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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:r3Cseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings r3Cseq_1.53.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/r3Cseq.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.53.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘r3Cseq’ can be installed ... OK
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
  ‘BSgenome.Mmusculus.UCSC.mm10.masked’
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
  ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assign3CseqSigContact: no visible global function definition for
  ‘fitted’
assign3CseqSigContact: no visible binding for global variable
  ‘relative.position’
assign3CseqSigContact: no visible binding for global variable
  ‘chromosome’
excludeReadsNearViewpoint: no visible global function definition for
  ‘subjectHits’
generate3CseqReport: no visible global function definition for ‘pdf’
generate3CseqReport: no visible global function definition for
  ‘dev.off’
get3CseqRefGene: no visible binding for global variable ‘hg18refGene’
get3CseqRefGene: no visible binding for global variable ‘hg19refGene’
get3CseqRefGene: no visible binding for global variable ‘mm9refGene’
get3CseqRefGene: no visible binding for global variable ‘mm10refGene’
get3CseqRefGene: no visible binding for global variable ‘rn5refGene’
getContrInteractionsInRefseq: no visible global function definition for
  ‘queryHits’
getContrInteractionsInRefseq: no visible global function definition for
  ‘subjectHits’
getExpInteractionsInRefseq: no visible global function definition for
  ‘queryHits’
getExpInteractionsInRefseq: no visible global function definition for
  ‘subjectHits’
getFragmentsPerWindow: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
getFragmentsPerWindow: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
getFragmentsPerWindow: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
getFragmentsPerWindow: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm10.masked’
getFragmentsPerWindow: no visible binding for global variable
  ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
getPowerLawFittedCoeficient: no visible binding for global variable
  ‘num’
getPowerLawFittedCoeficient: no visible binding for global variable
  ‘nr_reads’
getPowerLawFittedCoeficient: no visible global function definition for
  ‘coefficients’
getViewpoint: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
getViewpoint: no visible global function definition for ‘DNAString’
getViewpoint: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
getViewpoint: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
getViewpoint: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm10.masked’
getViewpoint: no visible binding for global variable
  ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable ‘BSgenome.Mmusculus.UCSC.mm10.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for ‘fitted’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘chromosome’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘par’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘abline’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘text’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘lines’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘rect’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘legend’
plotInteractionsNearViewpoint: no visible global function definition
  for ‘points’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘exp_RPMs’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘contr_RPMs’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘log2fold’
plotInteractionsPerChromosome: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotInteractionsPerChromosome: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotInteractionsPerChromosome: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotInteractionsPerChromosome: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotInteractionsPerChromosome: no visible binding for global variable
  ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotInteractionsPerChromosome: no visible global function definition
  for ‘fitted’
plotInteractionsPerChromosome: no visible global function definition
  for ‘abline’
plotInteractionsPerChromosome: no visible global function definition
  for ‘lines’
plotInteractionsPerChromosome: no visible global function definition
  for ‘legend’
plotInteractionsPerChromosome: no visible global function definition
  for ‘par’
plotOverviewInteractions: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotOverviewInteractions: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotOverviewInteractions: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotOverviewInteractions: no visible binding for global variable
  ‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotOverviewInteractions: no visible binding for global variable
  ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotOverviewInteractions: no visible global function definition for
  ‘axis’
plotOverviewInteractions: no visible global function definition for
  ‘polygon’
plotOverviewInteractions: no visible global function definition for
  ‘text’
plotOverviewInteractions: no visible global function definition for
  ‘rect’
plotOverviewInteractions: no visible global function definition for
  ‘legend’
getBatchInteractions,r3CseqInBatch: no visible global function
  definition for ‘na.omit’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable ‘BSgenome.Mmusculus.UCSC.mm10.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
getEnzymeRestrictionSequences,repbaseEnzyme-character: no visible
  binding for global variable ‘enzyme’
initialize,repbaseEnzyme: no visible binding for global variable
  ‘enzyme.db’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘chromosome’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘par’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘abline’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘text’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘lines’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘rect’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘legend’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘points’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘colorRampPalette’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘image’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for ‘axis’
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg18.masked BSgenome.Hsapiens.UCSC.hg19.masked
  BSgenome.Mmusculus.UCSC.mm10.masked
  BSgenome.Mmusculus.UCSC.mm9.masked
  BSgenome.Rnorvegicus.UCSC.rn5.masked DNAString abline axis chromosome
  coefficients colorRampPalette contr_RPMs dev.off enzyme enzyme.db
  exp_RPMs fitted hg18refGene hg19refGene image legend lines log2fold
  mm10refGene mm9refGene na.omit nr_reads num par pdf points polygon
  queryHits rect relative.position rn5refGene subjectHits text
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "image", "legend", "lines",
             "par", "points", "polygon", "rect", "text")
  importFrom("stats", "coefficients", "fitted", "na.omit")
to your NAMESPACE file.
* 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:
  getBatchInteractions.Rd: vsmooth.spline
  getInteractions.Rd: vsmooth.spline
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/r3Cseq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL r3Cseq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘r3Cseq’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package ‘Biostrings’ for request: ‘DNAString’ when loading ‘r3Cseq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘Biostrings’ for request: ‘DNAString’ when loading ‘r3Cseq’
** testing if installed package can be loaded from final location
No methods found in package ‘Biostrings’ for request: ‘DNAString’ when loading ‘r3Cseq’
** testing if installed package keeps a record of temporary installation path
* DONE (r3Cseq)