Last updated on 2025-09-26 20:48:51 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.3.1 | 28.45 | 221.84 | 250.29 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.3.1 | 19.58 | 154.36 | 173.94 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.3.1 | 384.73 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.3.1 | 383.12 | OK | |||
| r-devel-windows-x86_64 | 2.3.1 | 27.00 | 199.00 | 226.00 | OK | |
| r-patched-linux-x86_64 | 2.3.1 | 25.75 | 207.03 | 232.78 | OK | |
| r-release-linux-x86_64 | 2.3.1 | 27.59 | 207.09 | 234.68 | OK | |
| r-release-macos-arm64 | 2.3.1 | 101.00 | OK | |||
| r-release-macos-x86_64 | 2.3.1 | 223.00 | OK | |||
| r-release-windows-x86_64 | 2.3.1 | 27.00 | 190.00 | 217.00 | OK | |
| r-oldrel-macos-arm64 | 2.3.1 | 102.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.3.1 | 192.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.3.1 | 39.00 | 261.00 | 300.00 | OK |
Version: 2.3.1
Check: examples
Result: ERROR
Running examples in ‘RapidoPGS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.3.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Computing_RapidoPGSmulti.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- 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
Flavor: r-devel-linux-x86_64-debian-gcc