* using log directory 'd:/Rcompile/CRANpkg/local/4.2/SubtypeDrug.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* checking for file 'SubtypeDrug/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SubtypeDrug' version '0.1.9'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SubtypeDrug' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
Missing or unexported objects:
  'GSVA::gsvaParam' 'GSVA::ssgseaParam'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [38s] OK
* checking Rd files ... [2s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [22s] 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [19s] 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:
'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

* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING