Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 956/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCDOC 1.8.0  (landing page)
Maigné Élise
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/HiCDOC
git_branch: RELEASE_3_20
git_last_commit: 3496af8
git_last_commit_date: 2024-10-29 11:12:52 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for HiCDOC on teran2

To the developers/maintainers of the HiCDOC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCDOC.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: HiCDOC
Version: 1.8.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HiCDOC_1.8.0.tar.gz
StartedAt: 2024-11-20 04:19:33 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 04:26:25 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 411.4 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCDOC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HiCDOC_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/HiCDOC.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HiCDOC/DESCRIPTION’ ... OK
* this is package ‘HiCDOC’ version ‘1.8.0’
* 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: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) HiCDOC.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HiCDOC.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HiCDOC.Rd:34-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HiCDOC.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HiCDOC.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HiCDOC.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HiCDOC.Rd:55-58: Lost braces in \itemize; meant \describe ?
* 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 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
normalizeTechnicalBiases 54.016  0.342  54.281
HiCDOC                   49.886  0.175  49.756
plotDistanceEffect       16.129  0.548  15.929
* 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: 4 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/HiCDOC.Rcheck/00check.log’
for details.


Installation output

HiCDOC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HiCDOC
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘HiCDOC’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c constrainedClustering.cpp -o constrainedClustering.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c parseHiCFile.cpp -o parseHiCFile.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o HiCDOC.so RcppExports.o constrainedClustering.o parseHiCFile.o -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output

HiCDOC.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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(HiCDOC)
Loading required package: InteractionSet
Loading required package: GenomicRanges
Loading required package: stats4
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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, 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: GenomeInfoDb
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 3 | SKIP 0 | PASS 334 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 334 ]
> 
> proc.time()
   user  system elapsed 
 40.065   1.549  41.075 

Example timings

HiCDOC.Rcheck/HiCDOC-Ex.timings

nameusersystemelapsed
HiCDOC49.886 0.17549.756
HiCDOCDataSet-methods0.0620.0020.063
HiCDOCDataSet-parameters0.0080.0000.007
HiCDOCDataSetFromCool000
HiCDOCDataSetFromHiC000
HiCDOCDataSetFromHiCPro000
HiCDOCDataSetFromTabular0.1240.0010.120
detectCompartments1.9200.0701.864
exampleHiCDOCDataSet0.0110.0010.010
exampleHiCDOCDataSetProcessed0.0180.0000.018
filterSmallChromosomes0.0280.0000.029
filterSparseReplicates0.1070.0040.110
filterWeakPositions1.1710.0131.073
normalizeBiologicalBiases1.2180.0021.124
normalizeDistanceEffect2.4600.0002.518
normalizeTechnicalBiases54.016 0.34254.281
plotCentroids0.2890.0040.293
plotCompartmentChanges1.0210.0381.059
plotCompartments1.0460.0011.047
plotConcordanceDifferences0.1550.0010.157
plotConcordances0.2500.0010.251
plotDistanceEffect16.129 0.54815.929
plotInteractions0.5280.0050.517
plotSelfInteractionRatios0.2210.0010.222
reduceHiCDOCDataSet0.0260.0010.028