Jemma Wu
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/PloGO2 |
| git_branch: RELEASE_3_19 |
| git_last_commit: 7b91b7d |
| git_last_commit_date: 2024-04-30 11:23:06 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:03:08 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 1579/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Jemma Wu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: PloGO2 |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PloGO2_1.16.0.tar.gz |
| StartedAt: 2024-05-31 06:51:43 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 06:57:50 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 366.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: PloGO2.Rcheck |
| Warnings: NA |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PloGO2_1.16.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/PloGO2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘PloGO2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PloGO2’ version ‘1.16.0’
* 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 ‘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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PloGO 34.451 0.703 35.183
abundancePlot 20.996 0.220 21.185
writeAnnotation 17.515 0.136 17.651
processAnnotation 16.941 0.096 17.037
getGoID 16.091 0.100 16.191
processGoFile 8.984 0.064 9.047
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘PloGO2_vignette.Rnw’ using Sweave
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Loading required package: graph
Attaching package: ‘GOstats’
The following object is masked from ‘package:AnnotationDbi’:
makeGOGraph
Warning in fun(libname, pkgname) :
Package 'PloGO2' is deprecated and will be removed from Bioconductor
version 3.20
No encoding supplied: defaulting to UTF-8.
--- finished re-building ‘PloGO2_vignette.Rnw’
--- re-building ‘PloGO2_with_WGNCA_vignette.Rnw’ using Sweave
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Loading required package: graph
Attaching package: ‘GOstats’
The following object is masked from ‘package:AnnotationDbi’:
makeGOGraph
Warning in fun(libname, pkgname) :
Package 'PloGO2' is deprecated and will be removed from Bioconductor
version 3.20
Error: processing vignette 'PloGO2_with_WGNCA_vignette.Rnw' failed with diagnostics:
chunk 2 (label = wgcnaplots)
Error in library(heatmap3) : there is no package called ‘heatmap3’
--- failed re-building ‘PloGO2_with_WGNCA_vignette.Rnw’
SUMMARY: processing the following file failed:
‘PloGO2_with_WGNCA_vignette.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/PloGO2.Rcheck/00check.log’
for details.
PloGO2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL PloGO2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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)
PloGO2.Rcheck/PloGO2-Ex.timings
| name | user | system | elapsed | |
| ExcelToPloGO | 0 | 0 | 0 | |
| ExcelToPloPathway | 3.443 | 0.268 | 3.712 | |
| GOTermList | 0.130 | 0.028 | 0.161 | |
| PloGO | 34.451 | 0.703 | 35.183 | |
| PloPathway | 0.563 | 0.036 | 0.599 | |
| abundancePlot | 20.996 | 0.220 | 21.185 | |
| annotationPlot | 0.051 | 0.000 | 0.052 | |
| compareAnnot | 0 | 0 | 0 | |
| genAnnotationFiles | 0.253 | 0.039 | 0.292 | |
| genWegoFile | 0.000 | 0.000 | 0.001 | |
| getGoID | 16.091 | 0.100 | 16.191 | |
| plotAbundanceBar | 0.820 | 0.016 | 0.817 | |
| printSummary | 0 | 0 | 0 | |
| processAnnotation | 16.941 | 0.096 | 17.037 | |
| processGoFile | 8.984 | 0.064 | 9.047 | |
| processPathFile | 0.084 | 0.012 | 0.096 | |
| read.annot.file | 0.047 | 0.008 | 0.055 | |
| writeAnnotation | 17.515 | 0.136 | 17.651 | |