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BioC 3.0: CHECK report for r3Cseq on moscato1

This page was generated on 2015-04-10 09:47:31 -0700 (Fri, 10 Apr 2015).

Package 709/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
r3Cseq 1.12.1
Supat Thongjuea
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/r3Cseq
Last Changed Rev: 97464 / Revision: 102249
Last Changed Date: 2014-12-07 15:30:30 -0800 (Sun, 07 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: r3Cseq
Version: 1.12.1
Command: rm -rf r3Cseq.buildbin-libdir r3Cseq.Rcheck && mkdir r3Cseq.buildbin-libdir r3Cseq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=r3Cseq.buildbin-libdir r3Cseq_1.12.1.tar.gz >r3Cseq.Rcheck\00install.out 2>&1 && cp r3Cseq.Rcheck\00install.out r3Cseq-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=r3Cseq.buildbin-libdir --install="check:r3Cseq-install.out" --force-multiarch --no-vignettes --timings r3Cseq_1.12.1.tar.gz
StartedAt: 2015-04-10 04:38:02 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:43:49 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 346.9 seconds
RetCode: 0
Status:  OK  
CheckDir: r3Cseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf r3Cseq.buildbin-libdir r3Cseq.Rcheck && mkdir r3Cseq.buildbin-libdir r3Cseq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=r3Cseq.buildbin-libdir r3Cseq_1.12.1.tar.gz >r3Cseq.Rcheck\00install.out 2>&1 && cp r3Cseq.Rcheck\00install.out r3Cseq-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=r3Cseq.buildbin-libdir --install="check:r3Cseq-install.out" --force-multiarch --no-vignettes --timings r3Cseq_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/r3Cseq.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'r3Cseq/DESCRIPTION' ... OK
* this is package 'r3Cseq' version '1.12.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'GenomicRanges' 'Rsamtools' 'data.table' 'rtracklayer' 'VGAM'
  'qvalue' 'RColorBrewer' 'sqldf'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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.mm9.masked'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'GenomicRanges' 'RColorBrewer' 'Rsamtools' 'VGAM' 'data.table'
  'methods' 'qvalue' 'rtracklayer' 'sqldf'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDomainogramNearViewpoint,r3Cseq: warning in axis(1, at = c(seq(0,
  1, by = 0.1)), lab = c(seq(-distance, distance, distance/5)),
  cex.axis = 0.8, las = 2): partial argument match of 'lab' to 'labels'
plotDomainogramNearViewpoint,r3Cseq: warning in axis(2, at = c(0, 1),
  lab = c(paste(maximum_window/1000, "Kb"), "2 Kb"), cex.axis = 0.8,
  las = 2): partial argument match of 'lab' to 'labels'
assign3CseqSigContact: no visible global function definition for
  'space'
assign3CseqSigContact: no visible global function definition for
  'vsmooth.spline'
assign3CseqSigContact: no visible global function definition for
  'qvalue'
assign3CseqSigContact: no visible binding for global variable
  'relative.position'
assign3CseqSigContact: no visible binding for global variable
  'chromosome'
assign3CseqSigContact: no visible global function definition for
  'RangedData'
assign3CseqSigContact: no visible global function definition for
  'IRanges'
excludeReadsNearViewpoint: no visible global function definition for
  'space'
excludeReadsNearViewpoint: no visible global function definition for
  'RangedData'
excludeReadsNearViewpoint: no visible global function definition for
  'IRanges'
excludeReadsNearViewpoint: no visible global function definition for
  'subjectHits'
excludeReadsNearViewpoint: no visible global function definition for
  'findOverlaps'
generate3CseqReport: no visible global function definition for 'space'
get3CseqRefGene: no visible binding for global variable 'hg18refGene'
get3CseqRefGene: no visible binding for global variable 'hg19refGene'
get3CseqRefGene: no visible binding for global variable 'mm9refGene'
getContrInteractionsInRefseq: no visible global function definition for
  'GRanges'
getContrInteractionsInRefseq: no visible global function definition for
  'space'
getContrInteractionsInRefseq: no visible global function definition for
  'IRanges'
getContrInteractionsInRefseq: no visible global function definition for
  'findOverlaps'
getContrInteractionsInRefseq: no visible global function definition for
  'queryHits'
getContrInteractionsInRefseq: no visible global function definition for
  'subjectHits'
getContrInteractionsInRefseq: no visible global function definition for
  'sqldf'
getExpInteractionsInRefseq: no visible global function definition for
  'GRanges'
getExpInteractionsInRefseq: no visible global function definition for
  'space'
getExpInteractionsInRefseq: no visible global function definition for
  'IRanges'
getExpInteractionsInRefseq: no visible global function definition for
  'findOverlaps'
getExpInteractionsInRefseq: no visible global function definition for
  'queryHits'
getExpInteractionsInRefseq: no visible global function definition for
  'subjectHits'
getExpInteractionsInRefseq: no visible global function definition for
  'sqldf'
getFragmentsPerWindow: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg18.masked'
getFragmentsPerWindow: no visible global function definition for
  'seqlengths'
getFragmentsPerWindow: no visible global function definition for
  'RangedData'
getFragmentsPerWindow: no visible global function definition for
  'IRanges'
getFragmentsPerWindow: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19.masked'
getFragmentsPerWindow: no visible binding for global variable
  'BSgenome.Mmusculus.UCSC.mm9.masked'
getPowerLawFittedCoeficient: no visible global function definition for
  'data.table'
getPowerLawFittedCoeficient: no visible binding for global variable
  'num'
getPowerLawFittedCoeficient: no visible binding for global variable
  'nr_reads'
getPowerLawFittedCoeficient: no visible global function definition for
  'setkey'
getPowerLawFittedCoeficient: no visible global function definition for
  'setnames'
getViewpoint: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg18.masked'
getViewpoint: no visible global function definition for 'matchPattern'
getViewpoint: no visible global function definition for 'DNAString'
getViewpoint: no visible global function definition for
  'reverseComplement'
getViewpoint: no visible global function definition for 'RangedData'
getViewpoint: no visible global function definition for 'IRanges'
getViewpoint: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19.masked'
getViewpoint: no visible binding for global variable
  'BSgenome.Mmusculus.UCSC.mm9.masked'
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for 'space'
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for 'seqnames'
