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CHECK report for TCGAWorkflowData on malbec1

This page was generated on 2018-04-12 12:50:22 -0400 (Thu, 12 Apr 2018).

Package 306/326HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAWorkflowData 1.2.1
Tiago Chedraoui Silva
Snapshot Date: 2018-04-12 07:35:06 -0400 (Thu, 12 Apr 2018)
URL: https://git.bioconductor.org/packages/TCGAWorkflowData
Branch: RELEASE_3_6
Last Commit: c63b85a
Last Changed Date: 2017-12-05 08:25:52 -0400 (Tue, 05 Dec 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: TCGAWorkflowData
Version: 1.2.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCGAWorkflowData_1.2.1.tar.gz
StartedAt: 2018-04-12 10:41:31 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 10:46:18 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 286.9 seconds
RetCode: 0
Status:  OK 
CheckDir: TCGAWorkflowData.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCGAWorkflowData_1.2.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/TCGAWorkflowData.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.1’
* 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 76.8Mb
  sub-directories of 1Mb or more:
    data  76.1Mb
* 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 loading without being on the library search path ... 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 data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
TCGAWorkflowData 36.916  0.304  37.246
GBMmut           15.076  0.092  15.180
LGGmut           13.144  0.032  13.186
tmp.biogrid      12.652  0.012  12.670
mut              10.940  0.048  10.993
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.6-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’
for details.



Installation output

TCGAWorkflowData.Rcheck/00install.out

* installing *source* package ‘TCGAWorkflowData’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCGAWorkflowData)

Tests output

TCGAWorkflowData.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 38.760   0.520  39.299 

Example timings

TCGAWorkflowData.Rcheck/TCGAWorkflowData-Ex.timings

nameusersystemelapsed
GBMmut15.076 0.09215.180
LGGmut13.144 0.03213.186
TCGAWorkflowData36.916 0.30437.246
cnvMatrix0.0080.0000.007
exp0.5680.0160.587
gbm.exp0.4200.0080.428
gbm.samples0.5760.0120.590
genes0.1960.0040.196
genes_GR0.1960.0080.206
gistic.allbygene0.0080.0000.009
gistic.thresholedbygene0.0080.0000.008
histone.marks1.5920.0401.635
lgg.exp0.6600.0040.666
lgg.samples0.5320.0160.546
markersMatrix2.8280.0242.857
met0.5480.0080.558
mut10.940 0.04810.993
tmp.biogrid12.652 0.01212.670