##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCDOC_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/HiCDOC.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCDOC/DESCRIPTION’ ... OK
* this is package ‘HiCDOC’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘HiCDOC’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.checkCompartmentAssignment: no visible binding for global variable
  ‘chromosome’
.checkPca : f: no visible binding for global variable ‘compartment’
.checkResults: no visible binding for global variable
  ‘assignment.check’
.computePValues: no visible binding for global variable ‘condition’
.computePValues: no visible binding for global variable ‘chromosome’
.computePValues: no visible binding for global variable ‘index’
.computePValues: no visible global function definition for ‘.’
.computePValues: no visible binding for global variable ‘concordance’
.computePValues: no visible binding for global variable ‘condition.1’
.computePValues: no visible binding for global variable ‘condition.2’
.computePValues: no visible binding for global variable ‘concordance.1’
.computePValues: no visible binding for global variable ‘concordance.2’
.computePValues: no visible binding for global variable ‘compartment’
.computePValues: no visible binding for global variable ‘compartment.1’
.computePValues: no visible binding for global variable ‘compartment.2’
.computePValues: no visible binding for global variable ‘H0_value’
.computePValues: no visible binding for global variable ‘difference’
.computePValues : <anonymous>: no visible binding for global variable
  ‘difference’
.computePValues: no visible binding for global variable ‘pvalue’
.computePValues: no visible binding for global variable
  ‘pvalue.adjusted’
.computePValues: no visible binding for global variable ‘direction’
.computePca: no visible binding for global variable ‘chromosome’
.computePca: no visible global function definition for ‘.’
.computePca: no visible binding for global variable ‘condition’
.computePca: no visible binding for global variable ‘compartment’
.computePca: no visible binding for global variable ‘centroid’
.computeSelfInteractionRatios: no visible global function definition
  for ‘.’
.computeSelfInteractionRatios: no visible binding for global variable
  ‘index’
.computeSelfInteractionRatios: no visible binding for global variable
  ‘ratio’
.computeSelfInteractionRatios: no visible binding for global variable
  ‘variable’
.computeSelfInteractionRatios: no visible binding for global variable
  ‘chromosome’
.computeSelfInteractionRatios: no visible binding for global variable
  ‘condition’
.determineChromosomeSizes: no visible binding for global variable
  ‘minIndex’
.determineChromosomeSizes: no visible binding for global variable
  ‘index’
.determineChromosomeSizes: no visible global function definition for
  ‘.’
.determineChromosomeSizes: no visible binding for global variable
  ‘minStart’
.filterWeakPositionsOfChromosome: no visible global function definition
  for ‘.’
.filterWeakPositionsOfChromosome: no visible binding for global
  variable ‘index1’
.filterWeakPositionsOfChromosome: no visible binding for global
  variable ‘index2’
.filterWeakPositionsOfChromosome: no visible binding for global
  variable ‘value’
.filterWeakPositionsOfChromosome: no visible binding for global
  variable ‘variable’
.filterWeakPositionsOfChromosome: no visible binding for global
  variable ‘index’
.formatDetectCompartment: no visible binding for global variable
  ‘chromosome’
.formatDetectCompartment: no visible global function definition for ‘.’
