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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:53:24 -0500 (Thu, 16 Jan 2020).
| Package 42/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| alevinQC 1.3.0 Charlotte Soneson
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| 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 |
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### Running command:
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### /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.
alevinQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL alevinQC ### ############################################################################## ############################################################################## * 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)
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
alevinQC.Rcheck/alevinQC-Ex.timings
| name | user | system | elapsed | |
| alevinQCReport | 14.098 | 1.527 | 15.904 | |
| alevinQCShiny | 0.700 | 0.072 | 0.803 | |
| checkAlevinInputFiles | 0.003 | 0.001 | 0.004 | |
| plotAlevinBarcodeCollapse | 6.253 | 1.310 | 7.675 | |
| plotAlevinKneeNbrGenes | 3.221 | 1.383 | 4.607 | |
| plotAlevinKneeRaw | 7.305 | 2.354 | 9.671 | |
| plotAlevinQuant | 2.339 | 0.215 | 2.559 | |
| plotAlevinQuantPairs | 6.531 | 1.466 | 8.006 | |
| readAlevinQC | 0.761 | 0.073 | 0.834 | |