Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-12 13:20:42 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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 r3Cseq on nebbiolo1


To the developers/maintainers of the r3Cseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/r3Cseq.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 1557/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
r3Cseq 1.42.0  (landing page)
Supat Thongjuea or
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/r3Cseq
git_branch: RELEASE_3_15
git_last_commit: c9c2f38
git_last_commit_date: 2022-04-26 11:09:26 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: r3Cseq
Version: 1.42.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:r3Cseq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings r3Cseq_1.42.0.tar.gz
StartedAt: 2022-08-11 21:41:15 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 21:45:01 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 225.3 seconds
RetCode: 0
Status:   OK  
CheckDir: r3Cseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:r3Cseq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings r3Cseq_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/r3Cseq.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.42.0’
* 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 ‘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 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 ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/r3Cseq.Rcheck/00check.log’
for details.



Installation output

r3Cseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL r3Cseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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)

Tests output


Example timings

r3Cseq.Rcheck/r3Cseq-Ex.timings

nameusersystemelapsed
calculateBatchRPM000
calculateRPM000
contrInteractionRegions0.0000.0000.001
contrRPM000
contrRawData0.0010.0000.000
contrReadCount000
expInteractionRegions0.0000.0000.001
expRPM000
expRawData0.0010.0000.000
expReadCount000
export3Cseq2bedGraph0.0000.0000.001
export3CseqRawReads2bedGraph000
exportBatchInteractions2text0.0010.0000.000
exportInteractions2text000
generate3CseqReport0.0000.0000.001
getBatchInteractions000
getBatchRawReads000
getBatchReadCountPerRestrictionFragment000
getBatchReadCountPerWindow0.0000.0000.001
getContrInteractionsInRefseq000
getExpInteractionsInRefseq000
getInteractions000
getRawReads000
getReadCountPerRestrictionFragment0.0010.0000.000
getReadCountPerWindow000
getViewpoint000
plotDomainogramNearViewpoint0.0000.0000.001
plotInteractionsNearViewpoint000
plotInteractionsPerChromosome0.0000.0010.000
plotOverviewInteractions000
r3Cseq-class0.0000.0000.001
r3CseqCommon-class000
r3CseqInBatch-class0.0000.0010.000