BioC 3.2: CHECK report for occugene on zin1

Package: occugene

Version: 1.29.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings occugene_1.29.0.tar.gz

StartedAt: 2015-08-24 02:14:56 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:15:08 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 12.4 seconds

RetCode: 0

Status:  OK

CheckDir: occugene.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings occugene_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/occugene.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘occugene/DESCRIPTION’ ... OK
* this is package ‘occugene’ version ‘1.29.0’
* 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 ‘occugene’ can be installed ... [1s/1s] 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] 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
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/occugene.Rcheck/00check.log’
for details.

* 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
* DONE (occugene)

name	user	system	elapsed
binHist	0.000	0.000	0.001
binInsert	0	0	0
binInsertHist	0	0	0
checkFormat	0.022	0.001	0.023
delta0	0.043	0.000	0.043
eMult	0.455	0.000	0.456
etDelta	0.007	0.000	0.007
fCumul	0.000	0.000	0.001
fFit	0.041	0.000	0.040
loadAnnotation	0	0	0
loadInsertions	0.000	0.000	0.001
occup2Negenes	0.008	0.000	0.008
unbiasB0	0.359	0.000	0.359
unbiasDelta0	0.448	0.000	0.448
varMult	0.376	0.004	0.388