Package: occugene

Version: 1.42.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:occugene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings occugene_1.42.0.tar.gz

StartedAt: 2019-04-16 01:38:19 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:38:43 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 24.6 seconds

RetCode: 0

Status:  OK

CheckDir: occugene.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:occugene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings occugene_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/occugene.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘occugene/DESCRIPTION’ ... OK
* this is package ‘occugene’ version ‘1.42.0’
* 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 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 sizes of PDF files under ‘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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/occugene.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL occugene
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘occugene’ ...
** R
** data
** byte-compile and prepare 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	0	0
binInsert	0	0	0
binInsertHist	0	0	0
checkFormat	0.020	0.003	0.023
delta0	0.062	0.003	0.066
eMult	0.548	0.003	0.556
etDelta	0.006	0.002	0.008
fCumul	0.000	0.000	0.001
fFit	0.049	0.004	0.052
loadAnnotation	0	0	0
loadInsertions	0	0	0
occup2Negenes	0.009	0.002	0.012
unbiasB0	0.470	0.007	0.479
unbiasDelta0	0.550	0.007	0.559
varMult	0.529	0.001	0.532