Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:07 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for HiCDOC on nebbiolo2


To the developers/maintainers of the HiCDOC package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 907/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCDOC 1.0.0  (landing page)
Maigné Élise
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/HiCDOC
git_branch: RELEASE_3_16
git_last_commit: 8b0d83d
git_last_commit_date: 2022-11-01 11:27:16 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HiCDOC
Version: 1.0.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings HiCDOC_1.0.0.tar.gz
StartedAt: 2023-04-10 21:16:00 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:25:26 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 565.8 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCDOC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings HiCDOC_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/HiCDOC.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘HiCDOC/DESCRIPTION’ ... OK
* this is package ‘HiCDOC’ version ‘1.0.0’
* 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
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.2Mb
* 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 ... 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
  ‘value’
.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’
.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 global function definition for ‘.’
.predictCompartmentsAB: no visible binding for global variable ‘ratio’
.predictCompartmentsAB: no visible binding for global variable
  ‘chromosome’
.predictCompartmentsAB: no visible binding for global variable
  ‘compartment’
.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 ‘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 ‘compartment’
.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’
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 bin.1 bin.2
  centroid centroid.check change changed chromosome 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 minIndex minStart 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 ... 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
HiCDOC                   67.669  1.339  68.821
normalizeTechnicalBiases 58.314  0.456  58.638
plotDistanceEffect       23.844  0.808  24.646
* 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 ...
  ‘HiCDOC.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/HiCDOC.Rcheck/00check.log’
for details.



Installation output

HiCDOC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL HiCDOC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘HiCDOC’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/lib -L/usr/local/lib -o HiCDOC.so RcppExports.o constrainedClustering.o parseHiCFile.o -lz -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(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, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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 1 | SKIP 0 | PASS 333 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
 62.018   2.153  64.944 

Example timings

HiCDOC.Rcheck/HiCDOC-Ex.timings

nameusersystemelapsed
HiCDOC67.669 1.33968.821
HiCDOCDataSet-methods0.0990.0000.099
HiCDOCDataSet-parameters0.0110.0000.011
HiCDOCDataSetFromCool0.0010.0000.000
HiCDOCDataSetFromHiC000
HiCDOCDataSetFromHiCPro000
HiCDOCDataSetFromTabular0.1950.0240.219
detectCompartments2.7320.0522.678
exampleHiCDOCDataSet0.0150.0000.015
exampleHiCDOCDataSetProcessed0.0220.0000.021
filterSmallChromosomes0.0410.0040.045
filterSparseReplicates0.0960.0000.096
filterWeakPositions0.5130.0000.411
normalizeBiologicalBiases1.8420.0241.762
normalizeDistanceEffect1.8470.0041.754
normalizeTechnicalBiases58.314 0.45658.638
plotCentroids0.2710.0400.311
plotCompartmentChanges1.3680.0681.437
plotCompartments0.3480.0040.352
plotConcordanceDifferences0.2220.0000.222
plotConcordances0.3900.0080.398
plotDistanceEffect23.844 0.80824.646
plotInteractions0.7890.0040.781
plotSelfInteractionRatios0.3440.0000.344
reduceHiCDOCDataSet0.0410.0040.045