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This page was generated on 2021-10-23 15:51:47 -0400 (Sat, 23 Oct 2021).

CHECK results for HarmonizedTCGAData on nebbiolo2

To the developers/maintainers of the HarmonizedTCGAData package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 164/408HostnameOS / ArchINSTALLBUILDCHECK
HarmonizedTCGAData 1.15.0  (landing page)
Tianle Ma
Snapshot Date: 2021-10-23 09:30:01 -0400 (Sat, 23 Oct 2021)
git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData
git_branch: master
git_last_commit: 2803d02
git_last_commit_date: 2021-05-19 12:02:20 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HarmonizedTCGAData
Version: 1.15.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:HarmonizedTCGAData.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings HarmonizedTCGAData_1.15.0.tar.gz
StartedAt: 2021-10-23 12:23:24 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 12:25:33 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 129.1 seconds
RetCode: 0
Status:   OK  
CheckDir: HarmonizedTCGAData.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:HarmonizedTCGAData.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings HarmonizedTCGAData_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/HarmonizedTCGAData.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HarmonizedTCGAData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HarmonizedTCGAData’ version ‘1.15.0’
* 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 ‘HarmonizedTCGAData’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
Wall 7.614  0.548   9.219
* 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: OK


Installation output

HarmonizedTCGAData.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL HarmonizedTCGAData
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘HarmonizedTCGAData’ ...
** using staged installation
** 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 (HarmonizedTCGAData)

Tests output

HarmonizedTCGAData.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(HarmonizedTCGAData)
> 
> test_check("HarmonizedTCGAData")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 14.574   0.719  16.094 

Example timings

HarmonizedTCGAData.Rcheck/HarmonizedTCGAData-Ex.timings

nameusersystemelapsed
Wall7.6140.5489.219
project_ids3.4480.1683.954
surv.plot3.1010.0443.540