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CHECK report for TCGAWorkflowData on malbec1

This page was generated on 2020-04-14 17:46:26 -0400 (Tue, 14 Apr 2020).

Package 360/384HostnameOS / ArchINSTALLBUILDCHECK
TCGAWorkflowData 1.10.0
Tiago Chedraoui Silva
Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/TCGAWorkflowData
Branch: RELEASE_3_10
Last Commit: 41c09af
Last Changed Date: 2019-10-29 13:29:49 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: TCGAWorkflowData
Version: 1.10.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.10.0.tar.gz
StartedAt: 2020-04-14 13:43:15 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 13:50:45 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 450.1 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-3.10-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TCGAWorkflowData_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/TCGAWorkflowData.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.0’
* 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 or elapsed time > 5s
                   user system elapsed
TCGAWorkflowData 38.504  0.320  38.854
GBMmut           14.924  0.120  15.060
tmp.biogrid      13.088  0.076  13.171
LGGmut           12.364  0.048  12.420
mut              12.024  0.056  12.091
* 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-3.10-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’
for details.



Installation output

TCGAWorkflowData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL TCGAWorkflowData
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 47.552   0.816  48.411 

Example timings

TCGAWorkflowData.Rcheck/TCGAWorkflowData-Ex.timings

nameusersystemelapsed
GBMmut14.924 0.12015.060
LGGmut12.364 0.04812.420
TCGAWorkflowData38.504 0.32038.854
cnvMatrix0.0040.0000.007
exp0.5560.0040.561
exp.elmer0.5600.0120.576
gbm.exp0.4160.0040.417
gbm.samples0.5680.0040.572
genes0.1920.0040.195
genes_GR0.1880.0080.197
gistic.allbygene0.0080.0000.007
gistic.thresholedbygene0.0080.0000.007
histone.marks1.5960.0321.630
lgg.exp0.4200.0040.421
lgg.samples0.5600.0040.566
markersMatrix3.1840.0443.232
met0.5560.0120.570
met.elmer0.8280.0200.847
mut12.024 0.05612.091
tmp.biogrid13.088 0.07613.171