Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:22 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for GDCRNATools on tokay2


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 709/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GDCRNATools 1.14.0  (landing page)
Ruidong Li
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/GDCRNATools
git_branch: RELEASE_3_14
git_last_commit: 9b69c00
git_last_commit_date: 2021-10-26 12:41:09 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GDCRNATools
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GDCRNATools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GDCRNATools_1.14.0.tar.gz
StartedAt: 2022-01-20 20:16:03 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:23:09 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 425.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GDCRNATools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GDCRNATools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GDCRNATools_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GDCRNATools.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GDCRNATools/DESCRIPTION' ... OK
* this is package 'GDCRNATools' version '1.14.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GDCRNATools.Rcheck/00check.log'
for details.



Installation output

GDCRNATools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GDCRNATools_1.14.0.tar.gz && rm -rf GDCRNATools.buildbin-libdir && mkdir GDCRNATools.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GDCRNATools.buildbin-libdir GDCRNATools_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GDCRNATools_1.14.0.zip && rm GDCRNATools_1.14.0.tar.gz GDCRNATools_1.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 60 3963k   60 2407k    0     0  3237k      0  0:00:01 --:--:--  0:00:01 3235k
100 3963k  100 3963k    0     0  3698k      0  0:00:01  0:00:01 --:--:-- 3701k

install for i386

* installing *source* package 'GDCRNATools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GDCRNATools'
    finding HTML links ... done
    DEGAll                                  html  
    GDCRNATools-package                     html  
    enrichOutput                            html  
    gdcBarPlot                              html  
    gdcCEAnalysis                           html  
    gdcClinicalDownload                     html  
    gdcClinicalMerge                        html  
    gdcCorPlot                              html  
    gdcDEAnalysis                           html  
    gdcDEReport                             html  
    gdcEnrichAnalysis                       html  
    gdcEnrichPlot                           html  
    gdcExportNetwork                        html  
    gdcFilterDuplicate                      html  
    gdcFilterSampleType                     html  
    gdcHeatmap                              html  
    gdcKMPlot                               html  
    gdcMatchSamples                         html  
    gdcParseMetadata                        html  
    gdcRNADownload                          html  
    gdcRNAMerge                             html  
    gdcSurvivalAnalysis                     html  
    gdcVolcanoPlot                          html  
    gdcVoomNormalization                    html  
    lncTarget                               html  
    mirCounts                               html  
    pcTarget                                html  
    rnaCounts                               html  
    shinyCorPlot                            html  
    shinyKMPlot                             html  
    shinyPathview                           html  
** 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

install for x64

* installing *source* package 'GDCRNATools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GDCRNATools' as GDCRNATools_1.14.0.zip
* DONE (GDCRNATools)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GDCRNATools' successfully unpacked and MD5 sums checked

Tests output

GDCRNATools.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  15.90    1.21   18.65 

GDCRNATools.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  15.62    0.53   18.06 

Example timings

GDCRNATools.Rcheck/examples_i386/GDCRNATools-Ex.timings

nameusersystemelapsed
gdcBarPlot0.250.040.30
gdcCEAnalysis1.850.031.87
gdcClinicalDownload000
gdcClinicalMerge000
gdcCorPlot0.370.030.41
gdcDEAnalysis0.060.000.06
gdcDEReport0.020.000.02
gdcEnrichAnalysis000
gdcEnrichPlot0.170.040.20
gdcExportNetwork000
gdcFilterDuplicate1.280.073.72
gdcFilterSampleType1.170.002.95
gdcHeatmap0.070.000.06
gdcKMPlot0.400.110.52
gdcMatchSamples0.000.010.01
gdcParseMetadata1.210.003.08
gdcRNADownload000
gdcRNAMerge1.010.023.01
gdcSurvivalAnalysis0.030.020.05
gdcVolcanoPlot0.170.070.25
gdcVoomNormalization000
shinyCorPlot000
shinyKMPlot000
shinyPathview000

GDCRNATools.Rcheck/examples_x64/GDCRNATools-Ex.timings

nameusersystemelapsed
gdcBarPlot0.240.000.23
gdcCEAnalysis1.400.061.47
gdcClinicalDownload000
gdcClinicalMerge000
gdcCorPlot0.370.010.39
gdcDEAnalysis0.030.000.03
gdcDEReport0.020.000.01
gdcEnrichAnalysis0.000.020.02
gdcEnrichPlot0.160.000.16
gdcExportNetwork000
gdcFilterDuplicate0.970.033.44
gdcFilterSampleType1.080.022.95
gdcHeatmap0.200.010.22
gdcKMPlot0.550.050.59
gdcMatchSamples000
gdcParseMetadata0.920.002.80
gdcRNADownload000
gdcRNAMerge0.970.002.70
gdcSurvivalAnalysis0.050.000.05
gdcVolcanoPlot0.260.000.27
gdcVoomNormalization0.020.000.01
shinyCorPlot000
shinyKMPlot000
shinyPathview000