* using log directory 'd:/Rcompile/CRANpkg/local/4.6/RapidoPGS.Rcheck'
* using R Under development (unstable) (2025-10-13 r88918 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'RapidoPGS/DESCRIPTION' ... OK
* this is package 'RapidoPGS' version '2.3.1'
* 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 'RapidoPGS' 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s] OK
* checking whether the package can be unloaded cleanly ... [6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s] OK
* checking loading without being on the library search path ... [6s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s] OK
* checking Rd files ... [1s] 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 ... [5s] 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 ... [8s] ERROR
Running examples in 'RapidoPGS-Ex.R' failed
The error most likely occurred in:

> ### Name: rapidopgs_single
> ### Title: Compute PGS from GWAS summary statistics using posteriors from
> ###   Wakefield's approximate Bayes Factors
> ### Aliases: rapidopgs_single
> 
> ### ** Examples
> 
> sumstats <- data.table(SNPID=c("rs139096444","rs3843766","rs61977545", "rs544733737",
+ 		"rs2177641", "rs183491817", "rs72995775","rs78598863", "rs1411315"), 
+ 		CHR=c(4,20,14,2,4,6,6,21,13), 
+ 		BP=c(1479959, 13000913, 29107209, 203573414, 57331393, 11003529, 149256398, 
+ 				25630085, 79166661), 
+ 		REF=c("C","C","C","T","G","C","C","G","T"), 
+ 		ALT=c("A","T","T","A","A","A","T","A","C"), 
+ 		BETA=c(0.012,0.0079,0.0224,0.0033,0.0153,0.058,0.0742,0.001,-0.0131),
+ 		SE=c(0.0099,0.0066,0.0203,0.0171,0.0063,0.0255,0.043,0.0188,0.0074))
> 
> PGS  <- rapidopgs_single(sumstats,  trait = "cc")
Assigning LD blocks...
Loading required namespace: GenomeInfoDb
Failed with error:  'there is no package called 'GenomeInfoDb''
Error in .requirePackage(package) : 
  unable to load required package 'GenomeInfoDb'
Calls: rapidopgs_single ... vapply -> FUN -> is -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [17s] ERROR
Error(s) in re-building vignettes:
--- re-building 'Computing_RapidoPGSmulti.Rmd' using rmarkdown
--- finished re-building 'Computing_RapidoPGSmulti.Rmd'

--- re-building 'Computing_RapidoPGSsingle.Rmd' using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from Computing_RapidoPGSsingle.Rmd:126-128 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. └─RapidoPGS::rapidopgs_single(ds, trait = "cc", build = "hg38")
  2.   ├─ds[, `:=`(ld.block, findOverlaps(snpranges, blranges, select = "last"))]
  3.   └─data.table:::`[.data.table`(...)
  4.     └─base::eval(jsub, SDenv, parent.frame())
  5.       └─base::eval(jsub, SDenv, parent.frame())
  6.         ├─IRanges::findOverlaps(snpranges, blranges, select = "last")
  7.         └─GenomicRanges::findOverlaps(snpranges, blranges, select = "last")
  8.           └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...)
  9.             └─GenomicRanges:::findOverlaps_GNCList(...)
 10.               ├─base::merge(seqinfo(query), seqinfo(subject))
 11.               └─Seqinfo::merge(seqinfo(query), seqinfo(subject))
 12.                 └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
 13.                   └─base::vapply(args, function(arg) is(arg, class(x)), logical(1))
 14.                     └─Seqinfo (local) FUN(X[[i]], ...)
 15.                       └─methods::is(arg, class(x))
 16.                         └─methods::getClassDef(class1)
 17.                           └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Computing_RapidoPGSsingle.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building 'Computing_RapidoPGSsingle.Rmd'

SUMMARY: processing the following file failed:
  'Computing_RapidoPGSsingle.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [3s] OK
* DONE
Status: 2 ERRORs