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CHECK report for alevinQC on celaya2

This page was generated on 2020-01-16 13:53:24 -0500 (Thu, 16 Jan 2020).

Package 42/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alevinQC 1.3.0
Charlotte Soneson
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/alevinQC
Branch: master
Last Commit: 53a56cb
Last Changed Date: 2019-10-29 13:43:30 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 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: 1.3.0
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_1.3.0.tar.gz
StartedAt: 2020-01-16 01:37:37 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 01:40:23 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 165.8 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_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/alevinQC.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.0’
* 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 11.7Mb
  sub-directories of 1Mb or more:
    extdata  11.6Mb
* 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
.readAlevinQC_pre0.14: no visible binding for global variable ‘V1’
.readAlevinQC_pre0.14: no visible binding for global variable ‘V2’
.readAlevinQC_pre0.14: no visible binding for global variable ‘CB’
.readAlevinQC_pre0.14: no visible binding for global variable ‘V3’
.readAlevinQC_pre0.14: no visible binding for global variable ‘V4’
.readAlevinQC_pre0.14: no visible binding for global variable ‘V5’
.readAlevinQC_pre0.14: no visible binding for global variable
  ‘inFirstWhiteList’
.readAlevinQC_pre0.14: no visible binding for global variable
  ‘inFinalWhiteList’
.readAlevinQC_v0.14: no visible binding for global variable ‘V1’
.readAlevinQC_v0.14: no visible binding for global variable ‘V2’
.readAlevinQC_v0.14: no visible binding for global variable ‘CB’
.readAlevinQC_v0.14: no visible binding for global variable
  ‘MappingRate’
.readAlevinQC_v0.14: no visible binding for global variable
  ‘CorrectedReads’
.readAlevinQC_v0.14: no visible binding for global variable ‘DedupRate’
.readAlevinQC_v0.14: no visible binding for global variable
  ‘NumGenesOverMean’
.readAlevinQC_v0.14: no visible binding for global variable
  ‘MappedReads’
.readAlevinQC_v0.14: no visible binding for global variable
  ‘DeduplicatedReads’
.readAlevinQC_v0.14: no visible binding for global variable
  ‘NumGenesExpressed’
.readAlevinQC_v0.14: no visible binding for global variable ‘ranking’
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’
Undefined global functions or variables:
  CB CorrectedReads DedupRate DeduplicatedReads MappedReads MappingRate
  NumGenesExpressed NumGenesOverMean 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 (user + system) or elapsed time > 5s
                            user system elapsed
alevinQCReport            14.098  1.527  15.904
plotAlevinKneeRaw          7.305  2.354   9.671
plotAlevinQuantPairs       6.531  1.466   8.006
plotAlevinBarcodeCollapse  6.253  1.310   7.675
* 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-3.11-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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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: 40 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 43.706   8.696  53.165 

Example timings

alevinQC.Rcheck/alevinQC-Ex.timings

nameusersystemelapsed
alevinQCReport14.098 1.52715.904
alevinQCShiny0.7000.0720.803
checkAlevinInputFiles0.0030.0010.004
plotAlevinBarcodeCollapse6.2531.3107.675
plotAlevinKneeNbrGenes3.2211.3834.607
plotAlevinKneeRaw7.3052.3549.671
plotAlevinQuant2.3390.2152.559
plotAlevinQuantPairs6.5311.4668.006
readAlevinQC0.7610.0730.834