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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCDOC.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings HiCDOC_1.1.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/HiCDOC.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'HiCDOC/DESCRIPTION' ... OK
* this is package 'HiCDOC' version '1.1.1'
* 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 whether package 'HiCDOC' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 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 ... 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 ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/HiCDOC/libs/x64/HiCDOC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
HiCDOC                   52.33   3.98   56.29
normalizeTechnicalBiases 48.05   0.80   48.85
plotDistanceEffect       16.77   1.41   18.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    8.     └─pbapply::pbmapply(...)
    9.       └─base::mapply(...)
   10.         └─HiCDOC (local) `<fnctnWtT>`(...)
   11.           └─HiCDOC:::.setFromTabular(interactions, condition, replicate)
   12.             └─GenomicRanges::GRanges(allRegions)
   13.               └─methods::as(seqnames, "GRanges")
   14.                 └─GenomicRanges (local) asMethod(object)
   15.                   └─GenomicRanges::makeGRangesFromDataFrame(from, keep.extra.columns = TRUE)
   16.                     └─GenomicRanges::GRanges(...)
   17.                       └─GenomicRanges:::new_GRanges(...)
   18.                         └─GenomicRanges (local) stop_if_wrong_length("'seqnames'", ans_len)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 328 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/HiCDOC.Rcheck/00check.log'
for details.