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BioC 3.4: CHECK report for r3Cseq on morelia

This page was generated on 2017-04-15 16:23:52 -0400 (Sat, 15 Apr 2017).

Package 990/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
r3Cseq 1.20.0
Supat Thongjuea
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/r3Cseq
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: r3Cseq
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings r3Cseq_1.20.0.tar.gz
StartedAt: 2017-04-15 06:46:35 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 06:50:17 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 222.0 seconds
RetCode: 0
Status:  OK 
CheckDir: r3Cseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings r3Cseq_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/r3Cseq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.20.0’
* 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 loading without being on the library search path ... 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 ‘plot’
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 ‘plot’
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
  ‘plot’
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 ‘plot’
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 plot 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", "plot", "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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/r3Cseq.Rcheck/00check.log’
for details.

r3Cseq.Rcheck/00install.out:

* installing *source* package ‘r3Cseq’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biostrings" for requests: DNAString
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biostrings" for requests: DNAString
* DONE (r3Cseq)

r3Cseq.Rcheck/r3Cseq-Ex.timings:

nameusersystemelapsed
calculateBatchRPM000
calculateRPM000
contrInteractionRegions0.0000.0000.001
contrRPM000
contrRawData0.0000.0000.001
contrReadCount0.0000.0000.001
expInteractionRegions0.0000.0000.001
expRPM000
expRawData0.0000.0000.001
expReadCount0.0000.0000.001
export3Cseq2bedGraph0.0000.0000.001
export3CseqRawReads2bedGraph0.0010.0000.001
exportBatchInteractions2text0.0010.0000.000
exportInteractions2text0.0000.0000.001
generate3CseqReport0.0000.0000.001
getBatchInteractions0.0000.0000.001
getBatchRawReads000
getBatchReadCountPerRestrictionFragment000
getBatchReadCountPerWindow0.0000.0000.001
getContrInteractionsInRefseq000
getExpInteractionsInRefseq0.0010.0000.001
getInteractions0.0010.0000.001
getRawReads0.0010.0000.000
getReadCountPerRestrictionFragment0.0010.0000.000
getReadCountPerWindow0.0000.0010.001
getViewpoint0.0000.0000.001
plotDomainogramNearViewpoint0.0010.0000.000
plotInteractionsNearViewpoint0.0010.0000.001
plotInteractionsPerChromosome0.0010.0000.001
plotOverviewInteractions0.0010.0000.000
r3Cseq-class0.0010.0000.001
r3CseqCommon-class0.0010.0000.001
r3CseqInBatch-class0.0010.0000.000