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable 'BSgenome.Hsapiens.UCSC.hg19.masked'
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for 'seqlengths'
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 global function
  definition for 'RangedData'
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for 'IRanges'
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for 'countOverlaps'
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for 'vsmooth.spline'
makeInteractionMatrixNearCisPerWindow: no visible global function
  definition for 'qvalue'
plotInteractionsNearViewpoint: no visible global function definition
  for 'space'
plotInteractionsNearViewpoint: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg18.masked'
plotInteractionsNearViewpoint: no visible global function definition
  for 'seqlengths'
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
  'chromosome'
plotInteractionsNearViewpoint: no visible global function definition
  for 'brewer.pal'
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 global function definition
  for 'seqlengths'
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 global function definition
  for 'space'
plotInteractionsPerChromosome: no visible global function definition
  for 'brewer.pal'
plotOverviewInteractions: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg18.masked'
plotOverviewInteractions: no visible global function definition for
  'seqlengths'
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 global function definition for
  'brewer.pal'
plotOverviewInteractions: no visible global function definition for
  'space'
powerLawFittedRPM: no visible global function definition for 'zeta'
calculateBatchRPM,r3CseqInBatch: no visible global function definition
  for 'space'
calculateBatchRPM,r3CseqInBatch: no visible global function definition
  for 'RangedData'
calculateBatchRPM,r3CseqInBatch: no visible global function definition
  for 'IRanges'
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
  'space'
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
  'RangedData'
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
  'IRanges'
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
  'export'
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for 'RleList'
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
  variable 'BSgenome.Hsapiens.UCSC.hg18.masked'
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for 'seqlengths'
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for 'seqlevels<-'
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for 'seqlengths<-'
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for 'coverage'
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
  variable 'BSgenome.Hsapiens.UCSC.hg19.masked'
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
  variable 'BSgenome.Mmusculus.UCSC.mm9.masked'
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
  definition for 'export'
exportBatchInteractions2text,r3CseqInBatch: no visible global function
  definition for 'space'
exportInteractions2text,r3Cseq: no visible global function definition
  for 'space'
getBatchInteractions,r3CseqInBatch: no visible global function
  definition for 'space'
getBatchInteractions,r3CseqInBatch: no visible global function
  definition for 'qvalue'
getBatchInteractions,r3CseqInBatch: no visible global function
  definition for 'RangedData'
getBatchInteractions,r3CseqInBatch: no visible global function
  definition for 'IRanges'
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for 'ScanBamParam'
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for 'scanBamFlag'
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for 'scanBam'
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for 'width'
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for 'GRanges'
getBatchRawReads,r3CseqInBatch: no visible global function definition
  for 'IRanges'
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  global function definition for 'RangedData'
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  global function definition for 'IRanges'
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  global function definition for 'space'
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  global function definition for 'countOverlaps'
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
  definition for 'space'
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
  definition for 'countOverlaps'
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
  definition for 'RangedData'
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
  definition for 'IRanges'
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable 'BSgenome.Hsapiens.UCSC.hg18.masked'
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  global function definition for 'matchPattern'
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'
getEnzymeRestrictionSequences,repbaseEnzyme-character: no visible
  binding for global variable 'enzyme'
getRawReads,r3Cseq: no visible global function definition for
  'ScanBamParam'
getRawReads,r3Cseq: no visible global function definition for
  'scanBamFlag'
getRawReads,r3Cseq: no visible global function definition for 'scanBam'
getRawReads,r3Cseq: no visible global function definition for 'width'
getRawReads,r3Cseq: no visible global function definition for 'GRanges'
getRawReads,r3Cseq: no visible global function definition for 'IRanges'
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
  definition for 'RangedData'
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
  definition for 'IRanges'
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
  definition for 'countOverlaps'
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
  definition for 'space'
getReadCountPerWindow,r3Cseq: no visible global function definition for
  'countOverlaps'
getReadCountPerWindow,r3Cseq: no visible global function definition for
  'RangedData'
getReadCountPerWindow,r3Cseq: no visible global function definition for
  'space'
getReadCountPerWindow,r3Cseq: no visible global function definition for
  'IRanges'
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for 'space'
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable 'BSgenome.Hsapiens.UCSC.hg18.masked'
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for 'seqlengths'
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 'chromosome'
plotDomainogramNearViewpoint,r3Cseq: no visible global function
  definition for 'brewer.pal'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [10s] OK
** running examples for arch 'x64' ... [12s] 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/r3Cseq.Rcheck/00check.log'
for details.

