Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 759/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
funtooNorm 1.30.0 (landing page) Kathleen Klein
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.30.0 |
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_1.30.0.tar.gz |
StartedAt: 2024-11-19 22:13:47 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 22:23:03 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 555.7 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_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/funtooNorm.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘funtooNorm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘funtooNorm’ version ‘1.30.0’ * 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 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 funtooNorm 18.337 0.928 19.518 getSnpM 15.972 0.628 16.668 getNormM 15.243 0.713 16.109 getNormBeta 15.168 0.766 16.009 plotValidationGraph 15.323 0.597 15.963 fromRGChannelSet 9.937 0.575 10.615 * 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-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘funtooNorm’ ... ** 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 | 0.001 | 0.000 | 0.002 | |
agreement | 0.000 | 0.000 | 0.001 | |
fromRGChannelSet | 9.937 | 0.575 | 10.615 | |
funtooNorm | 18.337 | 0.928 | 19.518 | |
getGRanges | 4.607 | 0.247 | 4.863 | |
getNormBeta | 15.168 | 0.766 | 16.009 | |
getNormM | 15.243 | 0.713 | 16.109 | |
getRawBeta | 3.915 | 0.284 | 4.222 | |
getSnpM | 15.972 | 0.628 | 16.668 | |
plotValidationGraph | 15.323 | 0.597 | 15.963 | |
show-SampleSet-method | 3.190 | 0.170 | 3.373 | |