Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:35 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the basecallQC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basecallQC.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. |
Package 118/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
basecallQC 1.16.0 (landing page) Thomas Carroll
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: basecallQC |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings basecallQC_1.16.0.tar.gz |
StartedAt: 2021-10-14 08:56:02 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:01:38 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 336.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: basecallQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings basecallQC_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/basecallQC.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 ‘basecallQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘basecallQC’ version ‘1.16.0’ * 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 ‘basecallQC’ 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 ... OK * 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 (user + system) or elapsed time > 5s user system elapsed reportBCL 7.329 0.185 7.529 baseCallMetrics 5.633 0.339 5.975 demuxBoxplot 5.569 0.192 5.761 basecallQC 4.851 0.236 5.088 * 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: OK
basecallQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL basecallQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘basecallQC’ ... ** 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 (basecallQC)
basecallQC.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(basecallQC) Loading required package: rmarkdown Loading required package: knitr Loading required package: prettydoc Loading required package: yaml > > test_check("basecallQC") [ FAIL 0 | WARN 13 | SKIP 0 | PASS 5 ] > > proc.time() user system elapsed 20.046 0.657 20.692
basecallQC.Rcheck/basecallQC-Ex.timings
name | user | system | elapsed | |
BCL2FastQparams | 0.158 | 0.032 | 0.191 | |
baseCallMetrics | 5.633 | 0.339 | 5.975 | |
basecallQC | 4.851 | 0.236 | 5.088 | |
createBCLcommand | 0.460 | 0.012 | 0.472 | |
createBasemasks | 0.456 | 0.004 | 0.460 | |
demultiplexMetrics | 0.069 | 0.007 | 0.077 | |
demuxBarplot | 4.613 | 0.100 | 4.713 | |
demuxBoxplot | 5.569 | 0.192 | 5.761 | |
indexlengths | 0.032 | 0.000 | 0.032 | |
interOpsReport | 0.034 | 0.000 | 0.034 | |
makeFQTable | 4.643 | 0.064 | 4.706 | |
passFilterBar | 4.681 | 0.079 | 4.762 | |
passFilterBoxplot | 4.532 | 0.080 | 4.614 | |
passFilterTileplot | 4.406 | 0.056 | 4.463 | |
readlengths | 0.028 | 0.000 | 0.028 | |
reportBCL | 7.329 | 0.185 | 7.529 | |
summaryConvStatsTable | 4.592 | 0.028 | 4.620 | |
summaryDemuxTable | 4.664 | 0.012 | 4.676 | |
validateBCLSheet | 0.093 | 0.004 | 0.097 | |