Back to Build/check report for BioC 3.14 experimental data
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2021-11-24 18:35:27 -0500 (Wed, 24 Nov 2021).

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: 2021-11-24 08:30:01 -0500 (Wed, 24 Nov 2021)
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 20.04.3 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: 2021-11-24 16:05:01 -0500 (Wed, 24 Nov 2021)
EndedAt: 2021-11-24 16:10:38 -0500 (Wed, 24 Nov 2021)
EllapsedTime: 336.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TCGAWorkflowData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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 33.026  0.532  33.558
GBMmut           11.663  0.748  12.412
tmp.biogrid       9.642  0.007   9.650
mut               9.508  0.128   9.636
LGGmut            9.138  0.040   9.179
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL TCGAWorkflowData
###
##############################################################################
##############################################################################


* 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 
 34.046   1.185  35.212 

Example timings

TCGAWorkflowData.Rcheck/TCGAWorkflowData-Ex.timings

nameusersystemelapsed
GBMmut11.663 0.74812.412
LGGmut9.1380.0409.179
TCGAWorkflowData33.026 0.53233.558
cnvMatrix0.0060.0000.006
exp0.4510.0080.459
exp.elmer0.4540.0080.463
gbm.exp0.3380.0080.347
gbm.samples0.4620.0150.478
genes0.1530.0050.156
genes_GR0.1550.0000.154
gistic.allbygene0.0060.0000.005
gistic.thresholedbygene0.0050.0000.005
histone.marks1.0880.0801.167
lgg.exp0.3420.0120.354
lgg.samples0.4490.0200.469
markersMatrix2.5870.0642.651
met0.4380.0000.437
met.elmer0.4360.0040.440
mut9.5080.1289.636
tmp.biogrid9.6420.0079.650