CRAN Package Check Results for Package RapidoPGS

Last updated on 2025-10-09 15:50:16 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	2.3.1	27.11	218.93	246.04	ERROR
r-devel-linux-x86_64-debian-gcc	2.3.1	20.02	154.71	174.73	ERROR
r-devel-linux-x86_64-fedora-clang	2.3.1			383.35	ERROR
r-devel-linux-x86_64-fedora-gcc	2.3.1			399.40	OK
r-devel-windows-x86_64	2.3.1	28.00	199.00	227.00	ERROR
r-patched-linux-x86_64	2.3.1	27.96	206.66	234.62	OK
r-release-linux-x86_64	2.3.1	26.21	204.82	231.03	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	202.00	229.00	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	38.00	254.00	292.00	OK

Check Details

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 Flavors: r-devel-linux-x86_64-debian-clang, 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 Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.3.1
Check: examples
Result: 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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64

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-fedora-clang

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 --- 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-windows-x86_64