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CHECK report for TCGAWorkflowData on malbec2

This page was generated on 2021-01-18 15:58:40 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE TCGAWorkflowData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 360/385HostnameOS / ArchINSTALLBUILDCHECK
TCGAWorkflowData 1.15.0
Tiago Chedraoui Silva
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/TCGAWorkflowData
Branch: master
Last Commit: c1b3065
Last Changed Date: 2020-10-27 10:22:55 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS 

Summary

Package: TCGAWorkflowData
Version: 1.15.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.15.0.tar.gz
StartedAt: 2021-01-18 12:50:34 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 12:58:00 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 446.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: TCGAWorkflowData.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/TCGAWorkflowData.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘1.15.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 39.333  0.332  39.665
GBMmut           15.283  0.140  15.422
tmp.biogrid      13.695  0.044  13.740
mut              12.316  0.040  12.356
LGGmut           12.184  0.064  12.248
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’
for details.



Installation output

TCGAWorkflowData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL TCGAWorkflowData
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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 Under development (unstable) (2021-01-05 r79797) -- "Unsuffered Consequences"
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 
 43.517   0.667  44.168 

Example timings

TCGAWorkflowData.Rcheck/TCGAWorkflowData-Ex.timings

nameusersystemelapsed
GBMmut15.283 0.14015.422
LGGmut12.184 0.06412.248
TCGAWorkflowData39.333 0.33239.665
cnvMatrix0.0030.0040.007
exp0.5350.0120.548
exp.elmer0.5530.0000.553
gbm.exp0.4070.0120.419
gbm.samples0.5300.0080.538
genes0.1880.0000.188
genes_GR0.1940.0000.194
gistic.allbygene0.0070.0000.007
gistic.thresholedbygene0.0070.0000.007
histone.marks1.5930.0361.629
lgg.exp0.4180.0040.421
lgg.samples0.5430.0120.554
markersMatrix3.2200.0363.256
met0.8170.0080.824
met.elmer0.5730.0000.573
mut12.316 0.04012.356
tmp.biogrid13.695 0.04413.740