Last updated on 2024-04-19 07:56:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.8 | 63.05 | 518.98 | 582.03 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.9 | OK | ||||
| r-devel-linux-x86_64-fedora-clang | 0.1.9 | 786.46 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.9 | 756.06 | OK | |||
| r-prerel-macos-arm64 | 0.1.9 | 223.00 | OK | |||
| r-prerel-macos-x86_64 | 0.1.9 | 662.00 | NOTE | |||
| r-prerel-windows-x86_64 | 0.1.9 | 51.00 | 380.00 | 431.00 | OK | |
| r-patched-linux-x86_64 | 0.1.8 | 39.24 | 480.86 | 520.10 | ERROR | |
| r-release-linux-x86_64 | 0.1.8 | 46.13 | 505.85 | 551.98 | OK | |
| r-release-macos-arm64 | 0.1.9 | 12.00 | ERROR | |||
| r-release-macos-x86_64 | 0.1.9 | 9.00 | ERROR | |||
| r-release-windows-x86_64 | 0.1.8 | 68.00 | 513.00 | 581.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.9 | 165.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.1.8 | 65.00 | 407.00 | 472.00 | ERROR |
Version: 0.1.8
Check: examples
Result: ERROR
Running examples in ‘SubtypeDrug-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PrioSubtypeDrug
> ### Title: Prioritization of candidate cancer subtype-specific drugs
> ### (PrioSubtypeDrug)
> ### Aliases: PrioSubtypeDrug
>
> ### ** Examples
>
> require(GSVA)
Loading required package: GSVA
> require(parallel)
Loading required package: parallel
> ## Get simulated breast cancer gene expression profile data.
> Geneexp<-get("Geneexp")
> ## Obtain sample subtype data and calculate breast cancer subtype-specific drugs.
> Subtype<-system.file("extdata", "Subtype_labels.cls", package = "SubtypeDrug")
>
> ## Subpathway list data and drug subpathway association data
> ## were stored in packet `SubtypeDrugData`.
> ## `SubtypeDrugData` has been uploaded to the github repository.
> ## If subpathway list data and drug subpathway association data are needed,
> ## users can download and install through `install_github` function and
> ## set parameter url=""hanjunwei-lab/SubtypeDrugData".
> ## After installing and loading package `SubtypeDrugData`,
> ## users can use the following command to get the data.
> ## Get subpathway list data.
> ## If the gene expression profile contains gene Symbol.
> ## data(SpwSymbolList)
> ## If the gene expression profile contains gene Entrezid.
> ## data(SpwEntrezidList)
> ## Get drug subpathway association data.
> ## data(DrugSpwData)
>
> ## Identify breast subtype-specific drugs.
> ## Subtype_drugs<-PrioSubtypeDrug(Geneexp,Subtype,"Control",SpwSymbolList,drug.spw.data=DrugSpwData,
> ## E_FDR=1,S_FDR=1)
>
> ## Identify breast cancer-related drugs in only two types of samples: breast cancer and control.
> Cancer<-system.file("extdata", "Cancer_normal_labels.cls", package = "SubtypeDrug")
> ## Disease_drugs<-PrioSubtypeDrug(Geneexp,Cancer,"Control",SpwSymbolList,drug.spw.data=DrugSpwData,
> ## E_FDR=1,S_FDR=1)
>
> ## The function PrioSubtypeDrug() can also support user-defined data.
> Geneexp<-get("GeneexpT")
> ## User-defined drug regulation data should resemble the structure below
> UserDS<-get("UserDST")
> str(UserDS)
List of 2
$ chloramphenicol(1.24e-05M):List of 2
..$ Target_upregulation : chr [1:5] "04060_26" "04610_11" "04670_6" "05162_13" ...
..$ Target_downregulation: chr [1:5] "04150_14" "04610_11" "04625_34" "04670_6" ...
$ thioridazine(1e-06M) :List of 2
..$ Target_upregulation : chr [1:5] "04060_4" "04060_19" "04670_9" "05134_4" ...
..$ Target_downregulation: chr [1:5] "00790_8" "04060_8" "04064_14" "04390_10" ...
> ## Need to load gene set data consistent with drug regulation data.
