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CHECK report for esATAC on merida2

This page was generated on 2018-10-17 08:59:13 -0400 (Wed, 17 Oct 2018).

Package 462/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
esATAC 1.2.3
Zheng Wei , Wei Zhang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/esATAC
Branch: RELEASE_3_7
Last Commit: 331f58b
Last Changed Date: 2018-10-04 17:36:06 -0400 (Thu, 04 Oct 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: esATAC
Version: 1.2.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:esATAC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings esATAC_1.2.3.tar.gz
StartedAt: 2018-10-16 21:15:41 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:22:32 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 410.9 seconds
RetCode: 0
Status:  OK 
CheckDir: esATAC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:esATAC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings esATAC_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/esATAC.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘esATAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘esATAC’ version ‘1.2.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘esATAC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
* 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 ... 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
RMotifScanPair 5.639  0.349   6.044
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/esATAC.Rcheck/00check.log’
for details.



Installation output

esATAC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL esATAC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘esATAC’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c BedLine.cpp -o BedLine.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c BedUtils.cpp -o BedUtils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ChrDivi.cpp -o ChrDivi.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c CutCountPre.cpp -o CutCountPre.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c CutSiteCount.cpp -o CutSiteCount.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c LibComplexQC.cpp -o LibComplexQC.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c SortBed.cpp -o SortBed.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c rcpp_wrapper.cpp -o rcpp_wrapper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c renamer.cpp -o renamer.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c sam2bed.cc -o sam2bed.o
sam2bed.cc:111:16: warning: unused variable 'xspm' [-Wunused-variable]
    regmatch_t xspm[1];
               ^
sam2bed.cc:280:16: warning: unused variable 'xspm' [-Wunused-variable]
    regmatch_t xspm[1];
               ^
2 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o esATAC.so BedLine.o BedUtils.o ChrDivi.o CutCountPre.o CutSiteCount.o LibComplexQC.o RcppExports.o SortBed.o rcpp_wrapper.o renamer.o sam2bed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/esATAC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (esATAC)

Tests output

esATAC.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, colnames,
    dirname, 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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
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 object is masked from 'package:Biostrings':

    type

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

    aperm, apply


> 
> test_check("esATAC")
Opening FASTQ file '/private/tmp/RtmpwZpmKt/baseopr/reads_1.Renamer.fq'
Opening FASTQ file '/private/tmp/RtmpwZpmKt/baseopr/reads_2.Renamer.fq'
Trimming paired end reads ...
Opening FASTQ file '/private/tmp/RtmpwZpmKt/baseopr/reads_1.Renamer.fq'
Opening FASTQ file '/private/tmp/RtmpwZpmKt/baseopr/reads_2.Renamer.fq'
Opening FASTQ file '/private/tmp/RtmpwZpmKt/baseopr/reads_1.Renamer.fq'
Opening FASTQ file '/private/tmp/RtmpwZpmKt/baseopr/reads_2.Renamer.fq'
Trimming paired end reads ...
Opening FASTQ file '/private/tmp/RtmpwZpmKt/baseopr/reads_1.Renamer.fq'
Opening FASTQ file '/private/tmp/RtmpwZpmKt/baseopr/reads_2.Renamer.fq'
Opening FASTQ file '/private/tmp/RtmpwZpmKt/umr/reads_1.Renamer.fq'
Opening FASTQ file '/private/tmp/RtmpwZpmKt/umr/reads_2.Renamer.fq'
Trimming paired end reads ...
Opening FASTQ file '/private/tmp/RtmpwZpmKt/umr/reads_1.Renamer.fq'
Opening FASTQ file '/private/tmp/RtmpwZpmKt/umr/reads_2.Renamer.fq'
F-Seq Version 1.85
Settings: 
	window=2860
	bandwidth=100
	threshold = 8.719944
	est. fragment size = 0
	sequence length = 32
chr20: first=60385, last=13381774
....................
.....................
chr20: Completed in 0.554 seconds.
chr20: Found 1515 peaks.
-----------------------
finish temporary output:/private/tmp/RtmpwZpmKt/sam2bed/Example.SamToBed.bed.0
merge start
merge finish
finish
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 92 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 32.464   1.906  34.324 

Example timings

esATAC.Rcheck/esATAC-Ex.timings

nameusersystemelapsed
ATACProc-class1.7680.1031.903
BamToBed0.4340.0130.450
BedToBigWig0.0770.0050.082
BedUtils0.3030.0200.342
Bowtie2Mapping1.0060.2300.593
CutSiteCountR0.5400.0310.578
CutSitePre0.3180.0110.332
FastQC0.7430.0300.784
FragLenDistr0.0800.0030.085
FripQC2.5310.2362.067
LibComplexQC0.1660.0090.176
PeakCallingFseq0.3710.0180.394
PeakQC0.5540.0210.583
RGo0.0010.0000.001
RMotifScan0.0010.0000.002
RMotifScanPair5.6390.3496.044
RPeakAnno0.2080.0080.219
RPeakComp0.0620.0020.065
RSNPs0.1720.0070.181
RemoveAdapter0.2620.0020.267
Renamer0.0230.0010.025
Rsortbam0.0410.0010.042
SamToBam0.1830.0090.195
SamToBed0.3120.0070.321
TSSQC1.9610.1222.108
UnzipAndMerge0.0090.0010.011
atacPipe20.0020.0000.003
atacRepsPipe0.0020.0010.003
atacRepsPipe20.0040.0000.004
configureValue0.0020.0010.003
esATAC-package0.0020.0010.003
getMotifInfo0.0120.0000.012