CRAN Package Check Results for Package SubtypeDrug

Last updated on 2024-03-02 19:50:31 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.7 60.89 515.56 576.45 OK
r-devel-linux-x86_64-debian-gcc 0.1.7 47.87 390.70 438.57 OK
r-devel-linux-x86_64-fedora-clang 0.1.7 723.66 OK
r-devel-linux-x86_64-fedora-gcc 0.1.7 745.06 OK
r-devel-windows-x86_64 0.1.7 6.00 5.00 11.00 ERROR
r-patched-linux-x86_64 0.1.7 42.78 507.06 549.84 OK
r-release-linux-x86_64 0.1.7 40.03 501.72 541.75 OK
r-release-macos-arm64 0.1.7 9.00 ERROR
r-release-macos-x86_64 0.1.7 11.00 ERROR
r-release-windows-x86_64 0.1.7 68.00 530.00 598.00 OK
r-oldrel-macos-arm64 0.1.7 168.00 ERROR
r-oldrel-windows-x86_64 0.1.7 63.00 441.00 504.00 ERROR

Check Details

Version: 0.1.7
Check: whether package can be installed
Result: ERROR Installation failed. Flavor: r-devel-windows-x86_64

Version: 0.1.7
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: 0.1.7
Check: dependencies in R code
Result: WARN Missing or unexported objects: ‘GSVA::gsvaParam’ ‘GSVA::ssgseaParam’ Flavors: r-oldrel-macos-arm64, r-oldrel-windows-x86_64

Version: 0.1.7
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 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: 'gsvaParam' is not an exported object from 'namespace:GSVA' Execution halted Flavors: r-oldrel-macos-arm64, r-oldrel-windows-x86_64

Version: 0.1.7
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: 0.1.7
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-windows-x86_64