| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the CompGO package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CompGO.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 371/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Ashley J. Waardenberg
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CompGO |
| Version: 1.28.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:CompGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CompGO_1.28.0.tar.gz |
| StartedAt: 2021-10-14 21:28:49 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:33:32 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 283.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CompGO.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:CompGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CompGO_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CompGO.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CompGO/DESCRIPTION' ... OK
* this is package 'CompGO' version '1.28.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'CompGO' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'RDAVIDWebService' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CompGO.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 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
PCAplot: no visible global function definition for 'par'
PCAplot: no visible global function definition for 'text'
compareZscores: no visible global function definition for 'pnorm'
compareZscores: no visible global function definition for 'p.adjust'
compareZscores: no visible global function definition for 'setNames'
doZtrans.single: no visible binding for global variable 'Term'
doZtrans.single: no visible binding for global variable 'Z'
plotDendrogram: no visible global function definition for 'cor'
plotDendrogram: no visible global function definition for 'hclust'
plotDendrogram: no visible global function definition for 'dist'
plotInteractive: no visible global function definition for 'cor'
plotInteractive: no visible global function definition for 'hclust'
plotInteractive: no visible global function definition for 'dist'
plotInteractive: no visible global function definition for 'png'
plotInteractive: no visible global function definition for 'par'
plotInteractive: no visible global function definition for 'dev.off'
plotInteractive: no visible global function definition for 'text'
plotInteractive: no visible binding for global variable 'Var1'
plotInteractive: no visible binding for global variable 'Var2'
plotInteractive: no visible binding for global variable 'value'
plotPairwise: no visible global function definition for
'complete.cases'
plotPairwise: no visible global function definition for 'setNames'
plotPairwise: no visible global function definition for 'cor'
plotTwoGODags: no visible global function definition for 'goDag'
plotTwoGODags: no visible global function definition for 'nodes'
plotTwoGODags: no visible global function definition for
'nodeRenderInfo<-'
plotZRankedDAG: no visible global function definition for 'goDag'
plotZRankedDAG: no visible global function definition for 'nodes'
plotZRankedDAG: no visible global function definition for
'nodeRenderInfo<-'
plotZScores: no visible global function definition for 'complete.cases'
plotZScores: no visible global function definition for 'setNames'
plotZScores: no visible global function definition for 'cor'
slidingJaccard: no visible binding for global variable 'useRawPvals'
zTransformDirectory: no visible global function definition for
'read.table'
zTransformDirectory: no visible global function definition for
'complete.cases'
zTransformDirectory: no visible binding for global variable 'var'
Undefined global functions or variables:
Term Var1 Var2 Z complete.cases cor dev.off dist goDag hclust
nodeRenderInfo<- nodes p.adjust par png pnorm read.table setNames
text useRawPvals value var
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "par", "text")
importFrom("stats", "complete.cases", "cor", "dist", "hclust",
"p.adjust", "pnorm", "setNames", "var")
importFrom("utils", "read.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 files in 'vignettes' ... OK
* checking examples ... 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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/CompGO.Rcheck/00check.log'
for details.
CompGO.Rcheck/00install.out
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch CompGO
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* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'CompGO' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning message:
Package 'RDAVIDWebService' is deprecated and will be removed from
Bioconductor version 3.14
** help
*** installing help indices
converting help for package 'CompGO'
finding HTML links ... done
PCAplot html
annotateBedFromDb html
bed.sample html
compareZscores html
doZtrans.single html
gata4 html
getFnAnot_genome html
mef2a html
nkx25 html
p300 html
plotDendrogram html
plotInteractive html
plotPairwise html
plotTwoGODags html
plotZRankedDAG html
plotZScores html
slidingJaccard html
srf html
tbx5 html
viewKegg html
zTransformDirectory html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'RDAVIDWebService' is deprecated and will be removed from
Bioconductor version 3.14
** testing if installed package can be loaded from final location
Warning: Package 'RDAVIDWebService' is deprecated and will be removed from
Bioconductor version 3.14
** testing if installed package keeps a record of temporary installation path
* DONE (CompGO)
Making 'packages.html' ... done
CompGO.Rcheck/CompGO-Ex.timings
| name | user | system | elapsed | |
| annotateBedFromDb | 1.44 | 0.03 | 1.47 | |
| compareZscores | 0.17 | 0.00 | 0.20 | |
| doZtrans.single | 0.02 | 0.00 | 0.02 | |
| getFnAnot_genome | 0 | 0 | 0 | |
| plotPairwise | 0.50 | 0.02 | 0.51 | |
| plotTwoGODags | 4.73 | 0.03 | 4.77 | |
| plotZRankedDAG | 0 | 0 | 0 | |
| plotZScores | 0.52 | 0.00 | 0.51 | |
| slidingJaccard | 0.05 | 0.01 | 0.07 | |
| viewKegg | 0 | 0 | 0 | |
| zTransformDirectory | 0 | 0 | 0 | |