :
  2 windows fall off the target
8: In .local(target, windows, bin.num, bin.op, strand.aware) :
  2 windows fall off the target
> 
> proc.time()
   user  system elapsed 
  41.23    0.64   41.85


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.

> (require("genomation") & require("GenomicRanges") & require("GenomicAlignments") & require("rtracklayer") & require("readr") & require("Biostrings")) || stop("unable to load genomation package")
Loading required package: genomation
Loading required package: grid
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: GenomicAlignments
Loading required package: SummarizedExperiment
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


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
Loading required package: rtracklayer
Loading required package: readr
[1] TRUE
> genomation:::.test()
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
testing:min
testing:max
testing:median
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Parsed with column specification:
cols(
  X1 = col_character(),
  X2 = col_integer(),
  X3 = col_integer(),
  X4 = col_character(),
  X5 = col_integer(),
  X6 = col_character(),
  X7 = col_integer(),
  X8 = col_integer(),
  X9 = col_number()
)
Parsed with column specification:
cols(
  X1 = col_character(),
  X2 = col_integer(),
  X3 = col_integer(),
  X4 = col_character(),
  X5 = col_integer(),
  X6 = col_character(),
  X7 = col_integer(),
  X8 = col_integer(),
  X9 = col_number()
)


RUNIT TEST PROTOCOL -- Thu Apr 12 00:25:04 2018 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
genomation RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In .local(target, windows, strand.aware) :
  1 windows fall off the target
2: In .local(target, windows, strand.aware) :
  2 windows fall off the target
3: In .local(target, windows, strand.aware) :
  2 windows fall off the target
4: In .local(target, windows, strand.aware) :
  2 windows fall off the target
5: In .local(target, windows, strand.aware) :
  2 windows fall off the target
6: In .local(target, windows, strand.aware) :
  2 windows fall off the target
7: In .local(target, windows, bin.num, bin.op, strand.aware) :
  2 windows fall off the target
8: In .local(target, windows, bin.num, bin.op, strand.aware) :
  2 windows fall off the target
> 
> proc.time()
   user  system elapsed 
  46.53    0.60   47.12

name	user	system	elapsed
AnnotationByGeneParts-methods	0.92	0.01	0.93
ScoreMatrix-methods	3.81	0.19	4.00
ScoreMatrixBin-methods	2.16	0.14	2.30
ScoreMatrixList-methods	0.43	0.05	0.48
annotateWithFeature-methods	0.04	0.01	0.05
annotateWithFeatureFlank-methods	0.31	0.00	0.31
annotateWithFeatures-methods	0.54	0.02	0.55
annotateWithGeneParts-methods	0.61	0.01	0.62
binMatrix-methods	0.18	0.02	0.19
convertBed2Exons-methods	0.04	0.02	0.06
convertBed2Introns-methods	0.11	0.01	0.13
enrichmentMatrix-ScoreMatrix-method	5.63	0.31	19.14
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method	7.16	0.71	35.64
enrichmentMatrix-ScoreMatrixList-method	5.81	0.62	6.44
findFeatureComb-methods	0.27	0.00	0.27
getFeatsWithTargetsStats-methods	0.33	0.00	0.33
getFlanks-methods	0.09	0.00	0.09
getRandomEnrichment-methods	0.00	0.02	0.01
getTargetAnnotationStats-methods	0.73	0.04	0.79
gffToGRanges	0.24	0.00	0.23
heatMatrix	0.33	0.04	0.36
heatMeta	0.42	0.10	0.53
heatTargetAnnotation-methods	0.45	0.02	0.47
intersectScoreMatrixList-methods	0.22	0.02	0.23
multiHeatMatrix	0.41	0.07	0.49
orderBy-methods	0.36	0.05	0.40
patternMatrix-methods	0.10	0.05	0.16
plotMeta	0.47	0.09	0.56
plotTargetAnnotation-methods	0.28	0.00	0.28
readBed	0.23	0.02	0.25
readBroadPeak	0.05	0.00	0.04
readFeatureFlank-methods	0.08	0.02	0.10
readGeneric	0.03	0.01	0.04
readNarrowPeak	0.03	0.00	0.03
readTranscriptFeatures-methods	0.14	0.02	0.16
scaleScoreMatrix-methods	0.13	0.02	0.14
scaleScoreMatrixList	0.37	0.10	0.49

name	user	system	elapsed
AnnotationByGeneParts-methods	1.09	0.05	1.14
ScoreMatrix-methods	4.89	0.27	5.16
ScoreMatrixBin-methods	2.16	0.03	2.18
ScoreMatrixList-methods	0.43	0.01	0.46
annotateWithFeature-methods	0.05	0.00	0.05
annotateWithFeatureFlank-methods	0.39	0.00	0.39
annotateWithFeatures-methods	0.56	0.02	0.58
annotateWithGeneParts-methods	0.70	0.01	0.72
binMatrix-methods	0.12	0.04	0.16
convertBed2Exons-methods	0.07	0.00	0.06
convertBed2Introns-methods	0.12	0.00	0.13
enrichmentMatrix-ScoreMatrix-method	5.11	0.28	5.39
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method	5.17	0.62	5.79
enrichmentMatrix-ScoreMatrixList-method	4.70	0.61	5.32
findFeatureComb-methods	0.27	0.00	0.26
getFeatsWithTargetsStats-methods	0.75	0.05	0.80
getFlanks-methods	0.11	0.00	0.11
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.28	0.01	0.29
gffToGRanges	0.25	0.00	0.25
heatMatrix	0.28	0.08	0.36
heatMeta	0.42	0.16	0.58
heatTargetAnnotation-methods	0.48	0.03	0.51
intersectScoreMatrixList-methods	0.24	0.02	0.25
multiHeatMatrix	0.44	0.07	0.52
orderBy-methods	0.40	0.05	0.45
patternMatrix-methods	0.16	0.02	0.17
plotMeta	0.40	0.09	0.50
plotTargetAnnotation-methods	0.31	0.00	0.31
readBed	0.3	0.0	0.3
readBroadPeak	0.06	0.00	0.06
readFeatureFlank-methods	0.11	0.00	0.11
readGeneric	0.02	0.02	0.03
readNarrowPeak	0.04	0.00	0.05
readTranscriptFeatures-methods	0.14	0.01	0.16
scaleScoreMatrix-methods	0.16	0.02	0.17
scaleScoreMatrixList	0.42	0.01	0.43

CHECK report for genomation on tokay1

Summary

Command output

Installation output

Tests output

Example timings