Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:54:20 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE abseqR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 9/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
abseqR 1.6.0 JiaHong Fong
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: abseqR |
Version: 1.6.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:abseqR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings abseqR_1.6.0.tar.gz |
StartedAt: 2020-10-16 22:38:39 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 22:41:02 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 142.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: abseqR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:abseqR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings abseqR_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/abseqR.Rcheck’ * using R version 4.0.3 (2020-10-10) * 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 ‘1.6.0’ * 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-3.11-bioc/meat/abseqR.Rcheck/00check.log’ for details.
abseqR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL abseqR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-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)
abseqR.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 30 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ] > > proc.time() user system elapsed 45.283 0.445 45.752
abseqR.Rcheck/abseqR-Ex.timings
name | user | system | elapsed | |
AbSeqCRep-class | 0.627 | 0.140 | 0.928 | |
AbSeqRep-class | 0.027 | 0.016 | 0.044 | |
abseqReport | 0.032 | 0.012 | 0.045 | |
plus-AbSeqCRep-AbSeqCRep-method | 0.032 | 0.012 | 0.046 | |
plus-AbSeqCRep-AbSeqRep-method | 0.031 | 0.016 | 0.049 | |
plus-AbSeqRep-AbSeqCRep-method | 0.049 | 0.020 | 0.069 | |
plus-AbSeqRep-AbSeqRep-method | 0.054 | 0.016 | 0.070 | |
report | 0.036 | 0.028 | 0.066 | |