| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:28 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1516/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PloGO2 1.11.0 (landing page) Jemma Wu
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| Package: PloGO2 |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings PloGO2_1.11.0.tar.gz |
| StartedAt: 2023-04-11 22:33:24 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 22:41:52 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 508.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PloGO2.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings PloGO2_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PloGO2.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘PloGO2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PloGO2’ version ‘1.11.0’
* 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 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 loading without being on the library search path ... 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 37.264 0.480 37.774
abundancePlot 22.664 0.324 22.960
writeAnnotation 20.834 0.096 20.931
processAnnotation 17.132 0.084 17.216
getGoID 16.453 0.100 16.554
processGoFile 9.446 0.028 9.475
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘PloGO2_vignette.Rnw’... OK
‘PloGO2_with_WGNCA_vignette.Rnw’... failed
WARNING
Errors in running code in vignettes:
when running code in ‘PloGO2_with_WGNCA_vignette.Rnw’
...
\hline
\end{tabular}
\end{table}
> source(file.path(system.file("script", package = "PloGO2"),
+ "WGCNA_proteomics.R"))
When sourcing ‘PloGO2_with_WGNCA_vignette.R’:
Error: there is no package called ‘heatmap3’
Execution halted
* checking re-building of vignette outputs ... NOTE
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, sort, 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 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
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, sort, 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 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
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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/PloGO2.Rcheck/00check.log’
for details.
PloGO2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PloGO2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 ** testing if installed package can be loaded from final location ** 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 | 3.199 | 0.173 | 3.376 | |
| GOTermList | 0.139 | 0.028 | 0.175 | |
| PloGO | 37.264 | 0.480 | 37.774 | |
| PloPathway | 0.63 | 0.00 | 0.63 | |
| abundancePlot | 22.664 | 0.324 | 22.960 | |
| annotationPlot | 0.055 | 0.000 | 0.055 | |
| compareAnnot | 0 | 0 | 0 | |
| genAnnotationFiles | 0.287 | 0.020 | 0.307 | |
| genWegoFile | 0 | 0 | 0 | |
| getGoID | 16.453 | 0.100 | 16.554 | |
| plotAbundanceBar | 0.834 | 0.028 | 0.849 | |
| printSummary | 0 | 0 | 0 | |
| processAnnotation | 17.132 | 0.084 | 17.216 | |
| processGoFile | 9.446 | 0.028 | 9.475 | |
| processPathFile | 0.123 | 0.012 | 0.134 | |
| read.annot.file | 0.049 | 0.008 | 0.057 | |
| writeAnnotation | 20.834 | 0.096 | 20.931 | |