Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:34 -0400 (Fri, 15 Oct 2021).

CHECK results for abseqR on nebbiolo1

To the developers/maintainers of the abseqR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/abseqR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 9/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
abseqR 1.10.0  (landing page)
JiaHong Fong
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/abseqR
git_branch: RELEASE_3_13
git_last_commit: 9ad3c88
git_last_commit_date: 2021-05-19 12:39:19 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: abseqR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:abseqR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings abseqR_1.10.0.tar.gz
StartedAt: 2021-10-14 08:49:31 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 08:51:09 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 97.9 seconds
RetCode: 0
Status:   OK  
CheckDir: abseqR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:abseqR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings abseqR_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/abseqR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘abseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘abseqR’ version ‘1.10.0’
* 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 ‘abseqR’ 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.aminoAcidBar: no visible binding for global variable ‘position’
.aminoAcidBar: no visible binding for global variable ‘proportion’
.aminoAcidBar: no visible binding for global variable ‘aa’
.boxPlot: no visible binding for global variable ‘x’
.boxPlot: no visible binding for global variable ‘y’
.cloneDistHist: no visible binding for global variable ‘prop’
.cloneDistHist: no visible binding for global variable ‘..count..’
.cloneDistMarginal: no visible binding for global variable ‘prop’
.cloneDistMarginal: no visible binding for global variable ‘..scaled..’
.hmFromMatrix: no visible binding for global variable ‘Var2’
.hmFromMatrix: no visible binding for global variable ‘Var1’
.hmFromMatrix: no visible binding for global variable ‘value’
.plotDist: no visible binding for global variable ‘x’
.plotDist: no visible binding for global variable ‘y’
.plotDuplication: no visible binding for global variable ‘x’
.plotDuplication: no visible binding for global variable ‘y’
.plotDuplication: no visible binding for global variable ‘region’
.plotRarefaction: no visible binding for global variable ‘x’
.plotRarefaction: no visible binding for global variable ‘y’
.plotRarefaction: no visible binding for global variable ‘region’
.plotRarefaction: no visible binding for global variable ‘ci’
.plotRarefaction: no visible binding for global variable ‘compound’
.plotRecapture: no visible binding for global variable ‘x’
.plotRecapture: no visible binding for global variable ‘y’
.plotRecapture: no visible binding for global variable ‘region’
.plotRecapture: no visible binding for global variable ‘ci’
.plotRecapture: no visible binding for global variable ‘compound’
.plotSpectratype: no visible binding for global variable ‘percent’
.productivityPlot: no visible binding for global variable ‘Percentage’
.productivityPlot: no visible binding for global variable ‘Reason’
.regionAnalysis: no visible binding for global variable ‘cdr3’
.regionAnalysis: no visible binding for global variable ‘value’
.regionAnalysis: no visible binding for global variable ‘variable’
.scatterPlot: no visible binding for global variable ‘Count.x’
.scatterPlot: no visible binding for global variable ‘Count.y’
.scatterPlotComplex: no visible binding for global variable ‘prop.x’
.scatterPlotComplex: no visible binding for global variable ‘prop.y’
.topNDist: no visible binding for global variable ‘normPerc’
.topNDist: no visible binding for global variable ‘Clonotype’
Undefined global functions or variables:
  ..count.. ..scaled.. Clonotype Count.x Count.y Percentage Reason Var1
  Var2 aa cdr3 ci compound normPerc percent position prop prop.x prop.y
  proportion region value variable x y
* 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
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/abseqR.Rcheck/00check.log’
for details.



Installation output

abseqR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL abseqR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘abseqR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (abseqR)

Tests output

abseqR.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(abseqR)
> 
> test_check("abseqR")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 30 ]
> 
> proc.time()
   user  system elapsed 
 32.120   0.646  32.747 

Example timings

abseqR.Rcheck/abseqR-Ex.timings

nameusersystemelapsed
AbSeqCRep-class0.5420.0390.630
AbSeqRep-class0.0210.0150.037
abseqReport0.0240.0160.040
plus-AbSeqCRep-AbSeqCRep-method0.0150.0240.039
plus-AbSeqCRep-AbSeqRep-method0.0220.0160.039
plus-AbSeqRep-AbSeqCRep-method0.0200.0240.044
plus-AbSeqRep-AbSeqRep-method0.0230.0160.040
report0.0190.0240.045