Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

CHECK report for occugene on celaya2

This page was generated on 2020-01-16 13:30:35 -0500 (Thu, 16 Jan 2020).

Package 1166/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
occugene 1.47.0
Oliver Will
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/occugene
Branch: master
Last Commit: 8341a76
Last Changed Date: 2019-10-29 13:34:44 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: occugene
Version: 1.47.0
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_1.47.0.tar.gz
StartedAt: 2020-01-16 07:02:59 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 07:03:36 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 36.3 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_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/occugene.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.47.0’
* 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-3.11-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
binHist000
binInsert0.0000.0000.001
binInsertHist0.0010.0000.001
checkFormat0.0260.0050.032
delta00.0570.0030.060
eMult0.8140.0030.816
etDelta0.0070.0050.012
fCumul0.0010.0010.001
fFit0.0720.0070.079
loadAnnotation0.0000.0000.001
loadInsertions000
occup2Negenes0.0110.0040.014
unbiasB00.6960.0050.701
unbiasDelta00.6270.0050.632
varMult0.6920.0020.694