Back to Multiple platform build/check report for BioC 3.15
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-03-18 11:07:28 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for esATAC on riesling1


To the developers/maintainers of the esATAC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/esATAC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 607/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
esATAC 1.17.0  (landing page)
Zheng Wei
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/esATAC
git_branch: master
git_last_commit: 5fc63d5
git_last_commit_date: 2022-03-09 03:01:40 -0400 (Wed, 09 Mar 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: esATAC
Version: 1.17.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:esATAC.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings esATAC_1.17.0.tar.gz
StartedAt: 2022-03-17 19:02:52 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:10:34 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 461.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: esATAC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:esATAC.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings esATAC_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/esATAC.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'esATAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'esATAC' version '1.17.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'esATAC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
    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
* 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
Unexported objects imported by ':::' calls:
  'ShortRead:::.ShortReadQQA' 'ShortRead:::.qa_adapterContamination'
  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
atacPipe2: no visible global function definition for 'getObjsInPipe'
atacPipe2: no visible binding for global variable 'case.peak'
atacPipe2: no visible binding for global variable 'ctrl.peak'
atacPipe2: no visible binding for global variable 'pwm'
atacPipe2: no visible binding for global variable 'bed.case'
atacPipe2: no visible binding for global variable 'bed.ctrl'
atacPipe2: no visible binding for global variable 'caselist'
atacPipe2: no visible binding for global variable 'ctrllist'
atacPipe2: no visible global function definition for '.obtainConfigure'
atacPipe2: no visible binding for global variable 'param.tmp'
atacPipe2: no visible binding for global variable 'esATAC_report'
atacPipe2: no visible global function definition for 'getReportVal'
atacPipe2: no visible binding for global variable 'esATAC_result'
processing,BamToBed : <anonymous>: no visible global function
  definition for 'readGAlignments'
processing,BedToBigWig: no visible binding for global variable 'score'
Undefined global functions or variables:
  .obtainConfigure bed.case bed.ctrl case.peak caselist ctrl.peak
  ctrllist esATAC_report esATAC_result getObjsInPipe getReportVal
  param.tmp pwm readGAlignments score
* 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 ... WARNING
Undocumented arguments in documentation object 'PeakCallingMACS2'
  'genomeSize' 'pvalueThreshold'
Documented arguments not in \usage in documentation object 'PeakCallingMACS2':
  'threshold'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/esATAC/libs/x64/esATAC.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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
FastQC        2.19  18.12   21.79
CutSiteCountR 2.26  15.95   19.67
RSNPs         0.73  10.56   11.89
RPeakAnno     1.00   8.25   10.01
SamToBam      1.11   7.53    9.46
CutSitePre    1.00   7.03    8.76
FindAdapter   0.40   0.07   20.39
Renamer       0.33   0.05   18.82
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/esATAC.Rcheck/00check.log'
for details.



Installation output

esATAC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL esATAC
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'esATAC' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c BedLine.cpp -o BedLine.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c BedUtils.cpp -o BedUtils.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ChrDivi.cpp -o ChrDivi.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c CutCountPre.cpp -o CutCountPre.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c CutSiteCount.cpp -o CutSiteCount.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c LibComplexQC.cpp -o LibComplexQC.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c SortBed.cpp -o SortBed.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rcpp_wrapper.cpp -o rcpp_wrapper.o
rcpp_wrapper.cpp: In function 'int CutSiteCount_wrapper(Rcpp::List)':
rcpp_wrapper.cpp:334:7: warning: variable 'tmp_k' set but not used [-Wunused-but-set-variable]
   int tmp_k;
       ^~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c renamer.cpp -o renamer.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sam2bed.cc -o sam2bed.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o esATAC.dll tmp.def BedLine.o BedUtils.o ChrDivi.o CutCountPre.o CutSiteCount.o LibComplexQC.o RcppExports.o SortBed.o rcpp_wrapper.o renamer.o sam2bed.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'esATAC'
    finding HTML links ... done
    ATACProc-class                          html  
    BamToBed                                html  
    BedToBigWig                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bedToBigWig.html
    BedUtils                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bedUtils.html
    Bowtie2Mapping                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bowtie2Mapping.html
    finding level-2 HTML links ... done

    CutSiteCountR                           html  
    CutSitePre                              html  
    FRiPQC                                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/fripQC.html
    FastQC                                  html  
    FindAdapter                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/findAdapter.html
    FragLenDistr                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/fragLenDistr.html
    LibComplexQC                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/libComplexQC.html
    PeakCallingFseq                         html  
    PeakCallingMACS2                        html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/peakCallingMACS2.html
    PeakQC                                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/peakQC.html
    RGo                                     html  
    RMotifScan                              html  
    RMotifScanPair                          html  
    RPeakAnno                               html  
    RPeakComp                               html  
    RSNPs                                   html  
    RemoveAdapter                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/removeAdapter.html
    Renamer                                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/renamer.html
    Rsortbam                                html  
    SamToBam                                html  
    SamToBed                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/samToBed.html
    SingleRepReport                         html  
    TSSQC                                   html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/tssQC.html
    UnzipAndMerge                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/unzipAndMerge.html
    atacPipe2                               html  
    atacRepsPipe                            html  
    atacRepsPipe2                           html  
    esATAC-package                          html  
    getMotifInfo                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (esATAC)
Making 'packages.html' ... done

Tests output

esATAC.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(esATAC)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: pipeFrame

Attaching package: 'pipeFrame'

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

    report


> 
> test_check("esATAC")
[1] "2022-03-17 19:10:21 EDT"
[1] "2022-03-17 19:10:21 EDT"
[1] "2022-03-17 19:10:21 EDT"
[1] "2022-03-17 19:10:21 EDT"
[1] "2022-03-17 19:10:21 EDT"
[1] "2022-03-17 19:10:21 EDT"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
  14.32    1.32   18.42 

Example timings

esATAC.Rcheck/esATAC-Ex.timings

nameusersystemelapsed
BamToBed000
BedToBigWig0.040.000.05
BedUtils1.370.142.25
Bowtie2Mapping0.080.051.52
CutSiteCountR 2.2615.9519.67
CutSitePre1.007.038.76
FRiPQC1.630.302.46
FastQC 2.1918.1221.79
FindAdapter 0.40 0.0720.39
FragLenDistr0.050.000.05
LibComplexQC0.140.141.03
PeakCallingFseq0.250.141.11
PeakCallingMACS20.230.171.06
PeakQC0.440.121.25
RGo000
RMotifScan000
RMotifScanPair000
RPeakAnno 1.00 8.2510.01
RPeakComp0.030.020.05
RSNPs 0.7310.5611.89
RemoveAdapter0.130.050.39
Renamer 0.33 0.0518.82
Rsortbam0.070.000.07
SamToBam1.117.539.46
SamToBed0.270.201.17
TSSQC1.230.232.19
UnzipAndMerge0.020.000.03
atacPipe20.000.020.01
atacRepsPipe000
atacRepsPipe2000
esATAC-package000
getMotifInfo000