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CHECK report for qcmetrics on malbec2

This page was generated on 2019-10-16 12:03:31 -0400 (Wed, 16 Oct 2019).

Package 1283/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qcmetrics 1.22.0
Laurent Gatto
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/qcmetrics
Branch: RELEASE_3_9
Last Commit: c10c1d3
Last Changed Date: 2019-05-02 11:53:45 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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: qcmetrics
Version: 1.22.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:qcmetrics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings qcmetrics_1.22.0.tar.gz
StartedAt: 2019-10-16 04:11:19 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:12:28 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 69.3 seconds
RetCode: 0
Status:  OK 
CheckDir: qcmetrics.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:qcmetrics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings qcmetrics_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/qcmetrics.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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 ‘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 : : no visible global function definition for ‘ggplot’
n15qc : : no visible global function definition for ‘aes’
n15qc : : no visible global function definition for
  ‘geom_jitter’
n15qc : : no visible global function definition for
  ‘geom_boxplot’
n15qc : : no visible global function definition for
  ‘geom_hline’
n15qc : : 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 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/qcmetrics.Rcheck/00check.log’
for details.



Installation output

qcmetrics.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL qcmetrics
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output


Example timings

qcmetrics.Rcheck/qcmetrics-Ex.timings

nameusersystemelapsed
QcMetadata-class0.0030.0010.004
QcMetric-class0.0850.0040.090
QcMetrics-class0.2130.0000.229
psm4.3670.1634.535
qcReport-methods2.1360.2424.769