Package: qcmetrics

Version: 1.21.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qcmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qcmetrics_1.21.1.tar.gz

StartedAt: 2019-04-09 04:38:38 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:40:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 98.1 seconds

RetCode: 0

Status:  OK

CheckDir: qcmetrics.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:qcmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qcmetrics_1.21.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/qcmetrics.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qcmetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qcmetrics’ version ‘1.21.1’
* 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 ‘qcmetrics’ 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  as.data.frame.QcMetrics
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
n15qc: no visible global function definition for ‘fvarLabels’
n15qc: no visible global function definition for ‘fData’
n15qc : <anonymous>: no visible global function definition for ‘ggplot’
n15qc : <anonymous>: no visible global function definition for ‘aes’
n15qc : <anonymous>: no visible global function definition for
  ‘geom_jitter’
n15qc : <anonymous>: no visible global function definition for
  ‘geom_boxplot’
n15qc : <anonymous>: no visible global function definition for
  ‘geom_hline’
n15qc : <anonymous>: no visible global function definition for ‘labs’
n15qc: no visible global function definition for ‘fData<-’
n15qc: no visible global function definition for ‘combineFeatures’
n15qc: no visible global function definition for ‘exprs’
n15qc: no visible global function definition for ‘fileNames’
n15qc: no visible global function definition for ‘experimentData’
Undefined global functions or variables:
  aes combineFeatures experimentData exprs fData fData<- fileNames
  fvarLabels geom_boxplot geom_hline geom_jitter ggplot labs
* 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
Examples with CPU or elapsed time > 5s
     user system elapsed
psm 4.584  0.419   5.002
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/qcmetrics.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 qcmetrics
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘qcmetrics’ ...
** using staged installation
** R
** data
** 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 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 (qcmetrics)

name	user	system	elapsed
QcMetadata-class	0.004	0.001	0.005
QcMetric-class	0.107	0.004	0.112
QcMetrics-class	0.196	0.008	0.206
psm	4.584	0.419	5.002
qcReport-methods	3.256	1.467	4.576