Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-12 17:38 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 801/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneClassifiers 1.28.0  (landing page)
R Kuiper
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/geneClassifiers
git_branch: RELEASE_3_19
git_last_commit: b5d8c4d
git_last_commit_date: 2024-04-30 10:56:16 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for geneClassifiers on nebbiolo1

To the developers/maintainers of the geneClassifiers package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geneClassifiers.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.

raw results


Summary

Package: geneClassifiers
Version: 1.28.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:geneClassifiers.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings geneClassifiers_1.28.0.tar.gz
StartedAt: 2024-07-10 23:17:00 -0400 (Wed, 10 Jul 2024)
EndedAt: 2024-07-10 23:17:36 -0400 (Wed, 10 Jul 2024)
EllapsedTime: 35.1 seconds
RetCode: 0
Status:   OK  
CheckDir: geneClassifiers.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:geneClassifiers.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings geneClassifiers_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/geneClassifiers.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘geneClassifiers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneClassifiers’ version ‘1.28.0’
* 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 ‘geneClassifiers’ 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 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

geneClassifiers.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL geneClassifiers
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘geneClassifiers’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (geneClassifiers)

Tests output

geneClassifiers.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: x86_64-pc-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(geneClassifiers)
> 
> test_check("geneClassifiers")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 191 ]
> 
> proc.time()
   user  system elapsed 
  2.796   0.116   2.902 

Example timings

geneClassifiers.Rcheck/geneClassifiers-Ex.timings

nameusersystemelapsed
bracket-methods0.0800.0040.084
dim-methods0.0110.0000.011
getBatchCorrection-methods0.2250.0070.233
getCitations-methods0.0010.0010.001
getClassifications-methods0.0180.0000.018
getClassifier-methods0.0020.0000.002
getDecisionBoundaries-methods0.0010.0000.001
getDescription-methods0.0010.0000.001
getEventChain-methods0.0020.0000.002
getIntercept-methods0.0010.0000.002
getMeans-methods0.0030.0000.003
getName-methods0.0010.0000.002
getNormalizationMethod-methods0.0220.0040.027
getProbeNames-methods0.0000.0020.002
getScores-methods0.0180.0030.022
getSds-methods0.0010.0020.003
getTargetValue-methods0.0070.0010.009
getTrainingData-methods0.0310.0000.031
getWeightingType-methods0.0150.0000.015
getWeights-methods0.0010.0010.003
runClassifier-methods0.0160.0020.018
setNormalizationMethod-methods0.0150.0030.018
showClassifierList-methods0.0150.0030.019