Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 644/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnMCB 1.18.0  (landing page)
Xin Yu
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/EnMCB
git_branch: RELEASE_3_20
git_last_commit: 8348d44
git_last_commit_date: 2024-10-29 10:42:27 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for EnMCB on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: EnMCB
Version: 1.18.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EnMCB_1.18.0.tar.gz
StartedAt: 2024-11-20 07:32:57 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 07:36:10 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 193.3 seconds
RetCode: 0
Status:   OK  
CheckDir: EnMCB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EnMCB_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EnMCB.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnMCB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnMCB’ version ‘1.18.0’
* 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 loading without being on the library search path ... 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            17.086  0.064  17.185
ensemble_model          13.809  0.087  13.198
ensemble_prediction     12.584  0.076  11.957
pre_process_methylation  8.219  0.111   8.356
fast_roc_calculation     6.290  0.076   6.378
IdentifyMCB              5.651  0.100   5.759
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/EnMCB.Rcheck/00check.log’
for details.


Installation output

EnMCB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL EnMCB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  9.832   0.567  10.320 

Example timings

EnMCB.Rcheck/EnMCB-Ex.timings

nameusersystemelapsed
CompareMCB0.0280.0000.029
DiffMCB0.1790.0080.187
IdentifyMCB5.6510.1005.759
IdentifyMCB_parallel4.7020.0964.806
create_demo0.9510.0120.965
draw_survival_curve2.1920.1042.324
ensemble_model13.809 0.08713.198
ensemble_prediction12.584 0.07611.957
fast_roc_calculation6.2900.0766.378
metricMCB0.4890.0280.517
metricMCB.cv17.086 0.06417.185
multi_coxph0.0400.0040.044
pre_process_methylation8.2190.1118.356
univ_coxph0.1580.0000.158