CRAN Package Check Results for Package dynr

Last updated on 2020-01-24 23:50:30 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.15-1 34.20 219.12 253.32 WARN
r-devel-linux-x86_64-debian-gcc 0.1.15-1 28.04 171.49 199.53 OK
r-devel-linux-x86_64-fedora-clang 0.1.15-1 315.09 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1.15-1 306.64 NOTE
r-devel-windows-ix86+x86_64 0.1.15-1 141.00 253.00 394.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 0.1.15-1 126.00 340.00 466.00 NOTE
r-patched-linux-x86_64 0.1.15-1 28.26 199.91 228.17 OK
r-patched-solaris-x86 0.1.15-1 413.30 NOTE
r-release-linux-x86_64 0.1.15-1 26.78 198.04 224.82 OK
r-release-windows-ix86+x86_64 0.1.15-1 81.00 237.00 318.00 NOTE
r-release-osx-x86_64 0.1.15-1 NOTE
r-oldrel-windows-ix86+x86_64 0.1.15-1 73.00 214.00 287.00 NOTE
r-oldrel-osx-x86_64 0.1.15-1 NOTE

Check Details

Version: 0.1.15-1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'linearSDE.Rmd' using rmarkdown
    make[1]: Entering directory '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynr.Rcheck/vign_test/dynr/vignettes'
    clang-9 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/include -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -g -O3 -Wall -pedantic -mtune=native -c LinearSDE.c -o LinearSDE.o
    clang-9 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o LinearSDE.so LinearSDE.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
    make[1]: Leaving directory '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynr.Rcheck/vign_test/dynr/vignettes'
    make[1]: Entering directory '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynr.Rcheck/vign_test/dynr/vignettes'
    make[1]: Leaving directory '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynr.Rcheck/vign_test/dynr/vignettes'
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    dynr
     --- call from context ---
    checkHessian(x, transformation)
     --- call from argument ---
    if (class(V1) == "try-error") {
     failHess <- failHess + 1
     warning("Hessian is not invertible; used pseudo-inverse.\nModel might not be identified or is not at an optimal solution.\nRegard standard errors suspiciously.",
     call. = FALSE)
     V1 <- MASS::ginv(useHess)
    }
     --- R stacktrace ---
    where 1: checkHessian(x, transformation)
    where 2: endProcessing(output, transformation, conf.level)
    where 3: dynr.cook(model)
    where 4: eval(expr, envir, enclos)
    where 5: eval(expr, envir, enclos)
    where 6: withVisible(eval(expr, envir, enclos))
    where 7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 11: evaluate::evaluate(...)
    where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 14: block_exec(params)
    where 15: call_block(x)
    where 16: process_group.block(group)
    where 17: process_group(group)
    where 18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 19: process_file(text, output)
    where 20: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 21: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     output_dir = getwd(), ...)
    where 22: vweave_rmarkdown(...)
    where 23: engine$weave(file, quiet = quiet, encoding = enc)
    where 24: doTryCatch(return(expr), name, parentenv, handler)
    where 25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 26: tryCatchList(expr, classes, parentenv, handlers)
    where 27: tryCatch({
     engine$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)
     }
    }, error = function(e) {
     OK <<- FALSE
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 28: tools:::.buildOneVignette("linearSDE.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynr.Rcheck/vign_test/dynr",
     TRUE, FALSE, "linearSDE", "UTF-8", "/tmp/Rtmpp2vn7k/file2823596eb649.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (x, transformation)
    {
     failHess <- 0
     if (!is.finite(x$neg.log.likelihood)) {
     x$hessian.matrix <- matrix(NA, nrow(x$hessian.matrix),
     ncol(x$hessian.matrix))
     x <- failedProcessing(x, transformation)
     return(x)
     }
     if (any(!is.finite(x$hessian.matrix))) {
     warning("Found infinite, NaN, or missing values in Hessian. Add that to the list of things that are problematic:\nproblematic <- c('mankind instead of humankind', 'claims of Cherokee heritage', 'gender income gap', ..., 'your Hessian')",
     call. = FALSE)
     x <- failedProcessing(x, transformation)
     return(x)
     }
     diagH <- diag(x$hessian.matrix)
     zdiag <- diagH == 0
     if (any(zdiag)) {
     diagH[zdiag] <- 1e-13
     diag(x$hessian.matrix) <- diagH
     }
     if (is.positive.definite(x$hessian.matrix) || is.positive.definite2(x$hessian.matrix)) {
     useHess <- x$hessian.matrix
     }
     else {
     failHess <- failHess + 1
     msg <- "Hessian is not positive definite. The standard errors were computed using the nearest positive definite approximation to the Hessian matrix."
     warning(msg, call. = FALSE)
     useHess <- (Matrix::nearPD(x$hessian.matrix, conv.norm.type = "F"))$mat
     }
     V1 <- try(solve(useHess))
     if (class(V1) == "try-error") {
     failHess <- failHess + 1
     warning("Hessian is not invertible; used pseudo-inverse.\nModel might not be identified or is not at an optimal solution.\nRegard standard errors suspiciously.",
     call. = FALSE)
     V1 <- MASS::ginv(useHess)
     }
     x$inv.hessian <- V1
     x$hessian.status <- failHess
     return(x)
    }
    <bytecode: 0x11846e68>
    <environment: namespace:dynr>
     --- function search by body ---
    Function checkHessian in namespace dynr has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 133-134 (linearSDE.Rmd)
    Error: processing vignette 'linearSDE.Rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'linearSDE.Rmd'
    
    --- re-building 'InstallationForDevelopers.Rnw' using Sweave
    --- finished re-building 'InstallationForDevelopers.Rnw'
    
    --- re-building 'InstallationForUsers.Rnw' using Sweave
    --- finished re-building 'InstallationForUsers.Rnw'
    
    --- re-building 'LinearDiscreteTimeModels.Rnw' using Sweave
    --- finished re-building 'LinearDiscreteTimeModels.Rnw'
    
    --- re-building 'NonlinearContinuousTimeModels.Rnw' using Sweave
    --- finished re-building 'NonlinearContinuousTimeModels.Rnw'
    
    SUMMARY: processing the following file failed:
     'linearSDE.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.15-1
Check: installed package size
Result: NOTE
     installed size is 6.2Mb
     sub-directories of 1Mb or more:
     data 3.1Mb
     doc 1.5Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.1.15-1
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘Rdpack’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64