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CHECK report for esATAC on tokay2

This page was generated on 2020-10-17 11:56:32 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE esATAC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 564/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
esATAC 1.10.0
Zheng Wei
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/esATAC
Branch: RELEASE_3_11
Last Commit: a47e7d3
Last Changed Date: 2020-04-27 15:12:16 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: esATAC
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:esATAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings esATAC_1.10.0.tar.gz
StartedAt: 2020-10-17 03:55:28 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:08:41 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 793.2 seconds
RetCode: 0
Status:  OK  
CheckDir: esATAC.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:esATAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings esATAC_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/esATAC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.10.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'esATAC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  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 ... NOTE
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
processing,BedToBigWig: no visible binding for global variable 'score'
Undefined global functions or variables:
  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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-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         3.75  26.18   34.95
CutSiteCountR  4.63  24.66   44.00
CutSitePre     1.74  13.63   19.45
SamToBam       1.59  12.22   23.25
RPeakAnno      1.45  12.11   14.49
RSNPs          1.28  11.88   14.21
FRiPQC         2.87   0.75    5.46
FindAdapter    0.74   0.17   33.70
Renamer        0.73   0.10   47.12
Bowtie2Mapping 0.17   0.03   13.81
* 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: 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/esATAC.Rcheck/00check.log'
for details.



Installation output

esATAC.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch esATAC
###
##############################################################################
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* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
* installing *source* package 'esATAC' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c BedLine.cpp -o BedLine.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c BedUtils.cpp -o BedUtils.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ChrDivi.cpp -o ChrDivi.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CutCountPre.cpp -o CutCountPre.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CutSiteCount.cpp -o CutSiteCount.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c LibComplexQC.cpp -o LibComplexQC.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c SortBed.cpp -o SortBed.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c renamer.cpp -o renamer.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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 -LC:/Users/biocbuild/bbs-3.11-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-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  
    BedUtils                                html  
    Bowtie2Mapping                          html  
    finding level-2 HTML links ... done

    CutSiteCountR                           html  
    CutSitePre                              html  
    FRiPQC                                  html  
    FastQC                                  html  
    FindAdapter                             html  
    FragLenDistr                            html  
    LibComplexQC                            html  
    PeakCallingFseq                         html  
    PeakQC                                  html  
    RGo                                     html  
    RMotifScan                              html  
    RMotifScanPair                          html  
    RPeakAnno                               html  
    RPeakComp                               html  
    RSNPs                                   html  
    RemoveAdapter                           html  
    Renamer                                 html  
    Rsortbam                                html  
    SamToBam                                html  
    SamToBed                                html  
    SingleRepReport                         html  
    TSSQC                                   html  
    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
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** testing if installed package can be loaded from final location
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** 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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, 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, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

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: 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 objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: pipeFrame

Attaching package: 'pipeFrame'

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

    report


Warning message:
In options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
> 
> test_check("esATAC")
[1] "2020-10-17 04:08:23 EDT"
[1] "2020-10-17 04:08:23 EDT"
[1] "2020-10-17 04:08:23 EDT"
[1] "2020-10-17 04:08:23 EDT"
[1] "2020-10-17 04:08:23 EDT"
[1] "2020-10-17 04:08:23 EDT"
== testthat results  ===========================================================
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  19.39    1.03   30.65 

Example timings

esATAC.Rcheck/esATAC-Ex.timings

nameusersystemelapsed
BamToBed0.450.030.53
BedToBigWig0.120.000.12
BedUtils1.030.362.87
Bowtie2Mapping 0.17 0.0313.81
CutSiteCountR 4.6324.6644.00
CutSitePre 1.7413.6319.45
FRiPQC2.870.755.46
FastQC 3.7526.1834.95
FindAdapter 0.74 0.1733.70
FragLenDistr0.120.000.13
LibComplexQC0.280.221.57
PeakCallingFseq0.590.281.83
PeakQC0.810.222.55
RGo000
RMotifScan000
RMotifScanPair000
RPeakAnno 1.4512.1114.49
RPeakComp0.080.000.07
RSNPs 1.2811.8814.21
RemoveAdapter0.330.040.71
Renamer 0.73 0.1047.12
Rsortbam0.110.031.41
SamToBam 1.5912.2223.25
SamToBed0.420.302.22
TSSQC2.000.344.23
UnzipAndMerge0.040.030.06
atacPipe2000
atacRepsPipe000
atacRepsPipe2000
esATAC-package000
getMotifInfo0.010.000.02