> UserGS<-get("UserGST")
> str(UserGS)
List of 20
$ 04060_26 : chr [1:3] "ACVR1" "AMHR2" "AMH"
$ 04610_11 : chr [1:3] "C3" "CFB" "CFD"
$ 04670_6 : chr [1:3] "ITGB2" "F11R" "ITGAL"
$ 05162_13 : chr [1:3] "IL12A" "IL12B" "FCGR2B"
$ 05206_112: chr [1:3] "MIR143" "ATM" "TP53"
$ 04150_14 : chr [1:2] "SLC7A5" "SLC3A2"
$ 04610_11 : chr [1:3] "C3" "CFB" "CFD"
$ 04625_34 : chr [1:4] "MDM2" "IRF1" "IL12A" "IL12B"
$ 04670_6 : chr [1:3] "ITGB2" "F11R" "ITGAL"
$ 05162_13 : chr [1:3] "IL12A" "IL12B" "FCGR2B"
$ 04060_4 : chr [1:4] "IL10RB" "IL22RA1" "IL22RA2" "IL22"
$ 04060_19 : chr [1:3] "IL6ST" "IL11RA" "IL11"
$ 04670_9 : chr [1:3] "ITGB2" "ITGAM" "JAM3"
$ 05134_4 : chr [1:3] "ITGAM" "ITGB2" "C3"
$ 00100_6 : chr [1:6] "DHCR24" "LSS" "TM7SF2" "MSMO1" ...
$ 00790_8 : chr [1:4] "MOCS2" "MOCS1" "GPHN" "MOCOS"
$ 04060_8 : chr [1:3] "IL2RG" "IL7R" "IL7"
$ 04064_14 : chr [1:3] "PLCG1" "ZAP70" "LAT"
$ 04390_10 : chr [1:4] "YAP1" "WWTR1" "TP73" "BBC3"
$ 05165_16 : chr [1:3] "NFX1" "UBE3A" "TERT"
> Drugs<-PrioSubtypeDrug(Geneexp,Cancer,"Control",UserGS,spw.min.sz=1,
+ drug.spw.data=UserDS,drug.spw.min.sz=1,
+ nperm=10,E_FDR=1,S_FDR=1)
Error in .filterAndMapGenesAndGeneSets(param) :
The gene set list contains duplicated gene set names.
Calls: PrioSubtypeDrug ... gsva -> gsva -> .local -> .filterAndMapGenesAndGeneSets
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 0.1.8
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines at lines 139-147 [unnamed-chunk-5] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
The gene set list contains duplicated gene set names.
--- failed re-building ‘vignette.Rmd’
SUMMARY: processing the following file failed:
‘vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 0.1.9
Check: installed package size
Result: NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
data 5.0Mb
Flavor: r-prerel-macos-x86_64
Version: 0.1.9
Check: package dependencies
Result: ERROR
Package required but not available: ‘GSVA’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-release-macos-arm64, r-release-macos-x86_64
Version: 0.1.9
Check: dependencies in R code
Result: WARN
Missing or unexported objects:
‘GSVA::gsvaParam’ ‘GSVA::ssgseaParam’
Flavor: r-oldrel-macos-arm64
Version: 0.1.9
Check: examples
Result: ERROR
Running examples in ‘SubtypeDrug-Ex.R’ failed
The error most likely occurred in:
> ### Name: PrioSubtypeDrug
> ### Title: Prioritization of candidate cancer subtype-specific drugs
> ### (PrioSubtypeDrug)
> ### Aliases: PrioSubtypeDrug
>
> ### ** Examples
>
> require(GSVA)
Loading required package: GSVA
> require(parallel)
Loading required package: parallel
> ## Get simulated breast cancer gene expression profile data.
> Geneexp<-get("Geneexp")
> ## Obtain sample subtype data and calculate breast cancer subtype-specific drugs.
> Subtype<-system.file("extdata", "Subtype_labels.cls", package = "SubtypeDrug")
>
> ## Subpathway list data and drug subpathway association data
> ## were stored in packet `SubtypeDrugData`.
> ## `SubtypeDrugData` has been uploaded to the github repository.
> ## If subpathway list data and drug subpathway association data are needed,
> ## users can download and install through `install_github` function and
> ## set parameter url=""hanjunwei-lab/SubtypeDrugData".
