Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
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 1283/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
missMethyl 1.40.0 (landing page) Belinda Phipson
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the missMethyl package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/missMethyl.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: missMethyl |
Version: 1.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings missMethyl_1.40.0.tar.gz |
StartedAt: 2024-11-09 07:22:35 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 07:34:51 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 736.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: missMethyl.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings missMethyl_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/missMethyl.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘missMethyl/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘missMethyl’ version ‘1.40.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘missMethyl’ 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 ... WARNING '::' or ':::' import not declared from: ‘dplyr’ Package in Depends field not imported from: ‘IlluminaHumanMethylationEPICv2anno.20a1.hg38’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE goregion: no visible global function definition for ‘seqlevelsStyle<-’ Undefined global functions or variables: seqlevelsStyle<- * 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 RUVadj 10.670 0.271 10.942 topRUV 9.009 0.307 9.315 RUVfit 8.950 0.309 9.258 SWAN 6.982 0.598 7.580 getAdj 6.430 0.348 6.778 topGSA 6.071 0.223 6.301 * 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/missMethyl.Rcheck/00check.log’ for details.
missMethyl.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL missMethyl ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘missMethyl’ ... ** 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 (missMethyl)
missMethyl.Rcheck/missMethyl-Ex.timings
name | user | system | elapsed | |
RUVadj | 10.670 | 0.271 | 10.942 | |
RUVfit | 8.950 | 0.309 | 9.258 | |
SWAN | 6.982 | 0.598 | 7.580 | |
contrasts.varFit | 0.012 | 0.001 | 0.013 | |
densityByProbeType | 3.109 | 0.302 | 3.412 | |
getAdj | 6.430 | 0.348 | 6.778 | |
getINCs | 0.057 | 0.002 | 0.060 | |
getLeveneResiduals | 0.003 | 0.000 | 0.003 | |
getMappedEntrezIDs | 0 | 0 | 0 | |
gometh | 0 | 0 | 0 | |
goregion | 0.000 | 0.001 | 0.001 | |
gsameth | 0 | 0 | 0 | |
gsaregion | 0 | 0 | 0 | |
gsaseq | 0 | 0 | 0 | |
topGSA | 6.071 | 0.223 | 6.301 | |
topRUV | 9.009 | 0.307 | 9.315 | |
topVar | 0.003 | 0.000 | 0.003 | |
varFit | 0.003 | 0.000 | 0.003 | |