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This page was generated on 2024-02-20 13:14:57 -0500 (Tue, 20 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
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Package 425/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusOV 1.25.1  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-02-19 14:10:08 -0500 (Mon, 19 Feb 2024)
git_url: https://git.bioconductor.org/packages/consensusOV
git_branch: devel
git_last_commit: 0ce992b
git_last_commit_date: 2024-02-05 14:19:12 -0500 (Mon, 05 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for consensusOV on nebbiolo1


To the developers/maintainers of the consensusOV package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/consensusOV.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: consensusOV
Version: 1.25.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:consensusOV.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings consensusOV_1.25.1.tar.gz
StartedAt: 2024-02-19 21:14:13 -0500 (Mon, 19 Feb 2024)
EndedAt: 2024-02-19 21:21:17 -0500 (Mon, 19 Feb 2024)
EllapsedTime: 424.2 seconds
RetCode: 0
Status:   OK  
CheckDir: consensusOV.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:consensusOV.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings consensusOV_1.25.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/consensusOV.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘consensusOV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘consensusOV’ version ‘1.25.1’
* 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 ‘consensusOV’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
 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 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
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
get.consensus.subtypes 78.191  0.352  78.545
* 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

consensusOV.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘consensusOV’ ...
** using staged installation
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
** R
** data
*** moving datasets to lazyload DB
** 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 (consensusOV)

Tests output


Example timings

consensusOV.Rcheck/consensusOV-Ex.timings

nameusersystemelapsed
get.bentink.subtypes1.8550.1602.018
get.consensus.subtypes78.191 0.35278.545
get.hao.subtypes0.0520.0040.057
get.helland.subtypes0.0360.0100.047
get.konecny.subtypes0.0760.0040.079
get.subtypes0.0950.0000.095
get.verhaak.subtypes0.0690.0040.073