> ## After installing and loading package `SubtypeDrugData`,
> ## users can use the following command to get the data.
> ## Get subpathway list data.
> ## If the gene expression profile contains gene Symbol.
> ## data(SpwSymbolList)
> ## If the gene expression profile contains gene Entrezid.
> ## data(SpwEntrezidList)
> ## Get drug subpathway association data.
> ## data(DrugSpwData)
>
> ## Identify breast subtype-specific drugs.
> ## Subtype_drugs<-PrioSubtypeDrug(Geneexp,Subtype,"Control",SpwSymbolList,drug.spw.data=DrugSpwData,
> ## E_FDR=1,S_FDR=1)
>
> ## Identify breast cancer-related drugs in only two types of samples: breast cancer and control.
> Cancer<-system.file("extdata", "Cancer_normal_labels.cls", package = "SubtypeDrug")
> ## Disease_drugs<-PrioSubtypeDrug(Geneexp,Cancer,"Control",SpwSymbolList,drug.spw.data=DrugSpwData,
> ## E_FDR=1,S_FDR=1)
>
> ## The function PrioSubtypeDrug() can also support user-defined data.
> Geneexp<-get("GeneexpT")
> ## User-defined drug regulation data should resemble the structure below
> UserDS<-get("UserDST")
> str(UserDS)
List of 2
$ chloramphenicol(1.24e-05M):List of 2
..$ Target_upregulation : chr [1:5] "04060_26" "04610_11" "04670_6" "05162_13" ...
..$ Target_downregulation: chr [1:5] "04150_14" "04610_11" "04625_34" "04670_6" ...
$ thioridazine(1e-06M) :List of 2
..$ Target_upregulation : chr [1:5] "04060_4" "04060_19" "04670_9" "05134_4" ...
..$ Target_downregulation: chr [1:5] "00790_8" "04060_8" "04064_14" "04390_10" ...
> ## Need to load gene set data consistent with drug regulation data.
> UserGS<-get("UserGST")
> str(UserGS)
List of 17
$ 04060_26 : chr [1:3] "ACVR1" "AMHR2" "AMH"
$ 04610_11 : chr [1:3] "C3" "CFB" "CFD"
$ 04670_6 : chr [1:3] "ITGB2" "F11R" "ITGAL"
$ 05162_13 : chr [1:3] "IL12A" "IL12B" "FCGR2B"
$ 05206_112: chr [1:3] "MIR143" "ATM" "TP53"
$ 04150_14 : chr [1:2] "SLC7A5" "SLC3A2"
$ 04625_34 : chr [1:4] "MDM2" "IRF1" "IL12A" "IL12B"
$ 04060_4 : chr [1:4] "IL10RB" "IL22RA1" "IL22RA2" "IL22"
$ 04060_19 : chr [1:3] "IL6ST" "IL11RA" "IL11"
$ 04670_9 : chr [1:3] "ITGB2" "ITGAM" "JAM3"
$ 05134_4 : chr [1:3] "ITGAM" "ITGB2" "C3"
$ 00100_6 : chr [1:6] "DHCR24" "LSS" "TM7SF2" "MSMO1" ...
$ 00790_8 : chr [1:4] "MOCS2" "MOCS1" "GPHN" "MOCOS"
$ 04060_8 : chr [1:3] "IL2RG" "IL7R" "IL7"
$ 04064_14 : chr [1:3] "PLCG1" "ZAP70" "LAT"
$ 04390_10 : chr [1:4] "YAP1" "WWTR1" "TP73" "BBC3"
$ 05165_16 : chr [1:3] "NFX1" "UBE3A" "TERT"
> Drugs<-PrioSubtypeDrug(Geneexp,Cancer,"Control",UserGS,spw.min.sz=1,
+ drug.spw.data=UserDS,drug.spw.min.sz=1,
+ nperm=10,E_FDR=1,S_FDR=1)
Error: 'gsvaParam' is not an exported object from 'namespace:GSVA'
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.1.9
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 139-147 [unnamed-chunk-5] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
'gsvaParam' is not an exported object from 'namespace:GSVA'
--- failed re-building ‘vignette.Rmd’
SUMMARY: processing the following file failed:
‘vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.1.8
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-windows-x86_64