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CHECK report for SEtools on celaya2

This page was generated on 2020-01-16 13:55:16 -0500 (Thu, 16 Jan 2020).

Package 1569/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SEtools 1.1.0
Pierre-Luc Germain
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/SEtools
Branch: master
Last Commit: 8ee7008
Last Changed Date: 2019-10-29 13:43:40 -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 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SEtools
Version: 1.1.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SEtools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SEtools_1.1.0.tar.gz
StartedAt: 2020-01-16 08:49:00 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 08:53:37 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 276.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SEtools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SEtools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SEtools_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SEtools.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 ‘SEtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SEtools’ version ‘1.1.0’
* package encoding: UTF-8
* 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 ‘SEtools’ 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
.getBreaks: no visible global function definition for ‘quantile’
.getHMcols: no visible global function definition for
  ‘colorRampPalette’
.prepAssays : <anonymous> : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for ‘sd’
sehm: no visible binding for global variable ‘sd’
sortRows: no visible binding for global variable ‘sd’
sortRows: no visible global function definition for ‘aggregate’
sortRows: no visible binding for global variable ‘median’
sortRows: no visible global function definition for ‘dist’
Undefined global functions or variables:
  aggregate colorRampPalette dist median quantile sd
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "aggregate", "dist", "median", "quantile", "sd")
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 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/SEtools.Rcheck/00check.log’
for details.



Installation output

SEtools.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SEtools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SEtools’ ...
** 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 (SEtools)

Tests output


Example timings

SEtools.Rcheck/SEtools-Ex.timings

nameusersystemelapsed
crossHm4.0970.3564.453
log2FC0.0020.0010.003
meltSE0.0580.0020.059
mergeSEs0.1710.0030.173
resetAllSEtoolsOptions0.0000.0000.001
sehm0.1810.0080.192
sortRows0.0070.0030.010