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This page was generated on 2024-04-18 11:32:08 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
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 410/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
coMethDMR 1.6.0 (landing page) Fernanda Veitzman
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the coMethDMR 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: coMethDMR |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMethDMR_1.6.0.tar.gz |
StartedAt: 2024-04-17 09:48:18 -0400 (Wed, 17 Apr 2024) |
EndedAt: 2024-04-17 10:02:08 -0400 (Wed, 17 Apr 2024) |
EllapsedTime: 829.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: coMethDMR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMethDMR_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/coMethDMR.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * 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 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘coMethDMR/DESCRIPTION’ ... OK * this is package ‘coMethDMR’ version ‘1.6.0’ * package encoding: UTF-8 * 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 ‘coMethDMR’ 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 startup messages can be suppressed ... 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 ... NOTE File ‘coMethDMR/R/zzz.R’: .onLoad calls: packageStartupMessage("Checking for cached SeSAMe data.") packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.") See section ‘Good practice’ in '?.onAttach'. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed CoMethSingleRegion 47.043 1.322 54.167 lmmTest 38.685 1.027 44.256 SplitCpGDFbyRegion 27.504 0.807 31.652 CpGsInfoOneRegion 26.340 0.814 30.509 lmmTestAllRegions 23.397 0.842 26.814 GetCpGsInRegion 19.667 0.668 22.861 AnnotateResults 17.442 0.589 18.434 CoMethAllRegions 16.521 0.491 18.309 CloseBySingleRegion 11.595 0.907 13.927 CreateOutputDF 12.211 0.280 13.978 OrderCpGsByLocation 11.203 0.260 12.598 CpGsInfoAllRegions 10.687 0.349 12.132 ImportSesameData 7.968 0.229 9.658 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/coMethDMR.Rcheck/00check.log’ for details.
coMethDMR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL coMethDMR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘coMethDMR’ ... ** using staged installation ** R ** data ** 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 (coMethDMR)
coMethDMR.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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(coMethDMR) Checking for cached SeSAMe data. > > test_check("coMethDMR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ] > > proc.time() user system elapsed 82.269 3.326 91.982
coMethDMR.Rcheck/coMethDMR-Ex.timings
name | user | system | elapsed | |
AnnotateResults | 17.442 | 0.589 | 18.434 | |
CloseBySingleRegion | 11.595 | 0.907 | 13.927 | |
CoMethAllRegions | 16.521 | 0.491 | 18.309 | |
CoMethSingleRegion | 47.043 | 1.322 | 54.167 | |
CpGsInfoAllRegions | 10.687 | 0.349 | 12.132 | |
CpGsInfoOneRegion | 26.340 | 0.814 | 30.509 | |
CreateOutputDF | 12.211 | 0.280 | 13.978 | |
CreateParallelWorkers | 1.930 | 0.048 | 1.999 | |
CreateRdrop | 0.004 | 0.007 | 0.012 | |
FindComethylatedRegions | 0.019 | 0.004 | 0.024 | |
GetCpGsInRegion | 19.667 | 0.668 | 22.861 | |
GetResiduals | 0.311 | 0.009 | 0.326 | |
ImportSesameData | 7.968 | 0.229 | 9.658 | |
MarkComethylatedCpGs | 0.005 | 0.002 | 0.006 | |
MarkMissing | 0.004 | 0.001 | 0.005 | |
NameRegion | 0.001 | 0.001 | 0.001 | |
OrderCpGsByLocation | 11.203 | 0.260 | 12.598 | |
RegionsToRanges | 0.013 | 0.000 | 0.013 | |
SplitCpGDFbyRegion | 27.504 | 0.807 | 31.652 | |
WriteCloseByAllRegions | 0.041 | 0.001 | 0.042 | |
lmmTest | 38.685 | 1.027 | 44.256 | |
lmmTestAllRegions | 23.397 | 0.842 | 26.814 | |