• using R Under development (unstable) (2025-09-25 r88874)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-4) 15.2.0     GNU Fortran (Debian 15.2.0-4) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘RapidoPGS/DESCRIPTION’ ... OK
• this is package ‘RapidoPGS’ version ‘2.3.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘RapidoPGS’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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/7s] OK
• checking whether the package can be loaded with stated dependencies ... [6s/7s] OK
• checking whether the package can be unloaded cleanly ... [6s/8s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/7s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/6s] OK
• checking loading without being on the library search path ... [6s/7s] 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 ... [23s/31s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
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• 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 ... [4s/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 ... [5s/7s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [14s/19s] 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
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs