Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:28 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the EnMCB package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 546/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EnMCB 1.2.2 (landing page) Xin Yu
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: EnMCB |
Version: 1.2.2 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings EnMCB_1.2.2.tar.gz |
StartedAt: 2021-05-06 01:14:43 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 01:21:56 -0400 (Thu, 06 May 2021) |
EllapsedTime: 432.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: EnMCB.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings EnMCB_1.2.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/EnMCB.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (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 ‘1.2.2’ * 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 ... 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 ... NOTE auc_cal_cv_tvt: no visible binding for global variable ‘survival’ Undefined global functions or variables: survival * 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 ... WARNING Found the following significant warnings: Warning: 'survConcordance.fit' is deprecated. Warning: 'survConcordance.fit' is deprecated. Warning: 'survConcordance.fit' is deprecated. Warning: 'survConcordance.fit' is deprecated. Warning: 'survConcordance.fit' is deprecated. Warning: 'survConcordance.fit' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed IdentifyMCB 20.732 0.592 21.928 pre_process_methylation 9.700 0.224 9.942 fast_roc_calculation 9.076 0.084 9.172 ensemble_model 7.336 0.168 7.737 ensemble_prediction 6.260 0.024 6.383 * 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 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.12-bioc/meat/EnMCB.Rcheck/00check.log’ for details.
EnMCB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL EnMCB ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘EnMCB’ ... ** using staged installation ** R ** data ** 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 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 35.268 0.928 38.878
EnMCB.Rcheck/EnMCB-Ex.timings
name | user | system | elapsed | |
IdentifyMCB | 20.732 | 0.592 | 21.928 | |
create_demo | 0.380 | 0.032 | 0.415 | |
draw_survival_curve | 2.816 | 0.184 | 3.450 | |
ensemble_model | 7.336 | 0.168 | 7.737 | |
ensemble_prediction | 6.260 | 0.024 | 6.383 | |
fast_roc_calculation | 9.076 | 0.084 | 9.172 | |
metricMCB | 0.804 | 0.016 | 0.821 | |
metricMCB.cv | 1.572 | 0.012 | 1.589 | |
pre_process_methylation | 9.700 | 0.224 | 9.942 | |
univ_coxph | 0.168 | 0.020 | 0.200 | |