* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/ecap.Rcheck’
* using R Under development (unstable) (2022-03-29 r82022)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘ecap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ecap’ version ‘0.1.2’
* package encoding: UTF-8
* 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 ‘ecap’ can be installed ... [8s/33s] OK
* checking package directory ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [13s/63s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [5s/16s]
 [5s/18s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ecap)
  Loading required package: splines
  Loading required package: quadprog
  Loading required package: ggplot2
  > 
  > test_check("ecap")
   ----------- FAILURE REPORT -------------- 
   --- failure: length > 1 in coercion to logical ---
   --- srcref --- 
  : 
   --- package (from environment) --- 
  splines
   --- call from context --- 
  splines::splineDesign(Aknots, rep(k.pivot, 2L), 4, c(0, 1), derivs = deriv)
   --- call from argument --- 
  !outer.ok && nk < 2 * ord - 1
   --- R stacktrace ---
  where 1: splines::splineDesign(Aknots, rep(k.pivot, 2L), 4, c(0, 1), derivs = deriv)
  where 2: myns(fine_grid, knots = quantiles, intercept = T, Boundary.knots = knot.range)
  where 3: ecap(unadjusted_prob = p_obs, win_var = win_var, win_id = 1, 
      bias_indicator = FALSE)
  where 4: doTryCatch(return(expr), name, parentenv, handler)
  where 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 6: tryCatchList(expr, classes, parentenv, handlers)
  where 7: 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, nlines = 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))
  })
  where 8 at test-ecap.R#5: try(ecap(unadjusted_prob = p_obs, win_var = win_var, win_id = 1, 
      bias_indicator = FALSE))
  where 9: eval(code, test_env)
  where 10: eval(code, test_env)
  where 11: withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error)
  where 12: doTryCatch(return(expr), name, parentenv, handler)
  where 13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  where 15: doTryCatch(return(expr), name, parentenv, handler)
  where 16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), 
      names[nh], parentenv, handlers[[nh]])
  where 17: tryCatchList(expr, classes, parentenv, handlers)
  where 18: tryCatch(withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error), error = handle_fatal, 
      skip = function(e) {
      })
  where 19: test_code(desc, code, env = parent.frame(), reporter = reporter)
  where 20 at test-ecap.R#1: test_that("ecap model generation and prediction works", {
      p_obs <- runif(1000, 0, 1)
      p_new <- runif(1000, 0, 1)
      win_var <- rbinom(length(p_obs), 1, p_obs)
      ecap_fit <- try(ecap(unadjusted_prob = p_obs, win_var = win_var, 
          win_id = 1, bias_indicator = FALSE))
      ecap_fit_biased <- try(ecap(unadjusted_prob = p_obs, win_var = win_var, 
          win_id = 1, bias_indicator = FALSE))
      ecap_new <- try(predict(object = ecap_fit, new_unadjusted = p_new))
      expect_equivalent(length(p_obs), 1000)
      expect_equivalent(class(ecap_fit), "ecap")
      expect_equivalent(class(ecap_fit_biased), "ecap")
      expect_equivalent(class(ecap_new), "numeric")
  })
  where 21: eval(code, test_env)
  where 22: eval(code, test_env)
  where 23: withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error)
  where 24: doTryCatch(return(expr), name, parentenv, handler)
  where 25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 26: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  where 27: doTryCatch(return(expr), name, parentenv, handler)
  where 28: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), 
      names[nh], parentenv, handlers[[nh]])
  where 29: tryCatchList(expr, classes, parentenv, handlers)
  where 30: tryCatch(withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error), error = handle_fatal, 
      skip = function(e) {
      })
  where 31: test_code(NULL, exprs, env)
  where 32: source_file(path, child_env(env), wrap = wrap)
  where 33: FUN(X[[i]], ...)
