Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:02 -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: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:abseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings abseqR_1.6.0.tar.gz |
StartedAt: 2020-10-17 01:25:25 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 01:30:42 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 317.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: abseqR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:abseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings abseqR_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/abseqR.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AbSeqCRep-class 0.37 0.03 16.93 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.11-bioc/meat/abseqR.Rcheck/00check.log' for details.
abseqR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/abseqR_1.6.0.tar.gz && rm -rf abseqR.buildbin-libdir && mkdir abseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=abseqR.buildbin-libdir abseqR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL abseqR_1.6.0.zip && rm abseqR_1.6.0.tar.gz abseqR_1.6.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1521k 100 1521k 0 0 18.1M 0 --:--:-- --:--:-- --:--:-- 19.5M install for i386 * installing *source* package 'abseqR' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'abseqR' finding HTML links ... done AbSeqCRep-class html AbSeqRep-class html abseqReport html dot-UTR5Analysis html dot-abundanceAnalysis html dot-abundancePlot html dot-alignQualityHeatMaps html dot-allPrimerNames html dot-aminoAcidBar html dot-aminoAcidPlot html dot-analyzeUpstreamValidity html dot-annotAnalysis html dot-asRepertoireAlignLen html dot-asRepertoireBitscore html dot-asRepertoireChain html dot-asRepertoireDir html dot-asRepertoireList html dot-asRepertoireName html dot-asRepertoirePrimer3 html dot-asRepertoirePrimer5 html dot-asRepertoireQueryStart html dot-asRepertoireSubjectStart html dot-asRepertoireUpstream html dot-boxPlot html dot-calculateDInd html dot-calculateDiversityEstimates html dot-canonicalizeTitle html dot-capitalize html dot-checkVert html dot-cloneDistHist html dot-cloneDistMarginal html dot-clonotypeAnalysis html dot-collateReports html dot-commonPrimerNames html dot-correlationTest html dot-distanceMeasure html dot-diversityAnalysis html dot-emptyPlot html dot-findRepertoires html dot-generateAllSpectratypes html dot-generateDelayedReport html dot-generateReport html dot-getLineTypes html dot-getTotal html dot-hmFromMatrix html dot-inferAnalyzed html dot-loadMatrixFromDF html dot-loadSamplesFromString html dot-pairwiseComparison html dot-plotCirclize html dot-plotDist html dot-plotDiversityCurves html dot-plotDuplication html dot-plotErrorDist html dot-plotIGVErrors html dot-plotIGVUpstreamLenDist html dot-plotIGVUpstreamLenDistDetailed html dot-plotPrimerIGVStatus html dot-plotPrimerIntegrity html dot-plotRarefaction html dot-plotRecapture html dot-plotSamples html dot-plotSpectratype html dot-plotUpstreamLength html dot-plotUpstreamLengthDist html dot-primerAnalysis html dot-prodDistPlot html dot-productivityAnalysis html dot-productivityPlot html dot-readSummary html dot-regionAnalysis html dot-reportLBE html dot-saveAs html dot-scatterPlot html dot-scatterPlotComplex html dot-secretionSignalAnalysis html dot-substituteStringInFile html dot-summarySE html dot-topNDist html dot-vennIntersection html plus-AbSeqCRep-AbSeqCRep-method html plus-AbSeqCRep-AbSeqRep-method html plus-AbSeqRep-AbSeqCRep-method html plus-AbSeqRep-AbSeqRep-method html report html *** 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 install for x64 * installing *source* package 'abseqR' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'abseqR' as abseqR_1.6.0.zip * DONE (abseqR) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'abseqR' successfully unpacked and MD5 sums checked
abseqR.Rcheck/tests_i386/testthat.Rout R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 39.32 5.71 48.64 |
abseqR.Rcheck/tests_x64/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-w64-mingw32/x64 (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 43.53 6.09 59.70 |
abseqR.Rcheck/examples_i386/abseqR-Ex.timings
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abseqR.Rcheck/examples_x64/abseqR-Ex.timings
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