Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:29 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 128/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
basecallQC 1.28.0 (landing page) Thomas Carroll
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the basecallQC package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: basecallQC |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basecallQC_1.28.0.tar.gz |
StartedAt: 2024-05-06 19:47:01 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 19:49:27 -0400 (Mon, 06 May 2024) |
EllapsedTime: 145.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: basecallQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basecallQC_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/basecallQC.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘basecallQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘basecallQC’ version ‘1.28.0’ * 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 code 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 ... NOTE checkRd: (-1) basecallQC.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) basecallQC.Rd:40-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) basecallQC.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) basecallQC.Rd:45-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) basecallQC.Rd:47-48: Lost braces in \itemize; meant \describe ? checkRd: (-1) basecallQC.Rd:49-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) basecallQC.Rd:51-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) BCL2FastQparams.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) BCL2FastQparams.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) BCL2FastQparams.Rd:41-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) interOpsReport.Rd:32-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) interOpsReport.Rd:34-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) interOpsReport.Rd:38-41: Lost braces in \itemize; meant \describe ? * 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 ... 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 ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/basecallQC.Rcheck/00check.log’ for details.
basecallQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basecallQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 47 | SKIP 0 | PASS 5 ] [ FAIL 0 | WARN 47 | SKIP 0 | PASS 5 ] > > proc.time() user system elapsed 8.429 0.212 8.651
basecallQC.Rcheck/basecallQC-Ex.timings
name | user | system | elapsed | |
BCL2FastQparams | 0.084 | 0.007 | 0.090 | |
baseCallMetrics | 1.502 | 0.012 | 1.514 | |
basecallQC | 1.657 | 0.008 | 1.666 | |
createBCLcommand | 0.069 | 0.001 | 0.069 | |
createBasemasks | 0.066 | 0.000 | 0.067 | |
demultiplexMetrics | 0.015 | 0.001 | 0.015 | |
demuxBarplot | 1.211 | 0.005 | 1.215 | |
demuxBoxplot | 1.159 | 0.005 | 1.163 | |
indexlengths | 0.007 | 0.001 | 0.007 | |
interOpsReport | 0.006 | 0.000 | 0.005 | |
makeFQTable | 1.291 | 0.005 | 1.297 | |
passFilterBar | 1.292 | 0.003 | 1.296 | |
passFilterBoxplot | 1.314 | 0.004 | 1.317 | |
passFilterTileplot | 1.369 | 0.005 | 1.385 | |
readlengths | 0.009 | 0.001 | 0.009 | |
reportBCL | 2.184 | 0.062 | 2.287 | |
summaryConvStatsTable | 1.385 | 0.004 | 1.389 | |
summaryDemuxTable | 1.703 | 0.019 | 1.726 | |
validateBCLSheet | 0.019 | 0.001 | 0.019 | |