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This page was generated on 2021-10-20 12:04:42 -0400 (Wed, 20 Oct 2021).

CHECK results for GDCRNATools on nebbiolo2

To the developers/maintainers of the GDCRNATools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GDCRNATools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 705/2072HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GDCRNATools 1.13.1  (landing page)
Ruidong Li
Snapshot Date: 2021-10-19 14:50:04 -0400 (Tue, 19 Oct 2021)
git_url: https://git.bioconductor.org/packages/GDCRNATools
git_branch: master
git_last_commit: a757328
git_last_commit_date: 2021-08-03 03:15:18 -0400 (Tue, 03 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GDCRNATools
Version: 1.13.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GDCRNATools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GDCRNATools_1.13.1.tar.gz
StartedAt: 2021-10-19 20:08:16 -0400 (Tue, 19 Oct 2021)
EndedAt: 2021-10-19 20:12:37 -0400 (Tue, 19 Oct 2021)
EllapsedTime: 261.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GDCRNATools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GDCRNATools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GDCRNATools_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GDCRNATools.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GDCRNATools/DESCRIPTION’ ... OK
* this is package ‘GDCRNATools’ version ‘1.13.1’
* package encoding: UTF-8
* 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 ‘GDCRNATools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
deAnalysislimma: warning in topTable(fit2, coef = 1, n = Inf): partial
  argument match of 'n' to 'number'
gdcDEAnalysis: warning in topTable(fit2, coef = 1, n = Inf): partial
  argument match of 'n' to 'number'
cleanMirFun: no visible global function definition for ‘read.table’
cleanMirFun: no visible global function definition for ‘aggregate’
downloadClientFun: no visible global function definition for
  ‘download.file’
downloadClientFun: no visible global function definition for ‘unzip’
enrichBarPlotFun: no visible binding for global variable ‘Terms’
enrichBarPlotFun: no visible binding for global variable ‘FDR’
enrichBarPlotFun: no visible binding for global variable ‘Category’
enrichBubblePlotFun: no visible binding for global variable ‘Terms’
enrichBubblePlotFun: no visible binding for global variable
  ‘foldEnrichment’
enrichBubblePlotFun: no visible binding for global variable ‘FDR’
enrichBubblePlotFun: no visible binding for global variable ‘Counts’
gdcBarPlot: no visible binding for global variable ‘Regulation’
gdcClinicalDownload: no visible global function definition for
  ‘read.table’
gdcClinicalDownload: no visible global function definition for
  ‘write.table’
gdcCorPlot: no visible global function definition for ‘cor.test’
gdcDEAnalysis: no visible global function definition for ‘model.matrix’
gdcDEAnalysis: no visible global function definition for ‘p.adjust’
gdcGetURL: no visible global function definition for ‘URLencode’
gdcKMPlot: no visible global function definition for ‘pchisq’
gdcKMPlot: no visible global function definition for ‘qnorm’
gdcRNADownload: no visible global function definition for ‘read.table’
gdcRNADownload: no visible global function definition for ‘write.table’
gdcRNAMerge : <anonymous>: no visible global function definition for
  ‘read.table’
gdcRNAMerge: no visible global function definition for ‘read.table’
gdcRNAMerge : <anonymous>: no visible global function definition for
  ‘read.delim’
gdcRNAMerge: no visible global function definition for ‘read.delim’
hyperTestFun: no visible global function definition for ‘phyper’
kmTestFun: no visible global function definition for ‘pchisq’
kmTestFun: no visible global function definition for ‘qnorm’
manifestDownloadFun: no visible global function definition for
  ‘read.table’
mirCorTestFun: no visible global function definition for ‘cor.test’
multiRegFun: no visible global function definition for ‘cor.test’
Undefined global functions or variables:
  Category Counts FDR Regulation Terms URLencode aggregate cor.test
  download.file foldEnrichment model.matrix p.adjust pchisq phyper
  qnorm read.delim read.table unzip write.table
Consider adding
  importFrom("stats", "aggregate", "cor.test", "model.matrix",
             "p.adjust", "pchisq", "phyper", "qnorm")
  importFrom("utils", "URLencode", "download.file", "read.delim",
             "read.table", "unzip", "write.table")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/GDCRNATools.Rcheck/00check.log’
for details.



Installation output

GDCRNATools.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘GDCRNATools’ ...
** using staged installation
** R
** data
** inst
** 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 (GDCRNATools)

Tests output

GDCRNATools.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(GDCRNATools)


##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
> 
> test_check("GDCRNATools")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 13.539   0.917  16.405 

Example timings

GDCRNATools.Rcheck/GDCRNATools-Ex.timings

nameusersystemelapsed
gdcBarPlot0.2360.0160.252
gdcCEAnalysis1.3620.0801.443
gdcClinicalDownload000
gdcClinicalMerge000
gdcCorPlot0.3690.0040.373
gdcDEAnalysis0.0380.0000.037
gdcDEReport0.0140.0000.013
gdcEnrichAnalysis000
gdcEnrichPlot0.1280.0000.129
gdcExportNetwork0.0090.0000.009
gdcFilterDuplicate0.0880.0032.551
gdcFilterSampleType0.0860.0042.238
gdcHeatmap0.0550.0000.055
gdcKMPlot0.6860.0240.711
gdcMatchSamples0.0020.0000.003
gdcParseMetadata0.0750.0162.209
gdcRNADownload000
gdcRNAMerge0.0760.0082.685
gdcSurvivalAnalysis0.0560.0080.064
gdcVolcanoPlot0.1240.0400.164
gdcVoomNormalization0.0110.0040.014
shinyCorPlot0.0010.0000.001
shinyKMPlot0.0010.0000.000
shinyPathview000