JiaHong Fong
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/abseqR |
| Branch: RELEASE_3_8 |
| Last Commit: b96ae63 |
| Last Changed Date: 2018-10-30 11:42:11 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:53 -0400 (Sat, 13 Apr 2019).
| Package 9/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| abseqR 1.0.0 JiaHong Fong
| malbec1 | Linux (Ubuntu 16.04.6 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: abseqR |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:abseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings abseqR_1.0.0.tar.gz |
| StartedAt: 2019-04-13 00:23:52 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 00:28:05 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 252.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: abseqR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:abseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings abseqR_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/abseqR.Rcheck' * using R version 3.5.3 (2019-03-11) * 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 '1.0.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ** 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-3.8-bioc/meat/abseqR.Rcheck/00check.log' for details.
abseqR.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/abseqR_1.0.0.tar.gz && rm -rf abseqR.buildbin-libdir && mkdir abseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=abseqR.buildbin-libdir abseqR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL abseqR_1.0.0.zip && rm abseqR_1.0.0.tar.gz abseqR_1.0.0.zip
###
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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install for i386
* installing *source* package 'abseqR' ...
** 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
In R CMD INSTALL
install for x64
* installing *source* package 'abseqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'abseqR' as abseqR_1.0.0.zip
* DONE (abseqR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'abseqR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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abseqR.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 FAILED: 0
>
> proc.time()
user system elapsed
34.71 5.50 40.85
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abseqR.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 FAILED: 0
>
> proc.time()
user system elapsed
35.67 4.84 41.23
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abseqR.Rcheck/examples_i386/abseqR-Ex.timings
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abseqR.Rcheck/examples_x64/abseqR-Ex.timings
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