Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-03 11:38:19 -0400 (Fri, 03 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 628/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EnMCB 1.17.0 (landing page) Xin Yu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the EnMCB package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EnMCB.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: EnMCB |
Version: 1.17.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EnMCB_1.17.0.tar.gz |
StartedAt: 2024-05-02 03:48:59 -0400 (Thu, 02 May 2024) |
EndedAt: 2024-05-02 03:55:00 -0400 (Thu, 02 May 2024) |
EllapsedTime: 361.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EnMCB.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EnMCB_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EnMCB.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EnMCB/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EnMCB’ version ‘1.17.0’ * 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 ‘EnMCB’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 4.9Mb * 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 ... 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 metricMCB.cv 24.433 1.121 30.839 pre_process_methylation 11.215 2.911 17.159 ensemble_model 11.147 0.257 13.766 ensemble_prediction 10.652 0.289 13.204 IdentifyMCB 8.894 0.187 10.935 fast_roc_calculation 8.215 0.496 10.688 IdentifyMCB_parallel 8.321 0.135 10.209 draw_survival_curve 4.561 0.247 5.890 * 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-3.20-bioc/meat/EnMCB.Rcheck/00check.log’ for details.
EnMCB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EnMCB ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘EnMCB’ ... ** 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 (EnMCB)
EnMCB.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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(EnMCB) > > test_check("EnMCB") Start calculating the correlation, this may take a while... (or you can try to use IdentifyMCB_parallel function instead) | | | 0% | |################## | 25% | |################################### | 50% | |#################################################### | 75% | |######################################################################| 100% Now gathering the results, please wait ... Statistics ( 4 MCBs in total): chr2 : total MCBs: 1 Mean Length: 167 (Range: 167 167 ) chr6 : total MCBs: 1 Mean Length: 129 (Range: 129 129 ) chr8 : total MCBs: 2 Mean Length: 303.5 (Range: 181 426 ) [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 14.916 0.700 18.750
EnMCB.Rcheck/EnMCB-Ex.timings
name | user | system | elapsed | |
CompareMCB | 0.049 | 0.005 | 0.065 | |
DiffMCB | 0.336 | 0.014 | 0.428 | |
IdentifyMCB | 8.894 | 0.187 | 10.935 | |
IdentifyMCB_parallel | 8.321 | 0.135 | 10.209 | |
create_demo | 0.559 | 0.059 | 0.748 | |
draw_survival_curve | 4.561 | 0.247 | 5.890 | |
ensemble_model | 11.147 | 0.257 | 13.766 | |
ensemble_prediction | 10.652 | 0.289 | 13.204 | |
fast_roc_calculation | 8.215 | 0.496 | 10.688 | |
metricMCB | 0.792 | 0.051 | 1.024 | |
metricMCB.cv | 24.433 | 1.121 | 30.839 | |
multi_coxph | 0.108 | 0.017 | 0.146 | |
pre_process_methylation | 11.215 | 2.911 | 17.159 | |
univ_coxph | 0.236 | 0.010 | 0.302 | |