Jemma Wu
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/PloGO2 |
| git_branch: master |
| git_last_commit: 78eba39 |
| git_last_commit_date: 2021-10-26 12:58:58 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:18 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? 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 1437/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PloGO2 1.7.0 (landing page) Jemma Wu
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: PloGO2 |
| Version: 1.7.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PloGO2.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PloGO2_1.7.0.tar.gz |
| StartedAt: 2022-03-17 19:53:16 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:56:56 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 219.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PloGO2.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PloGO2.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PloGO2_1.7.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/PloGO2.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PloGO2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PloGO2' version '1.7.0'
* 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 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' ... NOTE
The following files look like leftovers/mistakes:
'Rplots.pdf'
Please remove them from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PloGO 27.37 2.56 29.95
writeAnnotation 15.52 0.10 15.63
abundancePlot 13.17 1.22 14.46
processAnnotation 12.59 0.67 13.27
getGoID 11.48 0.02 11.50
processGoFile 6.61 0.04 6.64
* 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 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/PloGO2.Rcheck/00check.log'
for details.
PloGO2.Rcheck/00install.out
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PloGO2
###
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* installing to library 'D:/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
converting help for package 'PloGO2'
finding HTML links ... done
ExcelToPloGO html
ExcelToPloPathway html
GOTermList html
PloGO html
PloPathway html
abundancePlot html
annotationPlot html
compareAnnot html
genAnnotationFiles html
genWegoFile html
getGoID html
plotAbundanceBar html
printSummary html
processAnnotation html
processGoFile html
processPathFile html
read.annot.file html
writeAnnotation html
** 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)
Making 'packages.html' ... done
PloGO2.Rcheck/PloGO2-Ex.timings
| name | user | system | elapsed | |
| ExcelToPloGO | 0 | 0 | 0 | |
| ExcelToPloPathway | 2.56 | 0.61 | 4.57 | |
| GOTermList | 0.13 | 0.00 | 0.12 | |
| PloGO | 27.37 | 2.56 | 29.95 | |
| PloPathway | 0.46 | 0.02 | 0.47 | |
| abundancePlot | 13.17 | 1.22 | 14.46 | |
| annotationPlot | 0.05 | 0.00 | 0.04 | |
| compareAnnot | 0 | 0 | 0 | |
| genAnnotationFiles | 0.42 | 0.15 | 0.78 | |
| genWegoFile | 0 | 0 | 0 | |
| getGoID | 11.48 | 0.02 | 11.50 | |
| plotAbundanceBar | 0.55 | 0.06 | 0.64 | |
| printSummary | 0 | 0 | 0 | |
| processAnnotation | 12.59 | 0.67 | 13.27 | |
| processGoFile | 6.61 | 0.04 | 6.64 | |
| processPathFile | 0.10 | 0.00 | 0.09 | |
| read.annot.file | 0.04 | 0.00 | 0.05 | |
| writeAnnotation | 15.52 | 0.10 | 15.63 | |