  where 34: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  where 35: doTryCatch(return(expr), name, parentenv, handler)
  where 36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 37: tryCatchList(expr, classes, parentenv, handlers)
  where 38: tryCatch(code, testthat_abort_reporter = function(cnd) {
      cat(conditionMessage(cnd), "\n")
      NULL
  })
  where 39: with_reporter(reporters$multi, lapply(test_paths, test_one_file, 
      env = env, wrap = wrap))
  where 40: test_files(test_dir = test_dir, test_package = test_package, 
      test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 
      env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 
      wrap = wrap, load_package = load_package)
  where 41: test_files(test_dir = path, test_paths = test_paths, test_package = package, 
      reporter = reporter, load_helpers = load_helpers, env = env, 
      stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 
      wrap = wrap, load_package = load_package, parallel = parallel)
  where 42: test_dir("testthat", package = package, reporter = reporter, 
      ..., load_package = "installed")
  where 43: test_check("ecap")
  
   --- value of length: 2 type: logical ---
  [1]  TRUE FALSE
   --- function from context --- 
  function (knots, x, ord = 4L, derivs = 0L, outer.ok = FALSE, 
      sparse = FALSE) 
  {
      if ((nk <- length(knots <- as.numeric(knots))) <= 0) 
          stop("must have at least 'ord' knots")
      if (is.unsorted(knots)) 
          knots <- sort.int(knots)
      x <- as.numeric(x)
      nx <- length(x)
      if (length(derivs) > nx) 
          stop("length of 'derivs' is larger than length of 'x'")
      if (length(derivs) < 1L) 
          stop("empty 'derivs'")
      ord <- as.integer(ord)
      if (ord > nk || ord < 1) 
          stop("'ord' must be positive integer, at most the number of knots")
      if (!outer.ok && nk < 2 * ord - 1) 
          stop(gettextf("need at least %s (=%d) knots", "2*ord -1", 
              2 * ord - 1), domain = NA)
      degree <- ord - 1L
      if (need.outer <- any(x < knots[ord] | knots[nk - degree] < 
          x)) {
          if (outer.ok) {
              in.x <- knots[1L] <= x & x <= knots[nk]
              if ((x.out <- !all(in.x))) {
                  x <- x[in.x]
                  nnx <- length(x)
              }
              dkn <- diff(knots)[(nk - 1L):1]
              knots <- knots[c(rep.int(1L, degree), seq_len(nk), 
                  rep.int(nk, max(0L, ord - match(TRUE, dkn > 0))))]
          }
          else stop(gettextf("the 'x' data must be in the range %g to %g unless you set '%s'", 
              knots[ord], knots[nk - degree], "outer.ok = TRUE"), 
              domain = NA)
      }
      temp <- .Call(C_spline_basis, knots, ord, x, derivs)
      ncoef <- nk - ord
      ii <- if (need.outer && x.out) {
          rep.int((1L:nx)[in.x], rep.int(ord, nnx))
      }
      else rep.int(1L:nx, rep.int(ord, nx))
      jj <- c(outer(1L:ord, attr(temp, "Offsets"), `+`))
      if (sparse) {
          if (is.null(tryCatch(loadNamespace("Matrix"), error = function(e) NULL))) 
              stop(gettextf("%s needs package 'Matrix' correctly installed", 
                  "splineDesign(*, sparse=TRUE)"), domain = NA)
          if (need.outer) {
              jj <- jj - degree - 1L
              ok <- 0 <= jj & jj < ncoef
              methods::as(methods::new("dgTMatrix", i = ii[ok] - 
                  1L, j = jj[ok], x = as.double(temp[ok]), Dim = c(nx, 
                  ncoef)), "CsparseMatrix")
          }
          else methods::as(methods::new("dgTMatrix", i = ii - 1L, 
              j = jj - 1L, x = as.double(temp), Dim = c(nx, ncoef)), 
              "CsparseMatrix")
      }
      else {
          design <- matrix(double(nx * ncoef), nx, ncoef)
          if (need.outer) {
              jj <- jj - degree
              ok <- 1 <= jj & jj <= ncoef
              design[cbind(ii, jj)[ok, , drop = FALSE]] <- temp[ok]
          }
          else design[cbind(ii, jj)] <- temp
          design
      }
  }
  <bytecode: 0x6b866a8>
  <environment: namespace:splines>
   --- function search by body ---
  Function splineDesign in namespace splines has this body.
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [6s/22s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘ecap-demo.Rmd’ using rmarkdown
Loading required package: splines
Loading required package: quadprog
Loading required package: ggplot2
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
splines
 --- call from context --- 
splineDesign(Aknots, rep(k.pivot, 2L), 4, c(0, 1), derivs = deriv)
 --- call from argument --- 
!outer.ok && nk < 2 * ord - 1
 --- R stacktrace ---
where 1: splineDesign(Aknots, rep(k.pivot, 2L), 4, c(0, 1), derivs = deriv)
where 2: myns(fine_grid, knots = quantiles, intercept = T, Boundary.knots = knot.range)
where 3: ecap(unadjusted_prob = p_obs_train, win_var = win_var_train, 
    win_id = 1, bias_indicator = T)
where 4: eval(expr, envir, enclos)
where 5: eval(expr, envir, enclos)
where 6: eval_with_user_handlers(expr, envir, enclos, user_handlers)
where 7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
where 8: withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)
where 9: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler))
where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), 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$message), stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options))
where 14: in_dir(input_dir(), expr)
where 15: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options)))
where 16: eng_r(options)
where 17: block_exec(params)
where 18: call_block(x)
where 19: process_group.block(group)
where 20: process_group(group)
where 21: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 22: process_file(text, output)
where 23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
where 25: vweave_rmarkdown(...)
where 26: engine$weave(file, quiet = quiet, encoding = enc)
where 27: doTryCatch(return(expr), name, parentenv, handler)
where 28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 29: tryCatchList(expr, classes, parentenv, handlers)
where 30: tryCatch({
    engine$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)))
})
where 31: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/ecap.Rcheck/vign_test/ecap")

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (knots, x, ord = 4L, derivs = 0L, outer.ok = FALSE, 
    sparse = FALSE) 
{
    if ((nk <- length(knots <- as.numeric(knots))) <= 0) 
        stop("must have at least 'ord' knots")
    if (is.unsorted(knots)) 
        knots <- sort.int(knots)
    x <- as.numeric(x)
    nx <- length(x)
    if (length(derivs) > nx) 
        stop("length of 'derivs' is larger than length of 'x'")
    if (length(derivs) < 1L) 
        stop("empty 'derivs'")
    ord <- as.integer(ord)
    if (ord > nk || ord < 1) 
        stop("'ord' must be positive integer, at most the number of knots")
    if (!outer.ok && nk < 2 * ord - 1) 
        stop(gettextf("need at least %s (=%d) knots", "2*ord -1", 
            2 * ord - 1), domain = NA)
    degree <- ord - 1L
    if (need.outer <- any(x < knots[ord] | knots[nk - degree] < 
        x)) {
        if (outer.ok) {
            in.x <- knots[1L] <= x & x <= knots[nk]
            if ((x.out <- !all(in.x))) {
                x <- x[in.x]
                nnx <- length(x)
            }
            dkn <- diff(knots)[(nk - 1L):1]
            knots <- knots[c(rep.int(1L, degree), seq_len(nk), 
                rep.int(nk, max(0L, ord - match(TRUE, dkn > 0))))]
        }
        else stop(gettextf("the 'x' data must be in the range %g to %g unless you set '%s'", 
            knots[ord], knots[nk - degree], "outer.ok = TRUE"), 
            domain = NA)
    }
    temp <- .Call(C_spline_basis, knots, ord, x, derivs)
    ncoef <- nk - ord
    ii <- if (need.outer && x.out) {
        rep.int((1L:nx)[in.x], rep.int(ord, nnx))
    }
    else rep.int(1L:nx, rep.int(ord, nx))
    jj <- c(outer(1L:ord, attr(temp, "Offsets"), `+`))
    if (sparse) {
        if (is.null(tryCatch(loadNamespace("Matrix"), error = function(e) NULL))) 
            stop(gettextf("%s needs package 'Matrix' correctly installed", 
                "splineDesign(*, sparse=TRUE)"), domain = NA)
        if (need.outer) {
            jj <- jj - degree - 1L
            ok <- 0 <= jj & jj < ncoef
            methods::as(methods::new("dgTMatrix", i = ii[ok] - 
                1L, j = jj[ok], x = as.double(temp[ok]), Dim = c(nx, 
                ncoef)), "CsparseMatrix")
        }
        else methods::as(methods::new("dgTMatrix", i = ii - 1L, 
            j = jj - 1L, x = as.double(temp), Dim = c(nx, ncoef)), 
            "CsparseMatrix")
    }
    else {
        design <- matrix(double(nx * ncoef), nx, ncoef)
        if (need.outer) {
            jj <- jj - degree
            ok <- 1 <= jj & jj <= ncoef
            design[cbind(ii, jj)[ok, , drop = FALSE]] <- temp[ok]
        }
        else design[cbind(ii, jj)] <- temp
        design
    }
}
<bytecode: 0x7117078>
<environment: namespace:splines>
 --- function search by body ---
Function splineDesign in namespace splines has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical

* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/ecap.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 6:29.73, 77.01 + 10.81