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This page was generated on 2024-07-12 12:32 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4675
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4391
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4371
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 760/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GDCRNATools 1.25.0  (landing page)
Ruidong Li
Snapshot Date: 2024-07-11 14:00 -0400 (Thu, 11 Jul 2024)
git_url: https://git.bioconductor.org/packages/GDCRNATools
git_branch: devel
git_last_commit: fd0461c
git_last_commit_date: 2024-04-30 11:03:29 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for GDCRNATools on lconway

To the developers/maintainers of the GDCRNATools package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GDCRNATools
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GDCRNATools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GDCRNATools_1.25.0.tar.gz
StartedAt: 2024-07-11 21:09:17 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 21:16:12 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 414.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GDCRNATools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GDCRNATools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GDCRNATools_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GDCRNATools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GDCRNATools/DESCRIPTION’ ... OK
* this is package ‘GDCRNATools’ version ‘1.25.0’
* 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 code 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    3.2Mb    1.6Mb    bzip2
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GDCRNATools.Rcheck/00check.log’
for details.


Installation output

GDCRNATools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GDCRNATools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 15.424   0.990  18.563 

Example timings

GDCRNATools.Rcheck/GDCRNATools-Ex.timings

nameusersystemelapsed
gdcBarPlot0.3980.0180.421
gdcCEAnalysis1.5520.0611.624
gdcClinicalDownload0.0000.0010.001
gdcClinicalMerge0.0000.0000.001
gdcCorPlot0.6350.0230.665
gdcDEAnalysis0.0460.0040.050
gdcDEReport0.0170.0020.019
gdcEnrichAnalysis0.0000.0010.001
gdcEnrichPlot0.2220.0250.249
gdcExportNetwork0.0140.0020.016
gdcFilterDuplicate0.1810.0152.967
gdcFilterSampleType0.1150.0072.630
gdcHeatmap0.0530.0050.059
gdcKMPlot0.5700.0160.591
gdcMatchSamples0.0010.0010.003
gdcParseMetadata0.1220.0072.624
gdcRNADownload0.0000.0000.001
gdcRNAMerge0.1110.0063.494
gdcSurvivalAnalysis0.0390.0030.043
gdcVolcanoPlot0.2720.0210.296
gdcVoomNormalization0.0130.0020.015
shinyCorPlot0.0010.0000.001
shinyKMPlot0.0010.0000.002
shinyPathview0.0010.0000.000