BioC 2.12: CHECK report for r3Cseq on moscato2

Package: r3Cseq

Version: 1.6.0

Command: rm -rf r3Cseq.buildbin-libdir && mkdir r3Cseq.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=r3Cseq.buildbin-libdir r3Cseq_1.6.0.tar.gz >r3Cseq-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=r3Cseq.buildbin-libdir --install="check:r3Cseq-install.out" --force-multiarch --no-vignettes --timings r3Cseq_1.6.0.tar.gz && mv r3Cseq.buildbin-libdir/* r3Cseq.Rcheck/ && rmdir r3Cseq.buildbin-libdir

StartedAt: 2013-10-09 03:43:26 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:48:30 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 304.4 seconds

RetCode: 0

Status: OK

CheckDir: r3Cseq.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/r3Cseq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.6.0'
* 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 whether package 'r3Cseq' can be installed ... 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
* 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
* 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 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 ...
** running examples for arch 'i386' ... [9s] OK
** running examples for arch 'x64' ... [13s] 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
  'E:/biocbld/bbs-2.12-bioc/meat/r3Cseq.Rcheck/00check.log'
for details.


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_1.6.0.zip
* DONE (r3Cseq)

BioC 2.12: CHECK report for r3Cseq on moscato2

Summary

Command output