Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:53 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for EnMCB on merida1


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 597/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnMCB 1.8.2  (landing page)
Xin Yu
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/EnMCB
git_branch: RELEASE_3_15
git_last_commit: 82f5dd1
git_last_commit_date: 2022-06-08 09:54:06 -0400 (Wed, 08 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: EnMCB
Version: 1.8.2
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_1.8.2.tar.gz
StartedAt: 2022-10-19 02:02:03 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 02:06:45 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 282.1 seconds
RetCode: 0
Status:   OK  
CheckDir: EnMCB.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.8.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/EnMCB.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.8.2’
* 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
DiffMCB: no visible binding for global variable ‘AdjustedPvalues’
Undefined global functions or variables:
  AdjustedPvalues
* 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
IdentifyMCB             29.493  0.668  30.220
metricMCB.cv            20.165  2.402  22.591
pre_process_methylation  9.085  2.717  11.819
ensemble_model          10.526  0.450  10.999
ensemble_prediction      8.674  0.266   8.951
fast_roc_calculation     7.099  1.110   8.218
* 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-3.15-bioc/meat/EnMCB.Rcheck/00check.log’
for details.



Installation output

EnMCB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EnMCB
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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)

Tests output

EnMCB.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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)
> 
> test_check("EnMCB")
Start calculating the correlation, this may take a while...
(or you can try to use IdentifyMCB_parallel function instead)

  |                                                                            
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  |##################                                                    |  25%
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  |###################################                                   |  50%
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  |####################################################                  |  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 
 33.034   0.875  33.930 

Example timings

EnMCB.Rcheck/EnMCB-Ex.timings

nameusersystemelapsed
CompareMCB0.0460.0030.049
DiffMCB0.1540.0090.162
IdentifyMCB29.493 0.66830.220
create_demo0.6080.0470.658
draw_survival_curve3.2620.2263.502
ensemble_model10.526 0.45010.999
ensemble_prediction8.6740.2668.951
fast_roc_calculation7.0991.1108.218
metricMCB0.7720.0100.782
metricMCB.cv20.165 2.40222.591
multi_coxph0.0680.0110.079
pre_process_methylation 9.085 2.71711.819
univ_coxph0.2440.0120.256