Last updated on 2020-08-07 01:50:20 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| Binarize | 1 | 11 | ||
| BiTrinA | 1 | 11 | ||
| BoolNet | 1 | 6 | 5 | |
| GiANT | 1 | 11 | ||
| MOCCA | 12 | |||
| ORION | 12 | |||
| TunePareto | 12 |
Current CRAN status: NOTE: 1, OK: 11
Version: 1.3
Check: Rd cross-references
Result: NOTE
Undeclared package ‘BoolNet’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: NOTE: 1, OK: 11
Version: 1.3
Check: Rd cross-references
Result: NOTE
Undeclared package ‘BoolNet’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: WARN: 1, NOTE: 6, OK: 5
Version: 2.1.5
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
'attractors.tex' 'cellcycle.sbml' 'cellcycle.txt' 'pajek_export.net'
'sequence.txt' 'testNet.bn'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64
Version: 2.1.5
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘BoolNet_package_vignette.Snw.Rnw’ using Sweave
Error: processing vignette 'BoolNet_package_vignette.Snw.Rnw' failed with diagnostics:
chunk 13
Error in net$interactions[[idx]][[functionIndices[idx]]] :
subscript out of bounds
--- failed re-building ‘BoolNet_package_vignette.Snw.Rnw’
SUMMARY: processing the following file failed:
‘BoolNet_package_vignette.Snw.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Current CRAN status: ERROR: 1, OK: 11
Version: 1.3
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘GlobalAncova’
Flavor: r-release-macos-x86_64
Version: 1.3
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘GlobalAncova’
Flavor: r-release-macos-x86_64
Version: 1.3
Check: examples
Result: ERROR
Running examples in ‘GiANT-Ex.R’ failed
The error most likely occurred in:
> ### Name: GiANT-package
> ### Title: Enrichment analysis
> ### Aliases: GiANT
>
> ### ** Examples
>
> # load data
> require(GlobalAncova)
Loading required package: GlobalAncova
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘GlobalAncova’
> data(vantVeer)
Warning in data(vantVeer) : data set ‘vantVeer’ not found
> data(phenodata)
Warning in data(phenodata) : data set ‘phenodata’ not found
> data(pathways)
Warning in data(pathways) : data set ‘pathways’ not found
>
> ##################################
> # Example 1: gene set analysis #
> ##################################
> res <- geneSetAnalysis(
+ # parameters for geneSetAnalysis
+ dat = vantVeer,
+ geneSets = pathways[1],
+ analysis = analysis.averageCorrelation(),
+ adjustmentMethod = "fdr",
+ # additional parameters for analysis.averageCorrelation
+ labs = phenodata$metastases,
+ method = "pearson",
+ numSamples = 50)
Error in geneSetAnalysis(dat = vantVeer, geneSets = pathways[1], analysis = analysis.averageCorrelation(), :
object 'pathways' not found
Execution halted
Flavor: r-release-macos-x86_64
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: OK: 12