BioC 2.14: CHECK report for occugene on moscato2

Package: occugene

Version: 1.24.0

Command: rm -rf occugene.buildbin-libdir && mkdir occugene.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=occugene.buildbin-libdir occugene_1.24.0.tar.gz >occugene-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=occugene.buildbin-libdir --install="check:occugene-install.out" --force-multiarch --no-vignettes --timings occugene_1.24.0.tar.gz

StartedAt: 2014-10-08 03:28:29 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:28:59 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 30.0 seconds

RetCode: 0

Status:  OK

CheckDir: occugene.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf occugene.buildbin-libdir && mkdir occugene.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=occugene.buildbin-libdir occugene_1.24.0.tar.gz >occugene-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=occugene.buildbin-libdir --install="check:occugene-install.out" --force-multiarch --no-vignettes --timings occugene_1.24.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/occugene.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'occugene/DESCRIPTION' ... OK
* this is package 'occugene' version '1.24.0'
* 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 'occugene' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
loadAnnotation: warning in read.table(fileName, head = T): partial
  argument match of 'head' to 'header'
loadInsertions: warning in read.table(fileName, head = T): partial
  argument match of 'head' to 'header'
* 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' ... [3s] OK
** running examples for arch 'x64' ... [3s] 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 was 1 note.
See
  'E:/biocbld/bbs-2.14-bioc/meat/occugene.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'occugene' ...
** 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 'occugene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'occugene' as occugene_1.24.0.zip
* DONE (occugene)

name	user	system	elapsed
binHist	0.02	0.00	0.01
binInsert	0	0	0
binInsertHist	0	0	0
checkFormat	0.02	0.00	0.02
delta0	0.05	0.00	0.05
eMult	0.59	0.00	0.59
etDelta	0.02	0.00	0.02
fCumul	0	0	0
fFit	0.06	0.00	0.06
loadAnnotation	0	0	0
loadInsertions	0	0	0
occup2Negenes	0	0	0
unbiasB0	0.51	0.00	0.52
unbiasDelta0	0.69	0.00	0.68
varMult	0.64	0.00	0.64

name	user	system	elapsed
binHist	0	0	0
binInsert	0	0	0
binInsertHist	0	0	0
checkFormat	0.02	0.02	0.03
delta0	0.06	0.00	0.06
eMult	0.72	0.00	0.71
etDelta	0.02	0.00	0.02
fCumul	0	0	0
fFit	0.06	0.00	0.06
loadAnnotation	0	0	0
loadInsertions	0	0	0
occup2Negenes	0.02	0.00	0.02
unbiasB0	0.73	0.00	0.73
unbiasDelta0	0.75	0.00	0.75
varMult	0.73	0.00	0.73