Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the EnMCB package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 570/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EnMCB 1.4.1 (landing page) Xin Yu
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: EnMCB |
Version: 1.4.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EnMCB_1.4.1.tar.gz |
StartedAt: 2021-10-14 18:42:54 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:50:47 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 472.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EnMCB.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EnMCB_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/EnMCB.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EnMCB/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EnMCB’ version ‘1.4.1’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 ... 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 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 22.427 2.067 24.543 IdentifyMCB 18.558 0.637 19.211 pre_process_methylation 10.375 3.884 14.309 ensemble_prediction 9.079 0.188 9.272 fast_roc_calculation 8.052 1.085 9.153 ensemble_model 8.305 0.432 8.742 * 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-3.13-bioc/meat/EnMCB.Rcheck/00check.log’ for details.
EnMCB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EnMCB ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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(EnMCB) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > 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 34.554 1.419 35.992
EnMCB.Rcheck/EnMCB-Ex.timings
name | user | system | elapsed | |
IdentifyMCB | 18.558 | 0.637 | 19.211 | |
create_demo | 0.555 | 0.019 | 0.575 | |
draw_survival_curve | 2.316 | 0.281 | 2.605 | |
ensemble_model | 8.305 | 0.432 | 8.742 | |
ensemble_prediction | 9.079 | 0.188 | 9.272 | |
fast_roc_calculation | 8.052 | 1.085 | 9.153 | |
metricMCB | 0.698 | 0.009 | 0.707 | |
metricMCB.cv | 22.427 | 2.067 | 24.543 | |
multi_coxph | 0.063 | 0.006 | 0.069 | |
pre_process_methylation | 10.375 | 3.884 | 14.309 | |
univ_coxph | 0.193 | 0.046 | 0.240 | |