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CHECK report for qcmetrics on merida1

This page was generated on 2019-04-16 11:57:13 -0400 (Tue, 16 Apr 2019).

Package 1221/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qcmetrics 1.20.1
Laurent Gatto
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/qcmetrics
Branch: RELEASE_3_8
Last Commit: b404c75
Last Changed Date: 2019-01-04 13:11:56 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: qcmetrics
Version: 1.20.1
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_1.20.1.tar.gz
StartedAt: 2019-04-16 02:05:55 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:07:01 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 65.5 seconds
RetCode: 0
Status:  OK 
CheckDir: qcmetrics.Rcheck
Warnings: 0

Command output

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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_1.20.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/qcmetrics.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.20.1’
* 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 ... OK
* 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
* 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-3.8-bioc/meat/qcmetrics.Rcheck/00check.log’
for details.



Installation output

qcmetrics.Rcheck/00install.out

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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/3.5/Resources/library’
* installing *source* package ‘qcmetrics’ ...
** 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
* DONE (qcmetrics)

Tests output


Example timings

qcmetrics.Rcheck/qcmetrics-Ex.timings

nameusersystemelapsed
QcMetadata-class0.0030.0010.003
QcMetric-class0.0380.0030.041
QcMetrics-class0.1710.0050.177
psm3.5880.1903.790
qcReport-methods2.5850.7483.244