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CHECK report for alevinQC on celaya2

This page was generated on 2019-10-16 13:04:19 -0400 (Wed, 16 Oct 2019).

Package 42/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alevinQC 1.0.0
Charlotte Soneson
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/alevinQC
Branch: RELEASE_3_9
Last Commit: 59ac8b3
Last Changed Date: 2019-05-02 11:54:14 -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: alevinQC
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:alevinQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings alevinQC_1.0.0.tar.gz
StartedAt: 2019-10-16 00:28:07 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:30:49 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 162.1 seconds
RetCode: 0
Status:  OK 
CheckDir: alevinQC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:alevinQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings alevinQC_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/alevinQC.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alevinQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alevinQC’ version ‘1.0.0’
* 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 ‘alevinQC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   8.1Mb
* 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
plotAlevinBarcodeCollapse: no visible binding for global variable
  ‘inFirstWhiteList’
plotAlevinBarcodeCollapse: no visible binding for global variable
  ‘collapsedFreq’
plotAlevinBarcodeCollapse: no visible binding for global variable
  ‘originalFreq’
plotAlevinKneeNbrGenes: no visible binding for global variable
  ‘inFirstWhiteList’
plotAlevinKneeNbrGenes: no visible binding for global variable
  ‘nbrGenesAboveZero’
plotAlevinKneeNbrGenes: no visible binding for global variable ‘x’
plotAlevinKneeRaw: no visible binding for global variable ‘ranking’
plotAlevinKneeRaw: no visible binding for global variable
  ‘originalFreq’
plotAlevinKneeRaw: no visible binding for global variable
  ‘inFirstWhiteList’
plotAlevinQuant: no visible binding for global variable
  ‘inFirstWhiteList’
plotAlevinQuant: no visible binding for global variable ‘collapsedFreq’
plotAlevinQuant: no visible binding for global variable ‘totalUMICount’
plotAlevinQuant: no visible binding for global variable
  ‘inFinalWhiteList’
plotAlevinQuant: no visible binding for global variable
  ‘nbrGenesAboveZero’
plotAlevinQuantPairs: no visible binding for global variable
  ‘inFirstWhiteList’
plotAlevinQuantPairs: no visible binding for global variable
  ‘inFinalWhiteList’
readAlevinQC: no visible binding for global variable ‘V1’
readAlevinQC: no visible binding for global variable ‘V2’
readAlevinQC: no visible binding for global variable ‘CB’
readAlevinQC: no visible binding for global variable ‘V3’
readAlevinQC: no visible binding for global variable ‘V4’
readAlevinQC: no visible binding for global variable ‘V5’
readAlevinQC: no visible binding for global variable ‘inFirstWhiteList’
readAlevinQC: no visible binding for global variable ‘inFinalWhiteList’
Undefined global functions or variables:
  CB V1 V2 V3 V4 V5 collapsedFreq inFinalWhiteList inFirstWhiteList
  nbrGenesAboveZero originalFreq ranking totalUMICount x
* 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
alevinQCReport            19.269  3.157  22.975
plotAlevinKneeRaw          7.880  2.305  10.211
plotAlevinBarcodeCollapse  5.840  1.748   7.592
plotAlevinQuantPairs       5.783  1.309   7.093
plotAlevinQuant            4.063  1.232   5.300
alevinQCShiny              3.629  1.424   5.063
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/alevinQC.Rcheck/00check.log’
for details.



Installation output

alevinQC.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL alevinQC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘alevinQC’ ...
** using staged installation
** 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 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 (alevinQC)

Tests output

alevinQC.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(alevinQC)
> 
> test_check("alevinQC")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 20 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 28.869   6.918  36.332 

Example timings

alevinQC.Rcheck/alevinQC-Ex.timings

nameusersystemelapsed
alevinQCReport19.269 3.15722.975
alevinQCShiny3.6291.4245.063
checkAlevinInputFiles0.0010.0010.002
plotAlevinBarcodeCollapse5.8401.7487.592
plotAlevinKneeNbrGenes3.0551.4294.492
plotAlevinKneeRaw 7.880 2.30510.211
plotAlevinQuant4.0631.2325.300
plotAlevinQuantPairs5.7831.3097.093
readAlevinQC2.8941.4834.378