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This page was generated on 2024-02-26 14:01:56 -0500 (Mon, 26 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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 219/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biotmle 1.27.0  (landing page)
Nima Hejazi
Snapshot Date: 2024-02-23 14:00:08 -0500 (Fri, 23 Feb 2024)
git_url: https://git.bioconductor.org/packages/biotmle
git_branch: devel
git_last_commit: e0507a8
git_last_commit_date: 2023-10-24 10:56:59 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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 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 biotmle on kunpeng2


To the developers/maintainers of the biotmle package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biotmle.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: biotmle
Version: 1.27.0
Command: /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:biotmle.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings biotmle_1.27.0.tar.gz
StartedAt: 2024-02-24 04:21:11 -0000 (Sat, 24 Feb 2024)
EndedAt: 2024-02-24 04:25:31 -0000 (Sat, 24 Feb 2024)
EllapsedTime: 260.5 seconds
RetCode: 0
Status:   OK  
CheckDir: biotmle.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:biotmle.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings biotmle_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biotmle.Rcheck’
* using R Under development (unstable) (2024-01-16 r85812)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘biotmle/DESCRIPTION’ ... OK
* this is package ‘biotmle’ version ‘1.27.0’
* 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 ‘biotmle’ 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
biomarkertmle 5.021  0.239   5.275
* 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: OK


Installation output

biotmle.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD INSTALL biotmle
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library’
* installing *source* package ‘biotmle’ ...
** using staged installation
** R
** 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 (biotmle)

Tests output

biotmle.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences"
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(biotmle)
biotmle v1.27.0: Targeted Learning with Moderated Statistics for Biomarker Discovery
> 
> test_check("biotmle")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 23.388   0.696  24.112 

Example timings

biotmle.Rcheck/biotmle-Ex.timings

nameusersystemelapsed
bioTMLE-class1.2410.0281.300
biomarkertmle5.0210.2395.275
heatmap_ic000
modtest_ic1.1950.0361.233
plot.bioTMLE000
volcano_ic000