Ruidong Li
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/GDCRNATools |
| git_branch: master |
| git_last_commit: 158729b |
| git_last_commit_date: 2021-10-26 12:41:09 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:34 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 712/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GDCRNATools 1.15.0 (landing page) Ruidong Li
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GDCRNATools |
| Version: 1.15.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GDCRNATools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GDCRNATools_1.15.0.tar.gz |
| StartedAt: 2022-03-17 19:08:55 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:12:59 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 244.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GDCRNATools.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GDCRNATools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GDCRNATools_1.15.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GDCRNATools.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.15.0'
* 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
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/GDCRNATools.Rcheck/00check.log'
for details.
GDCRNATools.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GDCRNATools
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
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
* DONE (GDCRNATools)
Making 'packages.html' ... done
GDCRNATools.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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
9.87 0.81 12.46
GDCRNATools.Rcheck/GDCRNATools-Ex.timings
| name | user | system | elapsed | |
| gdcBarPlot | 0.18 | 0.03 | 0.22 | |
| gdcCEAnalysis | 1.11 | 0.09 | 1.20 | |
| gdcClinicalDownload | 0 | 0 | 0 | |
| gdcClinicalMerge | 0 | 0 | 0 | |
| gdcCorPlot | 0.33 | 0.00 | 0.33 | |
| gdcDEAnalysis | 0.03 | 0.00 | 0.03 | |
| gdcDEReport | 0.02 | 0.00 | 0.01 | |
| gdcEnrichAnalysis | 0 | 0 | 0 | |
| gdcEnrichPlot | 0.11 | 0.00 | 0.11 | |
| gdcExportNetwork | 0.01 | 0.00 | 0.02 | |
| gdcFilterDuplicate | 0.08 | 0.02 | 2.28 | |
| gdcFilterSampleType | 0.05 | 0.00 | 2.19 | |
| gdcHeatmap | 0.11 | 0.00 | 0.11 | |
| gdcKMPlot | 0.33 | 0.06 | 0.39 | |
| gdcMatchSamples | 0 | 0 | 0 | |
| gdcParseMetadata | 0.07 | 0.00 | 2.28 | |
| gdcRNADownload | 0 | 0 | 0 | |
| gdcRNAMerge | 0.07 | 0.02 | 2.24 | |
| gdcSurvivalAnalysis | 0.03 | 0.00 | 0.03 | |
| gdcVolcanoPlot | 0.12 | 0.05 | 0.17 | |
| gdcVoomNormalization | 0.02 | 0.00 | 0.02 | |
| shinyCorPlot | 0 | 0 | 0 | |
| shinyKMPlot | 0.01 | 0.00 | 0.01 | |
| shinyPathview | 0 | 0 | 0 | |