Last updated on 2018-02-20 08:48:14 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2 | 1.90 | 42.43 | 44.33 | OK | --no-vignettes |
| r-devel-linux-x86_64-debian-gcc | 1.2 | 2.23 | 37.78 | 40.01 | OK | --no-vignettes |
| r-devel-linux-x86_64-fedora-clang | 1.2 | 38.29 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2 | 36.54 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.2 | 4.00 | 55.00 | 59.00 | OK | --no-vignettes |
| r-patched-linux-x86_64 | 1.2 | 1.05 | 49.45 | 50.50 | OK | --no-vignettes |
| r-patched-solaris-x86 | 1.2 | 76.80 | OK | --no-vignettes | ||
| r-release-linux-x86_64 | 1.2 | 1.28 | 47.99 | 49.27 | OK | --no-vignettes |
| r-release-windows-ix86+x86_64 | 1.2 | 4.00 | 73.00 | 77.00 | OK | --no-vignettes |
| r-release-osx-x86_64 | 1.2 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.2 | 4.00 | 83.00 | 87.00 | OK | --no-vignettes |
| r-oldrel-osx-x86_64 | 1.2 | OK |
Version: 1.2
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
‘GlobalAncova’ ‘globaltest’ ‘limma’ ‘DESeq’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64
Version: 1.2
Check: Rd cross-references
Result: NOTE
Packages unavailable to check Rd xrefs: ‘GlobalAncova’, ‘globaltest’, ‘DESeq’, ‘limma’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64
Version: 1.2
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[1:3],
+ analysis = analysis.averageCorrelation(),
+ adjustmentMethod = "fdr",
+ # additional parameters for analysis.averageCorrelation
+ labs = phenodata$metastases,
+ method = "pearson",
+ numSamples = 100)
Error in geneSetAnalysis(dat = vantVeer, geneSets = pathways[1:3], analysis = analysis.averageCorrelation(), :
object 'pathways' not found
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: GlobalAncova
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘GlobalAncova’
Warning in data(vantVeer) : data set ‘vantVeer’ not found
Warning in data(phenodata) : data set ‘phenodata’ not found
Warning in data(pathways) : data set ‘pathways’ not found
Error: processing vignette 'giant_package_vignette.Snw' failed with diagnostics:
chunk 5
Error in geneSetAnalysis(labs = phenodata$metastases, method = "pearson", :
object 'pathways' not found
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2
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[1:3],
+ analysis = analysis.averageCorrelation(),
+ adjustmentMethod = "fdr",
+ # additional parameters for analysis.averageCorrelation
+ labs = phenodata$metastases,
+ method = "pearson",
+ numSamples = 100)
Error in vector(mode = "list", length = length(geneSets)) :
object 'pathways' not found
Calls: geneSetAnalysis -> vector
Execution halted
Flavor: r-release-osx-x86_64
Version: 1.2
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘giant_package_vignette.Snw’
...
> data(pathways)
Warning in data(pathways) : data set ‘pathways’ not found
> resGsea <- geneSetAnalysis(labs = phenodata$metastases,
+ method = "pearson", numSamples = 1000, dat = vantVeer, geneSets = pathways,
+ an .... [TRUNCATED]
When sourcing ‘giant_package_vignette.R’:
Error: object 'pathways' not found
Execution halted
Flavor: r-release-osx-x86_64
Version: 1.2
Check: re-building of vignette outputs
Result: NOTE
Error in re-building vignettes:
...
Loading required package: GlobalAncova
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘GlobalAncova’
Warning in data(vantVeer) : data set ‘vantVeer’ not found
Warning in data(phenodata) : data set ‘phenodata’ not found
Warning in data(pathways) : data set ‘pathways’ not found
Error: processing vignette 'giant_package_vignette.Snw' failed with diagnostics:
chunk 5
Error in vector(mode = "list", length = length(geneSets)) :
object 'pathways' not found
Execution halted
Flavor: r-release-osx-x86_64