Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

CHECK report for occugene on merida1

This page was generated on 2021-05-06 12:35:58 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the occugene package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1242/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
occugene 1.50.0  (landing page)
Oliver Will
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/occugene
Branch: RELEASE_3_12
Last Commit: 2166673
Last Changed Date: 2020-10-27 10:30:02 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: occugene
Version: 1.50.0
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_1.50.0.tar.gz
StartedAt: 2021-05-06 04:18:36 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:19:07 -0400 (Thu, 06 May 2021)
EllapsedTime: 30.8 seconds
RetCode: 0
Status:   OK  
CheckDir: occugene.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/occugene.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘occugene/DESCRIPTION’ ... OK
* this is package ‘occugene’ version ‘1.50.0’
* 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-3.12-bioc/meat/occugene.Rcheck/00check.log’
for details.



Installation output

occugene.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL occugene
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘occugene’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (occugene)

Tests output


Example timings

occugene.Rcheck/occugene-Ex.timings

nameusersystemelapsed
binHist0.0000.0010.000
binInsert0.0010.0010.001
binInsertHist0.0010.0000.001
checkFormat0.0270.0060.033
delta00.0550.0030.059
eMult0.5700.0040.575
etDelta0.0040.0020.005
fCumul0.0010.0000.001
fFit0.0400.0040.045
loadAnnotation000
loadInsertions000
occup2Negenes0.0070.0020.009
unbiasB00.3620.0050.366
unbiasDelta00.5730.0080.583
varMult0.5710.0020.573