r3Cseq.Rcheck/00install.out:


install for i386

* installing *source* package 'r3Cseq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'r3Cseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'r3Cseq' as r3Cseq_1.12.1.zip
* DONE (r3Cseq)

r3Cseq.Rcheck/examples_i386/r3Cseq-Ex.timings:

nameusersystemelapsed
calculateBatchRPM000
calculateRPM000
contrInteractionRegions000
contrRPM000
contrRawData000
contrReadCount000
expInteractionRegions000
expRPM000
expRawData000
expReadCount000
export3Cseq2bedGraph000
export3CseqRawReads2bedGraph000
exportBatchInteractions2text000
exportInteractions2text000
generate3CseqReport000
getBatchInteractions000
getBatchRawReads000
getBatchReadCountPerRestrictionFragment000
getBatchReadCountPerWindow0.020.000.01
getContrInteractionsInRefseq000
getExpInteractionsInRefseq000
getInteractions000
getRawReads000
getReadCountPerRestrictionFragment000
getReadCountPerWindow000
getViewpoint000
plotDomainogramNearViewpoint000
plotInteractionsNearViewpoint000
plotInteractionsPerChromosome000
plotOverviewInteractions000
r3Cseq-class000
r3CseqCommon-class000
r3CseqInBatch-class000

r3Cseq.Rcheck/examples_x64/r3Cseq-Ex.timings:

nameusersystemelapsed
calculateBatchRPM000
calculateRPM000
contrInteractionRegions000
contrRPM000
contrRawData000
contrReadCount000
expInteractionRegions000
expRPM000
expRawData000
expReadCount000
export3Cseq2bedGraph000
export3CseqRawReads2bedGraph000
exportBatchInteractions2text000
exportInteractions2text000
generate3CseqReport000
getBatchInteractions000
getBatchRawReads000
getBatchReadCountPerRestrictionFragment000
getBatchReadCountPerWindow000
getContrInteractionsInRefseq000
getExpInteractionsInRefseq000
getInteractions000
getRawReads000
getReadCountPerRestrictionFragment000
getReadCountPerWindow000
getViewpoint000
plotDomainogramNearViewpoint000
plotInteractionsNearViewpoint000
plotInteractionsPerChromosome000
plotOverviewInteractions000
r3Cseq-class000
r3CseqCommon-class000
r3CseqInBatch-class000