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BioC 3.5: CHECK report for occugene on malbec2

This page was generated on 2017-10-18 14:12:54 -0400 (Wed, 18 Oct 2017).

Package 911/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
occugene 1.36.0
Oliver Will
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/occugene
Branch: RELEASE_3_5
Last Commit: 3f55b15
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: occugene
Version: 1.36.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings occugene_1.36.0.tar.gz
StartedAt: 2017-10-18 01:13:44 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:14:01 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 17.3 seconds
RetCode: 0
Status:  OK 
CheckDir: occugene.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings occugene_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/occugene.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.36.0’
* 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 ... 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
binInsertHist: no visible global function definition for ‘hist’
delta0: no visible global function definition for ‘coef’
eMult : unequalApproxEMult: no visible global function definition for
  ‘runif’
eMult : unequalApproxEMult: no visible binding for global variable
  ‘hist’
fFit : expModel: no visible global function definition for ‘nls’
loadAnnotation: no visible global function definition for ‘read.table’
loadInsertions: no visible global function definition for ‘read.table’
unbiasB0 : simB0: no visible global function definition for ‘coef’
unbiasB0: no visible global function definition for ‘coef’
varMult : unequalApproxVarMult: no visible global function definition
  for ‘runif’
varMult : unequalApproxVarMult: no visible binding for global variable
  ‘hist’
varMult : unequalApproxVarMult: no visible global function definition
  for ‘var’
Undefined global functions or variables:
  coef hist nls read.table runif var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coef", "nls", "runif", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 ... 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-3.5-bioc/meat/occugene.Rcheck/00check.log’
for details.


occugene.Rcheck/00install.out:

* 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)

occugene.Rcheck/occugene-Ex.timings:

nameusersystemelapsed
binHist000
binInsert000
binInsertHist000
checkFormat0.0160.0000.019
delta00.0640.0000.067
eMult0.460.000.46
etDelta0.0040.0000.004
fCumul0.0000.0000.001
fFit0.1280.0000.128
loadAnnotation000
loadInsertions0.0000.0000.001
occup2Negenes0.0040.0000.006
unbiasB00.2760.0000.276
unbiasDelta00.3640.0000.360
varMult0.4440.0000.447