Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-25 12:06 -0400 (Thu, 25 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4831 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 773/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
funtooNorm 1.33.0 (landing page) Kathleen Klein
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the funtooNorm package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/funtooNorm.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: funtooNorm |
Version: 1.33.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings funtooNorm_1.33.0.tar.gz |
StartedAt: 2025-09-24 19:29:05 -0400 (Wed, 24 Sep 2025) |
EndedAt: 2025-09-24 19:31:52 -0400 (Wed, 24 Sep 2025) |
EllapsedTime: 166.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: funtooNorm.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings funtooNorm_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/funtooNorm.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘funtooNorm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘funtooNorm’ version ‘1.33.0’ * 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 ‘funtooNorm’ can be installed ... OK * checking installed package size ... OK * checking package 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) fromRGChannelSet.Rd:5: Lost braces; missing escapes or markup? 5 | \title{Creates an object of class SampleSet from a RGChannelSet {minfi}} | ^ * 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 ... WARNING Documented arguments not in \usage in Rd file 'show-SampleSet-method.Rd': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘MyEndnoteLibrary.bib’ ‘funtooNorm.Rmd’ ‘funtooNorm.pdf’ ‘validationcurvesPCRlow.jpg’ Files named as vignettes but with no recognized vignette engine: ‘vignettes/funtooNorm.Rmd’ (Is a VignetteBuilder field missing?) * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getSnpM 7.447 0.487 8.513 getNormM 7.437 0.463 8.132 getNormBeta 7.367 0.507 8.088 funtooNorm 7.267 0.467 7.994 plotValidationGraph 5.921 0.321 6.546 fromRGChannelSet 4.922 0.189 5.197 * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/funtooNorm.Rcheck/00check.log’ for details.
funtooNorm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL funtooNorm ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘funtooNorm’ ... ** this is package ‘funtooNorm’ version ‘1.33.0’ ** 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 (funtooNorm)
funtooNorm.Rcheck/funtooNorm-Ex.timings
name | user | system | elapsed | |
SampleSet-class | 0.000 | 0.000 | 0.001 | |
agreement | 0 | 0 | 0 | |
fromRGChannelSet | 4.922 | 0.189 | 5.197 | |
funtooNorm | 7.267 | 0.467 | 7.994 | |
getGRanges | 2.297 | 0.225 | 2.606 | |
getNormBeta | 7.367 | 0.507 | 8.088 | |
getNormM | 7.437 | 0.463 | 8.132 | |
getRawBeta | 2.436 | 0.220 | 2.754 | |
getSnpM | 7.447 | 0.487 | 8.513 | |
plotValidationGraph | 5.921 | 0.321 | 6.546 | |
show-SampleSet-method | 1.557 | 0.178 | 1.788 | |