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Package 515/671HostnameOS / ArchBUILDCHECKBUILD BIN
r3Cseq 1.6.0
Supat Thongjuea
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/r3Cseq
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

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: 2013-05-01 09:48:42 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 09:53:50 -0700 (Wed, 01 May 2013)
EllapsedTime: 307.9 seconds
RetCode: 0
Status:  OK 
CheckDir: r3Cseq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/r3Cseq.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* 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 ... [29s/30s] 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 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 ... [14s/15s] 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.

r3Cseq.Rcheck/00install.out:

* 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)

r3Cseq.Rcheck/r3Cseq-Ex.timings:

nameusersystemelapsed
calculateBatchRPM0.0070.0020.010
calculateRPM0.0060.0020.009
contrInteractionRegions0.0110.0030.014
contrRPM0.0110.0030.014
contrRawData0.0060.0020.009
contrReadCount0.0060.0020.008
expInteractionRegions0.0100.0030.013
expRPM0.0070.0020.009
expRawData0.0060.0020.008
expReadCount0.0060.0020.008
export3Cseq2bedGraph0.0060.0010.007
export3CseqRawReads2bedGraph0.0110.0020.013
exportBatchInteractions2text0.0110.0010.013
exportInteractions2text0.0130.0010.014
generate3CseqReport0.0070.0020.009
getBatchInteractions0.0070.0020.010
getBatchRawReads0.0070.0020.008
getBatchReadCountPerRestrictionFragment0.0090.0020.013
getBatchReadCountPerWindow0.0100.0010.012
getContrInteractionsInRefseq0.0120.0010.013
getExpInteractionsInRefseq0.0070.0020.008
getInteractions0.0120.0040.016
getRawReads0.0080.0020.010
getReadCountPerRestrictionFragment0.0120.0050.017
getReadCountPerWindow0.0080.0020.015
getViewpoint0.0060.0020.007
plotDomainogramNearViewpoint0.0110.0010.012
plotInteractionsNearViewpoint0.3680.0020.374
plotInteractionsPerChromosome0.0060.0030.009
plotOverviewInteractions0.0060.0020.008
r3Cseq-class0.0090.0030.012
r3CseqCommon-class0.0070.0020.010
r3CseqInBatch-class0.0120.0030.015