BioC 2.13: CHECK report for r3Cseq on perceval

Package: r3Cseq

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch r3Cseq_1.8.0.tar.gz

StartedAt: 2014-04-05 03:40:34 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:46:00 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 325.4 seconds

RetCode: 0

Status:  OK

CheckDir: r3Cseq.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/r3Cseq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.8.0’
* 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 ... [31s/34s] 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
Packages in Depends field not imported from:
  ‘data.table’ ‘GenomicRanges’ ‘methods’ ‘qvalue’ ‘RColorBrewer’
  ‘Rsamtools’ ‘rtracklayer’ ‘sqldf’ ‘VGAM’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
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 binding for global variable
  ‘relative.position’
assign3CseqSigContact: no visible binding for global variable
  ‘chromosome’
get3CseqRefGene: no visible binding for global variable ‘hg18refGene’
get3CseqRefGene: no visible binding for global variable ‘hg19refGene’
get3CseqRefGene: no visible binding for global variable ‘mm9refGene’
getPowerLawFittedCoeficient: no visible binding for global variable
  ‘num’
getPowerLawFittedCoeficient: no visible binding for global variable
  ‘nr_reads’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘chromosome’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘exp_RPMs’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘contr_RPMs’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  binding for global variable ‘exp.read.length’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘chromosome’
* 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’ ... NOTE
The following directories should probably not be installed:
  ‘images’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘r3Cseq.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [16s/16s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/r3Cseq.Rcheck/00check.log’
for details.

* 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
* DONE (r3Cseq)

name	user	system	elapsed
calculateBatchRPM	0.006	0.003	0.009
calculateRPM	0.007	0.003	0.010
contrInteractionRegions	0.009	0.002	0.011
contrRPM	0.005	0.001	0.007
contrRawData	0.008	0.001	0.010
contrReadCount	0.005	0.001	0.006
expInteractionRegions	0.007	0.001	0.009
expRPM	0.006	0.002	0.008
expRawData	0.007	0.003	0.009
expReadCount	0.009	0.002	0.012
export3Cseq2bedGraph	0.006	0.002	0.008
export3CseqRawReads2bedGraph	0.006	0.001	0.007
exportBatchInteractions2text	0.006	0.003	0.008
exportInteractions2text	0.006	0.001	0.009
generate3CseqReport	0.010	0.002	0.011
getBatchInteractions	0.008	0.002	0.010
getBatchRawReads	0.003	0.002	0.005
getBatchReadCountPerRestrictionFragment	0.006	0.002	0.008
getBatchReadCountPerWindow	0.005	0.001	0.008
getContrInteractionsInRefseq	0.006	0.002	0.008
getExpInteractionsInRefseq	0.006	0.001	0.007
getInteractions	0.009	0.002	0.011
getRawReads	0.006	0.001	0.008
getReadCountPerRestrictionFragment	0.010	0.002	0.013
getReadCountPerWindow	0.006	0.001	0.008
getViewpoint	0.007	0.003	0.010
plotDomainogramNearViewpoint	0.007	0.002	0.010
plotInteractionsNearViewpoint	0.006	0.001	0.008
plotInteractionsPerChromosome	0.008	0.002	0.010
plotOverviewInteractions	0.005	0.001	0.007
r3Cseq-class	0.005	0.002	0.005
r3CseqCommon-class	0.007	0.002	0.008
r3CseqInBatch-class	0.008	0.002	0.010