Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-20 15:04:46 -0400 (Mon, 20 Sep 2021).

CHECK results for CompGO on nebbiolo1

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.

raw results

Package 371/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CompGO 1.28.0  (landing page)
Ashley J. Waardenberg
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/CompGO
git_branch: RELEASE_3_13
git_last_commit: e8e77da
git_last_commit_date: 2021-05-19 12:04:07 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CompGO
Version: 1.28.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CompGO.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CompGO_1.28.0.tar.gz
StartedAt: 2021-09-19 09:19:30 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 09:23:53 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 262.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CompGO.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CompGO.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CompGO_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CompGO.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 ‘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 for sufficient/correct file permissions ... 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 ‘/home/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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/CompGO.Rcheck/00check.log’
for details.



Installation output

CompGO.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CompGO
###
##############################################################################
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* installing to library ‘/home/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
** 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)

Tests output


Example timings

CompGO.Rcheck/CompGO-Ex.timings

nameusersystemelapsed
annotateBedFromDb0.6110.0280.639
compareZscores0.0580.0050.063
doZtrans.single0.0050.0000.006
getFnAnot_genome0.0000.0000.001
plotPairwise0.3380.0280.366
plotTwoGODags4.3700.1844.556
plotZRankedDAG000
plotZScores0.5180.0000.518
slidingJaccard0.0530.0000.053
viewKegg000
zTransformDirectory000