Back to Build/check report for BioC 3.14 experimental data
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This page was generated on 2022-01-19 14:50:25 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
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

CHECK results for TCGAWorkflowData on nebbiolo2


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

raw results

Package 382/408HostnameOS / ArchINSTALLBUILDCHECK
TCGAWorkflowData 1.18.0  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2022-01-19 07:30:01 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/TCGAWorkflowData
git_branch: RELEASE_3_14
git_last_commit: dc85e46
git_last_commit_date: 2021-10-26 12:29:09 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: TCGAWorkflowData
Version: 1.18.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.18.0.tar.gz
StartedAt: 2022-01-19 11:53:16 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 11:58:43 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 326.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TCGAWorkflowData.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/TCGAWorkflowData.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAWorkflowData/DESCRIPTION’ ... OK
* this is package ‘TCGAWorkflowData’ version ‘1.18.0’
* 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 ‘TCGAWorkflowData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 77.5Mb
  sub-directories of 1Mb or more:
    data  77.3Mb
* 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 ... WARNING
Undocumented data sets:
  ‘commonCNV’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
TCGAWorkflowData 27.263  0.524  27.787
GBMmut           11.074  0.156  11.230
tmp.biogrid       8.918  0.132   9.050
LGGmut            8.317  0.068   8.385
mut               8.146  0.100   8.247
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’
for details.



Installation output

TCGAWorkflowData.Rcheck/00install.out

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

Tests output

TCGAWorkflowData.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(TCGAWorkflowData)
> 
> test_check("TCGAWorkflowData")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 31.835   1.093  32.910 

Example timings

TCGAWorkflowData.Rcheck/TCGAWorkflowData-Ex.timings

nameusersystemelapsed
GBMmut11.074 0.15611.230
LGGmut8.3170.0688.385
TCGAWorkflowData27.263 0.52427.787
cnvMatrix0.0010.0040.005
exp0.4010.0280.429
exp.elmer0.4130.0040.417
gbm.exp0.3070.0040.311
gbm.samples0.5860.0280.614
genes0.1320.0040.135
genes_GR0.1330.0040.136
gistic.allbygene0.0050.0000.004
gistic.thresholedbygene0.0000.0050.004
histone.marks0.9870.0551.042
lgg.exp0.3100.0040.314
lgg.samples0.4120.0040.416
markersMatrix2.2820.0642.347
met0.4090.0080.417
met.elmer0.4200.0160.436
mut8.1460.1008.247
tmp.biogrid8.9180.1329.050