Package: decontam

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:decontam.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings decontam_1.3.1.tar.gz

StartedAt: 2019-04-09 00:21:09 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:21:58 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 48.7 seconds

RetCode: 0

Status:  OK

CheckDir: decontam.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:decontam.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings decontam_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/decontam.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decontam/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decontam’ version ‘1.3.1’
* 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 ‘decontam’ 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
plot_condition: no visible binding for global variable ‘Condition’
plot_condition: no visible binding for global variable ‘DNA_conc’
plot_frequency: no visible binding for global variable ‘DNA_conc’
plot_frequency: no visible binding for global variable
  ‘taxon_abundance’
plot_frequency: no visible binding for global variable ‘Type’
plot_frequency: no visible binding for global variable ‘contam’
plot_frequency: no visible binding for global variable ‘non.contam’
Undefined global functions or variables:
  Condition DNA_conc Type contam non.contam taxon_abundance
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
isNotContaminant 5.889  0.278   6.198
* 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-3.9-bioc/meat/decontam.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 decontam
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘decontam’ ...
** R
** inst
** 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 (decontam)

name	user	system	elapsed
isContaminant	3.869	0.123	4.070
isNotContaminant	5.889	0.278	6.198
plot_condition	1.274	0.062	1.346
plot_frequency	1.902	0.048	1.960