CRAN Package Check Results for Package sensR

Last updated on 2020-02-10 07:51:53 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.5-1 14.04 125.03 139.07 ERROR
r-devel-linux-x86_64-debian-gcc 1.5-1 10.71 95.17 105.88 ERROR
r-devel-linux-x86_64-fedora-clang 1.5-1 169.71 ERROR
r-devel-linux-x86_64-fedora-gcc 1.5-1 174.80 ERROR
r-devel-windows-ix86+x86_64 1.5-1 37.00 153.00 190.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.5-1 41.00 153.00 194.00 OK
r-patched-linux-x86_64 1.5-1 13.13 125.68 138.81 OK
r-patched-solaris-x86 1.5-1 230.40 OK
r-release-linux-x86_64 1.5-1 13.51 126.86 140.37 OK
r-release-windows-ix86+x86_64 1.5-1 28.00 144.00 172.00 OK
r-release-osx-x86_64 1.5-1 OK
r-oldrel-windows-ix86+x86_64 1.5-1 13.00 182.00 195.00 OK
r-oldrel-osx-x86_64 1.5-1 OK

Check Details

Version: 1.5-1
Check: examples
Result: ERROR
    Running examples in 'sensR-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: clm2twoAC
    > ### Title: Extract 2-AC coefficient table from a cumulative link model
    > ### Aliases: clm2twoAC
    > ### Keywords: models
    >
    > ### ** Examples
    >
    >
    > ## Example of a simple 2-AC model. First the conventional way:
    > twoAC(c(2, 2, 6))
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    sensR
     --- call from context ---
    estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
    if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
    }
     --- R stacktrace ---
    where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
    where 2: twoAC(c(2, 2, 6))
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (data, vcov = TRUE, warn = TRUE)
    {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
    }
    <bytecode: 0x9d1b4e0>
    <environment: namespace:sensR>
     --- function search by body ---
    Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(vcov) != "try-error") { : the condition has length > 1
    Calls: twoAC -> estimate.2AC
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.5-1
Check: tests
Result: ERROR
     Running 'betabin.R' [3s/4s]
     Comparing 'betabin.Rout' to 'betabin.Rout.save' ... OK
     Running 'discrim.R' [2s/3s]
     Comparing 'discrim.Rout' to 'discrim.Rout.save' ... OK
     Running 'test-all.R' [9s/12s]
     Running 'testdouble.R' [3s/4s]
     Running 'twoAC.R' [3s/5s]
    Running the tests in 'tests/twoAC.R' failed.
    Complete output:
     > library(sensR)
     >
     > ## Testing border line cases:
     > twoAC(c(5, 0, 15))
     Results for the 2-AC protocol with data c(5, 0, 15):
     Estimate Std. Error
     tau 0.0000 NA
     d.prime 0.9539 NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 2.287737 p-value = 0.022153
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 0, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 0, 15):
     Estimate Std. Error
     tau 0.0000 NA
     d.prime 0.9539 NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(0, 5, 15))
     Results for the 2-AC protocol with data c(0, 5, 15):
     Estimate Std. Error
     tau NA NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 4.560089 p-value = 5.1132e-06
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 15, 0))
     Results for the 2-AC protocol with data c(5, 15, 0):
     Estimate Std. Error
     tau NA NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = -2.632769 p-value = 0.0084692
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 0, 0))
     Results for the 2-AC protocol with data c(5, 0, 0):
     Estimate Std. Error
     tau 0 NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = -2.632769 p-value = 0.0084692
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(0, 0, 15))
     Results for the 2-AC protocol with data c(0, 0, 15):
     Estimate Std. Error
     tau 0 NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 4.560089 p-value = 5.1132e-06
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(0, 5, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(0, 5, 15):
     Estimate Std. Error
     tau NA NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(5, 15, 0), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 15, 0):
     Estimate Std. Error
     tau NA NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(5, 0, 0), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 0, 0):
     Estimate Std. Error
     tau 0 NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(0, 0, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(0, 0, 15):
     Estimate Std. Error
     tau 0 NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     >
     > ## Testing twoAC functions:
     > (fm1 <- twoAC(c(2, 2, 6)))
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     sensR
     --- call from context ---
     estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     --- R stacktrace ---
     where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     where 2: twoAC(c(2, 2, 6))
    
     --- value of length: 2 type: logical ---
     [1] TRUE TRUE
     --- function from context ---
     function (data, vcov = TRUE, warn = TRUE)
     {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
     }
     <bytecode: 0x9309588>
     <environment: namespace:sensR>
     --- function search by body ---
     Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(vcov) != "try-error") { : the condition has length > 1
     Calls: twoAC -> estimate.2AC
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.5-1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'methodology.Rnw' using Sweave
    --- finished re-building 'methodology.Rnw'
    
