Charlotte Soneson
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/alevinQC |
| Branch: RELEASE_3_10 |
| Last Commit: 8ca336f |
| Last Changed Date: 2019-10-29 13:11:30 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:48:46 -0400 (Wed, 15 Apr 2020).
| Package 42/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| alevinQC 1.2.0 Charlotte Soneson
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: alevinQC |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2020-04-15 00:18:53 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 00:20:59 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 125.8 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/alevinQC.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.0’
* 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 or elapsed time > 5s
user system elapsed
alevinQCReport 11.318 0.763 12.261
plotAlevinKneeRaw 6.635 1.228 7.941
plotAlevinQuantPairs 5.368 0.765 6.182
plotAlevinBarcodeCollapse 4.820 0.712 5.568
* 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-3.10-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/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)
alevinQC.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
35.194 4.400 40.208
alevinQC.Rcheck/alevinQC-Ex.timings
| name | user | system | elapsed | |
| alevinQCReport | 11.318 | 0.763 | 12.261 | |
| alevinQCShiny | 0.726 | 0.044 | 0.774 | |
| checkAlevinInputFiles | 0.003 | 0.001 | 0.003 | |
| plotAlevinBarcodeCollapse | 4.820 | 0.712 | 5.568 | |
| plotAlevinKneeNbrGenes | 2.702 | 0.794 | 3.527 | |
| plotAlevinKneeRaw | 6.635 | 1.228 | 7.941 | |
| plotAlevinQuant | 1.654 | 0.051 | 1.721 | |
| plotAlevinQuantPairs | 5.368 | 0.765 | 6.182 | |
| readAlevinQC | 0.622 | 0.034 | 0.669 | |