Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:41 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 PloGO2 on nebbiolo1


To the developers/maintainers of the PloGO2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PloGO2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1467/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PloGO2 1.8.2  (landing page)
Jemma Wu , Dana Pascovici
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/PloGO2
git_branch: RELEASE_3_15
git_last_commit: f2c093f
git_last_commit_date: 2022-09-15 02:25:41 -0400 (Thu, 15 Sep 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PloGO2
Version: 1.8.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings PloGO2_1.8.2.tar.gz
StartedAt: 2022-10-18 21:09:49 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:14:18 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 268.5 seconds
RetCode: 0
Status:   OK  
CheckDir: PloGO2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings PloGO2_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/PloGO2.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PloGO2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PloGO2’ version ‘1.8.2’
* 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 ‘PloGO2’ 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 ... 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
Children: no visible global function definition for ‘Ontology’
ExcelToPloGO: no visible binding for global variable ‘Term’
ExcelToPloGO: no visible binding for global variable ‘Ontology’
GOGraphWrapper: no visible global function definition for ‘Ontology’
GOParent: no visible global function definition for ‘Ontology’
GOTermList: no visible global function definition for ‘Ontology’
PloGO: no visible global function definition for ‘read.delim’
PloGO: no visible global function definition for ‘unzip’
PloGO: no visible global function definition for ‘read.csv’
PloPathway: no visible global function definition for ‘unzip’
PloPathway : <anonymous>: no visible global function definition for
  ‘read.table’
PloPathway: no visible global function definition for ‘read.csv’
abundancePlot: no visible binding for global variable ‘eps’
aggregateAbundance : <anonymous>: no visible global function definition
  for ‘Term’
aggregateAbundance : <anonymous>: no visible global function definition
  for ‘aggregate’
annotationPlot : <anonymous>: no visible global function definition for
  ‘Term’
compareAnnot: no visible global function definition for ‘fisher.test’
compareAnnot : <anonymous>: no visible global function definition for
  ‘Term’
compareAnnot: no visible global function definition for ‘p.adjust’
countAndAbundance: no visible global function definition for ‘par’
countAndAbundance: no visible global function definition for ‘barplot’
countAndAbundance: no visible global function definition for ‘axTicks’
countAndAbundance: no visible global function definition for ‘axis’
countAndAbundance: no visible global function definition for ‘title’
genAnnotationFiles: no visible global function definition for
  ‘read.csv’
genAnnotationFiles: no visible global function definition for
  ‘write.table’
genWegoFile: no visible global function definition for ‘useMart’
genWegoFile: no visible global function definition for ‘useDataset’
genWegoFile: no visible global function definition for ‘getBM’
genWegoFile: no visible global function definition for ‘aggregate’
genWegoFile: no visible global function definition for ‘write.table’
getGoID: no visible binding for global variable ‘Term’
getUniprotBatch: no visible binding for global variable ‘IDList’
inGraph: no visible global function definition for ‘nodes’
plotAbundanceBar: no visible global function definition for ‘par’
plotAbundanceBar: no visible global function definition for ‘barplot’
plotAbundanceBar: no visible global function definition for ‘rainbow’
plotAbundanceBar: no visible global function definition for ‘legend’
plotMat: no visible global function definition for ‘colorRampPalette’
plotMat : <anonymous>: no visible global function definition for ‘Term’
processAnnotFile: no visible global function definition for ‘read.csv’
processGoFile : <anonymous>: no visible global function definition for
  ‘Term’
processGoFile: no visible global function definition for ‘read.csv’
processPathFile: no visible global function definition for ‘read.csv’
read.annot.file: no visible global function definition for ‘read.table’
read.annot.file: no visible global function definition for ‘aggregate’
tabulateAnnot : <anonymous>: no visible global function definition for
  ‘Term’
writeGOannot: no visible global function definition for ‘read.csv’
writeGOannot: no visible global function definition for ‘write.csv’
writeGOannot: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  IDList Ontology Term aggregate axTicks axis barplot colorRampPalette
  eps fisher.test getBM legend nodes p.adjust par rainbow read.csv
  read.delim read.table title unzip useDataset useMart write.csv
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "axTicks", "axis", "barplot", "legend", "par",
             "title")
  importFrom("stats", "aggregate", "fisher.test", "p.adjust")
  importFrom("utils", "read.csv", "read.delim", "read.table", "unzip",
             "write.csv", "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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
PloGO             38.031  0.608  38.647
abundancePlot     20.607  0.296  20.908
processAnnotation 18.645  0.208  18.853
writeAnnotation   18.252  0.068  18.320
getGoID           16.266  0.088  16.355
processGoFile      8.779  0.032   8.811
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/PloGO2.Rcheck/00check.log’
for details.



Installation output

PloGO2.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL PloGO2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘PloGO2’ ...
** using staged installation
** R
** 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 (PloGO2)

Tests output


Example timings

PloGO2.Rcheck/PloGO2-Ex.timings

nameusersystemelapsed
ExcelToPloGO0.0000.0010.000
ExcelToPloPathway3.1720.2403.415
GOTermList0.1250.0240.157
PloGO38.031 0.60838.647
PloPathway0.5490.0040.553
abundancePlot20.607 0.29620.908
annotationPlot0.0730.0040.078
compareAnnot0.0010.0000.000
genAnnotationFiles0.2580.0400.298
genWegoFile0.0000.0000.001
getGoID16.266 0.08816.355
plotAbundanceBar0.8400.0080.848
printSummary000
processAnnotation18.645 0.20818.853
processGoFile8.7790.0328.811
processPathFile0.0940.0080.102
read.annot.file0.0550.0040.058
writeAnnotation18.252 0.06818.320