BioC 2.12: CHECK report for r3Cseq on petty

Package: r3Cseq

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch r3Cseq_1.6.0.tar.gz

StartedAt: 2013-10-08 23:34:38 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:40:22 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 343.8 seconds

RetCode: 0

Status:  OK

CheckDir: r3Cseq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/r3Cseq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'r3Cseq/DESCRIPTION' ... OK
* this is package 'r3Cseq' version '1.6.0'
* 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 ... [34s/36s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-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	0.002	0.008
calculateRPM	0.010	0.001	0.012
contrInteractionRegions	0.009	0.001	0.011
contrRPM	0.009	0.000	0.014
contrRawData	0.021	0.001	0.021
contrReadCount	0.006	0.003	0.011
expInteractionRegions	0.008	0.002	0.010
expRPM	0.005	0.001	0.007
expRawData	0.010	0.001	0.011
expReadCount	0.009	0.002	0.010
export3Cseq2bedGraph	0.009	0.001	0.011
export3CseqRawReads2bedGraph	0.005	0.000	0.005
exportBatchInteractions2text	0.009	0.000	0.010
exportInteractions2text	0.005	0.002	0.007
generate3CseqReport	0.005	0.002	0.006
getBatchInteractions	0.005	0.002	0.007
getBatchRawReads	0.006	0.001	0.007
getBatchReadCountPerRestrictionFragment	0.006	0.001	0.007
getBatchReadCountPerWindow	0.008	0.001	0.008
getContrInteractionsInRefseq	0.008	0.000	0.008
getExpInteractionsInRefseq	0.005	0.002	0.008
getInteractions	0.005	0.002	0.008
getRawReads	0.006	0.002	0.007
getReadCountPerRestrictionFragment	0.006	0.002	0.007
getReadCountPerWindow	0.006	0.001	0.006
getViewpoint	0.010	0.001	0.011
plotDomainogramNearViewpoint	0.009	0.001	0.011
plotInteractionsNearViewpoint	0.005	0.002	0.007
plotInteractionsPerChromosome	0.006	0.002	0.007
plotOverviewInteractions	0.006	0.001	0.009
r3Cseq-class	0.004	0.001	0.007
r3CseqCommon-class	0.005	0.000	0.006
r3CseqInBatch-class	0.009	0.001	0.011