.formatDetectCompartment: no visible binding for global variable
  ‘index’
.formatDetectCompartment: no visible binding for global variable
  ‘condition’
.formatDetectCompartment: no visible binding for global variable
  ‘compartment’
.formatDetectCompartment: no visible binding for global variable
  ‘concordance’
.formatDetectCompartment: no visible binding for global variable
  ‘significance’
.formatDetectCompartment: no visible binding for global variable
  ‘pvalue.adjusted’
.formatDetectCompartment: no visible binding for global variable
  ‘condition.1’
.formatDetectCompartment: no visible binding for global variable
  ‘condition.2’
.formatDetectCompartment: no visible binding for global variable
  ‘pvalue’
.formatDetectCompartment: no visible binding for global variable
  ‘direction’
.formatDetectCompartment: no visible binding for global variable
  ‘centroid.check’
.formatDetectCompartment: no visible binding for global variable
  ‘PC1.check’
.formatDetectCompartment: no visible binding for global variable
  ‘assignment.check’
.messageCheck: no visible binding for global variable ‘chromosome’
.normalizeDistanceEffectOfChromosome: no visible binding for global
  variable ‘value’
.normalizeDistanceEffectOfChromosome: no visible binding for global
  variable ‘logvalue’
.normalizeDistanceEffectOfChromosome: no visible binding for global
  variable ‘logdistance’
.normalizeDistanceEffectOfChromosome: no visible binding for global
  variable ‘bias’
.parseOneCool: no visible binding for global variable ‘chromosome’
.parseOneCool: no visible binding for global variable ‘index’
.parseOneCool: no visible binding for global variable ‘id1’
.parseOneCool: no visible binding for global variable ‘id2’
.parseOneHiCPro: no visible binding for global variable ‘chromosome’
.parseOneHiCPro: no visible binding for global variable ‘index’
.parseOneHiCPro: no visible binding for global variable ‘startIndex’
.parseOneHiCPro: no visible binding for global variable ‘stopIndex’
.plotInteractionsGrid: no visible binding for global variable ‘start1’
.plotInteractionsGrid: no visible binding for global variable ‘start2’
.plotInteractionsWrap: no visible binding for global variable ‘start1’
.plotInteractionsWrap: no visible binding for global variable ‘start2’
.predictCompartmentsAB: no visible binding for global variable
  ‘offDiagonal’
.predictCompartmentsAB: no visible binding for global variable ‘ratio’
.predictCompartmentsAB: no visible global function definition for ‘.’
.predictCompartmentsAB: no visible binding for global variable
  ‘chromosome’
.predictCompartmentsAB: no visible binding for global variable
  ‘cluster’
.predictCompartmentsAB: no visible binding for global variable ‘A’
.predictCompartmentsAB: no visible binding for global variable ‘1’
.predictCompartmentsAB: no visible binding for global variable ‘2’
.predictCompartmentsAB: no visible binding for global variable
  ‘compartment’
.predictCompartmentsAB: no visible binding for global variable ‘change’
.predictCompartmentsAB: no visible binding for global variable
  ‘concordance’
.reduceHiCDOCChromosomes: no visible binding for global variable
  ‘chromosome’
.reduceHiCDOCConditions: no visible binding for global variable
  ‘condition’
.setFromTabular: no visible binding for global variable ‘chromosome’
.setFromTabular: no visible binding for global variable ‘position 1’
.setFromTabular: no visible binding for global variable ‘position 2’
.setFromTabular: no visible global function definition for ‘.’
.setFromTabular: no visible binding for global variable ‘bin.1’
.setFromTabular: no visible binding for global variable ‘bin.2’
.setFromTabular: no visible binding for global variable ‘variable’
.setFromTabular: no visible binding for global variable ‘indexC’
.setFromTabular: no visible binding for global variable ‘index’
.tieCentroids: no visible binding for global variable ‘cluster’
.tieCentroids: no visible binding for global variable ‘condition’
.tieCentroids: no visible binding for global variable ‘chromosome’
.tieCentroids: no visible global function definition for ‘.’
.tieCentroids: no visible binding for global variable ‘centroid’
.tieCentroids: no visible binding for global variable ‘cluster.1’
.tieCentroids: no visible binding for global variable ‘cluster.2’
.tieCentroids: no visible binding for global variable ‘change’
.tieCentroids: no visible binding for global variable ‘concordance’
.tieCentroids: no visible binding for global variable ‘compartment’
normalizeTechnicalBiases: no visible global function definition for ‘.’
