Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-14 11:05:53 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4159
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4055
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3997
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4114
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 eegc on nebbiolo1


To the developers/maintainers of the eegc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/eegc.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 567/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eegc 1.21.0  (landing page)
Xiaoyuan Zhou
Snapshot Date: 2022-01-13 13:55:14 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/eegc
git_branch: master
git_last_commit: c70bd39
git_last_commit_date: 2021-10-26 12:29:44 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'DESeq2' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'clusterProfiler' which is not available

Summary

Package: eegc
Version: 1.21.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:eegc.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings eegc_1.21.0.tar.gz
StartedAt: 2022-01-13 19:11:26 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 19:18:36 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 429.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: eegc.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:eegc.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings eegc_1.21.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/eegc.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eegc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eegc’ version ‘1.21.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘eegc’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data  10.5Mb
* 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
categorizeGene : <anonymous>: no visible global function definition for
  ‘quantile’
densityPlot: no visible binding for global variable ‘density’
densityPlot: no visible global function definition for ‘lines’
densityPlot: no visible global function definition for ‘axis’
densityPlot: no visible global function definition for ‘adjustcolor’
densityPlot: no visible global function definition for ‘legend’
densityPlot : <anonymous>: no visible global function definition for
  ‘quantile’
densityPlot: no visible global function definition for ‘text’
densityPlot: no visible global function definition for ‘dev.copy2pdf’
diffGene: no visible global function definition for ‘model.matrix’
diffGene: no visible binding for global variable ‘treat’
diffGene: no visible binding for global variable ‘control’
diffGene: no visible global function definition for ‘results’
diffGene: no visible global function definition for ‘p.adjust’
dotPercentage: no visible global function definition for ‘lines’
dotPercentage: no visible global function definition for ‘axis’
dotPercentage: no visible global function definition for ‘text’
dotPercentage: no visible global function definition for ‘par’
enrichment : enrichment : <anonymous>: no visible global function
  definition for ‘phyper’
enrichment : enrichment: no visible global function definition for
  ‘p.adjust’
grnPlot: no visible global function definition for ‘title’
grnPlot: no visible global function definition for ‘legend’
markerScatter: no visible global function definition for
  ‘colorRampPalette’
markerScatter: no visible global function definition for ‘points’
markerScatter: no visible global function definition for ‘lm’
markerScatter: no visible global function definition for ‘abline’
markerScatter: no visible global function definition for ‘text’
markerScatter: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline adjustcolor axis colorRampPalette control density dev.copy2pdf
  legend lines lm model.matrix p.adjust par phyper points quantile
  results text title treat
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette",
             "dev.copy2pdf")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points", "text", "title")
  importFrom("stats", "density", "lm", "model.matrix", "p.adjust",
             "phyper", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'barplotEnrich.Rd':
  ‘[DOSE]{barplot.enrichResult}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 LazyData ... WARNING
  LazyData DB of 10.5 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
functionEnrich 212.424  2.824 221.441
* 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 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/eegc.Rcheck/00check.log’
for details.



Installation output

eegc.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL eegc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘eegc’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (eegc)

Tests output


Example timings

eegc.Rcheck/eegc-Ex.timings

nameusersystemelapsed
barplotEnrich000
categorizeGene0.8150.0120.826
densityPlot0.0040.0000.004
diffGene0.2620.0180.281
dotPercentage0.0010.0000.002
enrichment1.9440.0992.044
functionEnrich212.424 2.824221.441
grnPlot0.0000.0010.001
heatmapPlot0.2450.0070.252
markerScatter0.2150.0040.218
networkAnalyze0.1170.0040.121