##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:esATAC.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings esATAC_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/esATAC.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘esATAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘esATAC’ version ‘1.29.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘esATAC’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
    libs      2.3Mb
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Bowtie2Mapping.Rd: bowtie2, bowtie2_build, bowtie2_usage
  RMotifScan.Rd: GRanges, getRefRc, PFMatrix, PFMatrixList, PWMatrix,
    PWMatrixList
  RMotifScanPair.Rd: getRefRc, PFMatrix, PFMatrixList, PWMatrix,
    PWMatrixList
  RPeakAnno.Rd: annotatePeak, GRanges
  RPeakComp.Rd: GRanges
  SingleRepReport.Rd: Step-class
  atacPipe2.Rd: PFMatrix, PFMatrixList, PWMatrix, PWMatrixList
  atacRepsPipe.Rd: PFMatrix, PFMatrixList, PWMatrix, PWMatrixList,
    printMap
  atacRepsPipe2.Rd: PFMatrix, PFMatrixList, PWMatrix, PWMatrixList
  esATAC-package.Rd: PFMatrix, PFMatrixList, PWMatrix, PWMatrixList,
    printMap
  getMotifInfo.Rd: PFMatrix, PFMatrixList
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
FindAdapter 0.426  0.052  19.502
Renamer     0.421  0.017  18.723
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/esATAC.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL esATAC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘esATAC’ ...
** this is package ‘esATAC’ version ‘1.29.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c BedLine.cpp -o BedLine.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c BedUtils.cpp -o BedUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c ChrDivi.cpp -o ChrDivi.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c CutCountPre.cpp -o CutCountPre.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c CutSiteCount.cpp -o CutSiteCount.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c LibComplexQC.cpp -o LibComplexQC.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c SortBed.cpp -o SortBed.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c rcpp_wrapper.cpp -o rcpp_wrapper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c renamer.cpp -o renamer.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX  -DR_EVN_FLAG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c sam2bed.cc -o sam2bed.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/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 -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-esATAC/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (esATAC)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

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: 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] "2025-01-24 22:16:09 EST"
[1] "2025-01-24 22:16:09 EST"
[1] "2025-01-24 22:16:09 EST"
[1] "2025-01-24 22:16:09 EST"
[1] "2025-01-24 22:16:09 EST"
[1] "2025-01-24 22:16:09 EST"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 19.115   1.291  20.385