Last updated on 2020-10-30 08:49:07 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.5 | 29.47 | 404.98 | 434.45 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.5 | 26.19 | 301.72 | 327.91 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.5 | 323.52 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.5 | 332.09 | WARN | |||
| r-devel-windows-ix86+x86_64 | 1.2.5 | 64.00 | 338.00 | 402.00 | NOTE | |
| r-patched-linux-x86_64 | 1.2.5 | 32.02 | 381.20 | 413.22 | OK | |
| r-patched-solaris-x86 | 1.2.5 | 408.00 | WARN | |||
| r-release-linux-x86_64 | 1.2.5 | 26.16 | 381.85 | 408.01 | OK | |
| r-release-macos-x86_64 | 1.2.5 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 1.2.5 | 47.00 | 463.00 | 510.00 | NOTE | |
| r-oldrel-macos-x86_64 | 1.2.5 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.2.5 | 43.00 | 301.00 | 344.00 | NOTE |
Version: 1.2.5
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘metaboGSE.Rmd’ using rmarkdown
Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
Loading required package: ape
Loading required package: glpkAPI
using GLPK version 4.65
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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: graph
Attaching package: 'graph'
The following objects are masked from 'package:ape':
complement, edges
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:Matrix':
expand
The following object is masked from 'package:base':
expand.grid
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
The following objects are masked from 'package:sybil':
algorithm, algorithm<-, allGenes, genes
Building most specific GOs .....
( 2320 GO terms found. )
Build GO DAG topology ..........
Quitting from lines 166-204 (metaboGSE.Rmd)
Error: processing vignette 'metaboGSE.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘metaboGSE.Rmd’
SUMMARY: processing the following file failed:
‘metaboGSE.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2.5
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'unix'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.2.5
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘metaboGSE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
Loading required package: ape
Loading required package: glpkAPI
using GLPK version 4.65
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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: graph
Attaching package: 'graph'
The following objects are masked from 'package:ape':
complement, edges
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:Matrix':
expand
The following object is masked from 'package:base':
expand.grid
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
The following objects are masked from 'package:sybil':
algorithm, algorithm<-, allGenes, genes
Building most specific GOs .....
( 2320 GO terms found. )
Build GO DAG topology ..........
Quitting from lines 166-204 (metaboGSE.Rmd)
Error: processing vignette 'metaboGSE.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘metaboGSE.Rmd’
SUMMARY: processing the following file failed:
‘metaboGSE.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.2.5
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘KEGGREST’
Flavor: r-release-macos-x86_64
Version: 1.2.5
Check: examples
Result: ERROR
Running examples in ‘metaboGSE-Ex.R’ failed
The error most likely occurred in:
> ### Name: pwDesc
> ### Title: Description of gene set IDs
> ### Aliases: pwDesc
>
> ### ** Examples
>
> pwDesc("GO:0006696")
Error in loadNamespace(name) : there is no package called ‘GO.db’
Calls: pwDesc ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-oldrel-macos-x86_64