CRAN Package Check Results for Package doBy

Last updated on 2019-12-08 23:47:21 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 4.6-3 13.06 109.85 122.91 ERROR
r-devel-linux-x86_64-debian-gcc 4.6-3 10.69 91.48 102.17 OK
r-devel-linux-x86_64-fedora-clang 4.6-3 158.54 OK
r-devel-linux-x86_64-fedora-gcc 4.6-3 147.56 OK
r-devel-windows-ix86+x86_64 4.6-3 23.00 197.00 220.00 OK
r-devel-windows-ix86+x86_64-gcc8 4.6-3 25.00 145.00 170.00 OK
r-patched-linux-x86_64 4.6-3 13.26 106.17 119.43 OK
r-patched-solaris-x86 4.6-3 209.30 OK
r-release-linux-x86_64 4.6-3 11.13 105.62 116.75 OK
r-release-windows-ix86+x86_64 4.6-3 19.00 140.00 159.00 OK
r-release-osx-x86_64 4.6-3 OK
r-oldrel-windows-ix86+x86_64 4.6-3 13.00 119.00 132.00 OK
r-oldrel-osx-x86_64 4.6-3 OK

Check Details

Version: 4.6-3
Check: examples
Result: ERROR
    Running examples in 'doBy-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: linest-matrix
    > ### Title: Linear estimates matrix
    > ### Aliases: linest-matrix LE_matrix LE_matrix.default
    > ### aggregate_linest_list get_linest_list
    > ### Keywords: utilities
    >
    > ### ** Examples
    >
    >
    > ## Two way anova:
    >
    > data(warpbreaks)
    >
    > ## An additive model
    > m0 <- lm(breaks ~ wool + tension, data=warpbreaks)
    >
    > ## Estimate mean for each wool type, for tension="M":
    > K <- LE_matrix(m0, at=list(wool=c("A", "B"), tension="M"))
    > K
     (Intercept) woolB tensionM tensionH
    [1,] 1 0 1 0
    [2,] 1 1 1 0
    >
    > ## Vanilla computation:
    > K %*% coef(m0)
     [,1]
    [1,] 29.27778
    [2,] 23.50000
    >
    > ## Alternative; also providing standard errors etc:
    > linest(m0, K)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    doBy
     --- call from context ---
    null_basis(object)
     --- call from argument ---
    if (class(m) != "try-error") .null_basis(m) else stop("Can not find null basis for 'object'")
     --- R stacktrace ---
    where 1: null_basis(object)
    where 2: is_estimable(L, null_basis(object))
    where 3: linest.lm(m0, K)
    where 4: linest(m0, K)
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (object)
    {
     .null_basis <- function(object) {
     S <- svd(object)
     id <- S$d < 1e-15
     if (any(id)) {
     null.basis <- S$v[, id, drop = FALSE]
     null.basis
     }
     else {
     matrix(nrow = ncol(object), ncol = 0)
     }
     }
     if (is.character(object)) {
     stop("'object' of type 'character' not valid")
     }
     if (is.vector(object)) {
     object <- matrix(object, ncol = 1)
     }
     if (inherits(object, c("matrix", "Matrix"))) {
     .null_basis(object)
     }
     else {
     m <- try(model.matrix(object), silent = TRUE)
     if (class(m) != "try-error")
     .null_basis(m)
     else stop("Can not find null basis for 'object'")
     }
    }
    <bytecode: 0x7d88610>
    <environment: namespace:doBy>
     --- function search by body ---
    Function null_basis in namespace doBy has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(m) != "try-error") .null_basis(m) else stop("Can not find null basis for 'object'") :
     the condition has length > 1
    Calls: linest -> linest.lm -> is_estimable -> null_basis
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 4.6-3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'doby.Rnw' using knitr
    --- finished re-building 'doby.Rnw'
    
    --- re-building 'linest-lsmeans.Rnw' using knitr
    Warning in dir.create("figures") : 'figures' already exists
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    doBy
     --- call from context ---
    null_basis(object)
     --- call from argument ---
    if (class(m) != "try-error") .null_basis(m) else stop("Can not find null basis for 'object'")
     --- R stacktrace ---
    where 1: null_basis(object)
    where 2: is_estimable(L, null_basis(object))
    where 3: linest.lm(tooth1, L)
    where 4: linest(tooth1, L)
    where 5: eval(expr, envir, enclos)
    where 6: eval(expr, envir, enclos)
    where 7: withVisible(eval(expr, envir, enclos))
    where 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 12: evaluate::evaluate(...)
    where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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: 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$render, options)))
    where 15: block_exec(params)
    where 16: call_block(x)
    where 17: process_group.block(group)
    where 18: process_group(group)
    where 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 20: process_file(text, output)
    where 21: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",
     file)) knit2pandoc else knit)(file, encoding = encoding,
     quiet = quiet, envir = globalenv(), ...)
    where 22: engine$weave(file, quiet = quiet, encoding = enc)
    where 23: doTryCatch(return(expr), name, parentenv, handler)
    where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 25: tryCatchList(expr, classes, parentenv, handlers)
    where 26: tryCatch({
     engine$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 27: tools:::.buildOneVignette("linest-lsmeans.Rnw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/doBy.Rcheck/vign_test/doBy",
     TRUE, FALSE, "linest-lsmeans", "UTF-8", "/tmp/RtmpupOhVw/file202dd1c15.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (object)
    {
     .null_basis <- function(object) {
     S <- svd(object)
     id <- S$d < 1e-15
     if (any(id)) {
     null.basis <- S$v[, id, drop = FALSE]
     null.basis
     }
     else {
     matrix(nrow = ncol(object), ncol = 0)
     }
     }
     if (is.character(object)) {
     stop("'object' of type 'character' not valid")
     }
     if (is.vector(object)) {
     object <- matrix(object, ncol = 1)
     }
     if (inherits(object, c("matrix", "Matrix"))) {
     .null_basis(object)
     }
     else {
     m <- try(model.matrix(object), silent = TRUE)
     if (class(m) != "try-error")
     .null_basis(m)
     else stop("Can not find null basis for 'object'")
     }
    }
    <bytecode: 0xca26ad0>
    <environment: namespace:doBy>
     --- function search by body ---
    Function null_basis in namespace doBy has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 189-191 (linest-lsmeans.Rnw)
    Error: processing vignette 'linest-lsmeans.Rnw' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'linest-lsmeans.Rnw'
    
    SUMMARY: processing the following file failed:
     'linest-lsmeans.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang