CRAN Package Check Results for Package MetaSKAT

Last updated on 2020-12-11 06:47:39 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.81 15.89 78.67 94.56 OK
r-devel-linux-x86_64-debian-gcc 0.81 11.81 61.38 73.19 OK
r-devel-linux-x86_64-fedora-clang 0.81 132.79 OK
r-devel-linux-x86_64-fedora-gcc 0.81 110.20 OK
r-devel-windows-ix86+x86_64 0.81 38.00 139.00 177.00 OK
r-patched-linux-x86_64 0.81 14.19 74.76 88.95 OK
r-patched-solaris-x86 0.81 160.00 WARN
r-release-linux-x86_64 0.81 14.59 74.31 88.90 OK
r-release-macos-x86_64 0.81 OK
r-release-windows-ix86+x86_64 0.81 31.00 141.00 172.00 OK
r-oldrel-macos-x86_64 0.81 OK
r-oldrel-windows-ix86+x86_64 0.81 31.00 126.00 157.00 OK

Check Details

Version: 0.81
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘MetaSKAT.Rnw’ using Sweave
    Loading required package: Matrix
    Loading required package: SPAtest
    Read SetID file
    
    SetID file has10sets
    
    Read Bim file
    
    Bim file has828markers
    
    Merge datasets and get set info
    
    Save was done successfully!
    
    Close the opened Bed file: /home/ripley/R/packages/tests32/MetaSKAT.Rcheck/vign_test/MetaSKAT/vignettes/01.bed
    
    Read SetID file
    
    SetID file has10sets
    
    Read Bim file
    
    Bim file has828markers
    
    Close the opened MSSD file: ./01.MSSD
    
    Merge datasets and get set info
    
    Save was done successfully!
    
    Close the opened Bed file: /home/ripley/R/packages/tests32/MetaSKAT.Rcheck/vign_test/MetaSKAT/vignettes/02.bed
    
    Read SetID file
    
    SetID file has10sets
    
    Read Bim file
    
    Bim file has828markers
    
    Close the opened MSSD file: ./02.MSSD
    
    Merge datasets and get set info
    
    Save was done successfully!
    
    Close the opened Bed file: /home/ripley/R/packages/tests32/MetaSKAT.Rcheck/vign_test/MetaSKAT/vignettes/03.bed
    
    Number of cohorts = 3
    
    997 samples, 10 sets, 528 SNPs and 465 unique SNPs
    
    
     *** caught segfault ***
    address 7195a620, cause 'memory not mapped'
    
    Traceback:
     1: Open_MSSD_File_2Read(File.Mat.vec, File.Info.vec)
     2: eval(expr, .GlobalEnv)
     3: eval(expr, .GlobalEnv)
     4: withVisible(eval(expr, .GlobalEnv))
     5: doTryCatch(return(expr), name, parentenv, handler)
     6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
     9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
    10: evalFunc(ce, options)
    11: tryCatchList(expr, classes, parentenv, handlers)
    12: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
    13: driver$runcode(drobj, chunk, chunkopts)
    14: utils::Sweave(...)
    15: engine$weave(file, quiet = quiet, encoding = enc)
    16: doTryCatch(return(expr), name, parentenv, handler)
    17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    18: tryCatchList(expr, classes, parentenv, handlers)
    19: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    20: tools:::buildVignettes(dir = "/home/ripley/R/packages/tests32/MetaSKAT.Rcheck/vign_test/MetaSKAT", ser_elibs = "/tmp/Rtmp.JaOKx/file2f254141ed0.rds")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86