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This page was generated on 2024-03-28 11:39:47 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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

Package 1559/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PloGO2 1.15.1  (landing page)
Jemma Wu , Dana Pascovici
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/PloGO2
git_branch: devel
git_last_commit: ff8899a
git_last_commit_date: 2024-02-29 13:44:41 -0400 (Thu, 29 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for PloGO2 on lconway


To the developers/maintainers of the PloGO2 package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: PloGO2
Version: 1.15.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PloGO2_1.15.1.tar.gz
StartedAt: 2024-03-27 23:12:10 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 23:18:18 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 368.1 seconds
RetCode: 0
Status:   OK  
CheckDir: PloGO2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PloGO2_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PloGO2.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PloGO2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PloGO2’ version ‘1.15.1’
* 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 code 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 whether startup messages can be suppressed ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
PloGO             47.685  2.593  50.708
abundancePlot     24.779  0.954  25.991
getGoID           23.447  0.265  24.071
writeAnnotation   21.967  1.137  23.336
processAnnotation 21.795  1.037  23.030
processGoFile     11.991  0.286  12.395
ExcelToPloPathway  4.623  0.938   5.870
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/PloGO2.Rcheck/00check.log’
for details.


Installation output

PloGO2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PloGO2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
Warning in fun(libname, pkgname) :
  Package 'PloGO2' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'PloGO2' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (PloGO2)

Tests output


Example timings

PloGO2.Rcheck/PloGO2-Ex.timings

nameusersystemelapsed
ExcelToPloGO0.0000.0000.001
ExcelToPloPathway4.6230.9385.870
GOTermList0.1620.0130.177
PloGO47.685 2.59350.708
PloPathway0.7860.0370.830
abundancePlot24.779 0.95425.991
annotationPlot0.1090.0070.116
compareAnnot0.0000.0010.000
genAnnotationFiles0.3880.1900.634
genWegoFile0.0000.0010.001
getGoID23.447 0.26524.071
plotAbundanceBar0.8190.0360.862
printSummary0.0000.0010.001
processAnnotation21.795 1.03723.030
processGoFile11.991 0.28612.395
processPathFile0.1280.0110.140
read.annot.file0.0720.0070.079
writeAnnotation21.967 1.13723.336