normalizeTechnicalBiases: no visible binding for global variable
  ‘seqnames1’
normalizeTechnicalBiases: no visible binding for global variable
  ‘start1’
normalizeTechnicalBiases: no visible binding for global variable
  ‘start2’
normalizeTechnicalBiases: no visible binding for global variable
  ‘chromosome’
plotCentroids: no visible binding for global variable ‘PC1’
plotCentroids: no visible binding for global variable ‘PC2’
plotCentroids: no visible binding for global variable ‘compartment’
plotCentroids: no visible binding for global variable ‘condition’
plotCompartments: no visible binding for global variable ‘position’
plotCompartments: no visible binding for global variable ‘compartment’
plotCompartments: no visible binding for global variable ‘condition’
plotConcordanceDifferences: no visible binding for global variable
  ‘changed’
plotConcordanceDifferences: no visible binding for global variable
  ‘compartment.1’
plotConcordanceDifferences: no visible binding for global variable
  ‘compartment.2’
plotConcordanceDifferences: no visible binding for global variable
  ‘difference’
plotConcordances: no visible binding for global variable ‘condition’
plotConcordances: no visible binding for global variable
  ‘pvalue.adjusted’
plotConcordances: no visible binding for global variable ‘concordance’
plotInteractions: no visible global function definition for ‘.’
plotInteractions: no visible binding for global variable ‘seqnames1’
plotInteractions: no visible binding for global variable ‘start1’
plotInteractions: no visible binding for global variable ‘start2’
plotInteractions: no visible binding for global variable ‘variable’
plotInteractions: no visible binding for global variable ‘condition’
plotSelfInteractionRatios: no visible global function definition for
  ‘.’
plotSelfInteractionRatios: no visible binding for global variable
  ‘condition’
plotSelfInteractionRatios: no visible binding for global variable
  ‘index’
plotSelfInteractionRatios: no visible binding for global variable
  ‘compartment’
plotSelfInteractionRatios: no visible binding for global variable
  ‘ratio’
concordances,HiCDOCDataSet: no visible binding for global variable
  ‘centroid.check’
concordances,HiCDOCDataSet: no visible binding for global variable
  ‘PC1.check’
concordances,HiCDOCDataSet: no visible binding for global variable
  ‘assignment.check’
concordances,HiCDOCDataSet: no visible binding for global variable
  ‘chromosome’
Undefined global functions or variables:
  . 1 2 A H0_value PC1 PC1.check PC2 assignment.check bias bin.1 bin.2
  centroid centroid.check change changed chromosome cluster cluster.1
  cluster.2 compartment compartment.1 compartment.2 concordance
  concordance.1 concordance.2 condition condition.1 condition.2
  difference direction id1 id2 index index1 index2 indexC logdistance
  logvalue minIndex minStart offDiagonal position position 1 position 2
  pvalue pvalue.adjusted ratio seqnames1 significance start1 start2
  startIndex stopIndex value variable
* 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:
  HiCDOC.Rd: BiocParallel
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 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 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
HiCDOC                    115.819  4.596 202.520
normalizeTechnicalBiases  103.276  4.865 142.783
plotDistanceEffect         18.333  1.429  25.469
detectCompartments          4.999  0.109  13.024
normalizeDistanceEffect     4.802  0.194  12.686
plotCompartmentChanges      4.712  0.094   5.944
normalizeBiologicalBiases   3.937  0.088  10.171
* 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 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-3.22-bioc/meat/HiCDOC.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCDOC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘HiCDOC’ ...
** this is package ‘HiCDOC’ version ‘1.12.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c constrainedClustering.cpp -o constrainedClustering.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c parseHiCFile.cpp -o parseHiCFile.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o HiCDOC.so RcppExports.o constrainedClustering.o parseHiCFile.o -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-HiCDOC/00new/HiCDOC/libs
** R
** data
** 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 (HiCDOC)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(HiCDOC)
Loading required package: InteractionSet
Loading required package: GenomicRanges
Loading required package: stats4
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

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: Seqinfo
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

> 
> test_check("HiCDOC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 355 ]
> 
> proc.time()
   user  system elapsed 
 86.032   3.700 110.300