    --- re-building 'twoACexamples.Rnw' using Sweave
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    sensR
     --- call from context ---
    estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
    if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
    }
     --- R stacktrace ---
    where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
    where 2: twoAC(c(2, 2, 6))
    where 3: eval(expr, .GlobalEnv)
    where 4: eval(expr, .GlobalEnv)
    where 5: withVisible(eval(expr, .GlobalEnv))
    where 6: doTryCatch(return(expr), name, parentenv, handler)
    where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 8: tryCatchList(expr, classes, parentenv, handlers)
    where 9: 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))
    })
    where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
    where 11: evalFunc(ce, options)
    where 12: tryCatchList(expr, classes, parentenv, handlers)
    where 13: tryCatch(evalFunc(ce, options), finally = {
     cat("\n")
     sink()
    })
    where 14: driver$runcode(drobj, chunk, chunkopts)
    where 15: utils::Sweave(...)
    where 16: engine$weave(file, quiet = quiet, encoding = enc)
    where 17: doTryCatch(return(expr), name, parentenv, handler)
    where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 19: tryCatchList(expr, classes, parentenv, handlers)
    where 20: 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 21: tools:::.buildOneVignette("twoACexamples.Rnw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sensR.Rcheck/vign_test/sensR",
     TRUE, FALSE, "twoACexamples", "UTF-8", "/tmp/RtmpUEae3N/file2f483571095e.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (data, vcov = TRUE, warn = TRUE)
    {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
    }
    <bytecode: 0xa2614f8>
    <environment: namespace:sensR>
     --- function search by body ---
    Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
    
    Error: processing vignette 'twoACexamples.Rnw' failed with diagnostics:
     chunk 2 (label = example1-1)
    Error in if (class(vcov) != "try-error") { : the condition has length > 1
    
    --- failed re-building 'twoACexamples.Rnw'
    
    SUMMARY: processing the following file failed:
     'twoACexamples.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.5-1
Check: examples
Result: ERROR
    Running examples in ‘sensR-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: clm2twoAC
    > ### Title: Extract 2-AC coefficient table from a cumulative link model
    > ### Aliases: clm2twoAC
    > ### Keywords: models
    >
    > ### ** Examples
    >
    >
    > ## Example of a simple 2-AC model. First the conventional way:
    > twoAC(c(2, 2, 6))
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    sensR
     --- call from context ---
    estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
    if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
    }
     --- R stacktrace ---
    where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
    where 2: twoAC(c(2, 2, 6))
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (data, vcov = TRUE, warn = TRUE)
    {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
    }
    <bytecode: 0x5556e509ad90>
    <environment: namespace:sensR>
     --- function search by body ---
    Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(vcov) != "try-error") { : the condition has length > 1
    Calls: twoAC -> estimate.2AC
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.5-1
Check: tests
Result: ERROR
     Running ‘betabin.R’ [2s/4s]
     Comparing ‘betabin.Rout’ to ‘betabin.Rout.save’ ... OK
     Running ‘discrim.R’ [2s/3s]
     Comparing ‘discrim.Rout’ to ‘discrim.Rout.save’ ... OK
     Running ‘test-all.R’ [7s/10s]
     Running ‘testdouble.R’ [2s/4s]
     Running ‘twoAC.R’ [3s/4s]
    Running the tests in ‘tests/twoAC.R’ failed.
    Complete output:
     > library(sensR)
     >
     > ## Testing border line cases:
     > twoAC(c(5, 0, 15))
     Results for the 2-AC protocol with data c(5, 0, 15):
     Estimate Std. Error
     tau 0.0000 NA
     d.prime 0.9539 NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 2.287737 p-value = 0.022153
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 0, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 0, 15):
     Estimate Std. Error
     tau 0.0000 NA
     d.prime 0.9539 NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(0, 5, 15))
     Results for the 2-AC protocol with data c(0, 5, 15):
     Estimate Std. Error
     tau NA NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 4.560089 p-value = 5.1132e-06
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 15, 0))
     Results for the 2-AC protocol with data c(5, 15, 0):
     Estimate Std. Error
     tau NA NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = -2.632769 p-value = 0.0084692
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 0, 0))
     Results for the 2-AC protocol with data c(5, 0, 0):
     Estimate Std. Error
     tau 0 NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = -2.632769 p-value = 0.0084692
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(0, 0, 15))
     Results for the 2-AC protocol with data c(0, 0, 15):
     Estimate Std. Error
     tau 0 NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 4.560089 p-value = 5.1132e-06
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(0, 5, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(0, 5, 15):
     Estimate Std. Error
     tau NA NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(5, 15, 0), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 15, 0):
     Estimate Std. Error
     tau NA NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(5, 0, 0), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 0, 0):
     Estimate Std. Error
     tau 0 NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(0, 0, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(0, 0, 15):
     Estimate Std. Error
     tau 0 NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     >
     > ## Testing twoAC functions:
     > (fm1 <- twoAC(c(2, 2, 6)))
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     sensR
     --- call from context ---
     estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     --- R stacktrace ---
     where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     where 2: twoAC(c(2, 2, 6))
    
     --- value of length: 2 type: logical ---
     [1] TRUE TRUE
     --- function from context ---
     function (data, vcov = TRUE, warn = TRUE)
     {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
     }
     <bytecode: 0x55f2256588a0>
     <environment: namespace:sensR>
     --- function search by body ---
     Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(vcov) != "try-error") { : the condition has length > 1
     Calls: twoAC -> estimate.2AC
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.5-1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘methodology.Rnw’ using Sweave
    --- finished re-building ‘methodology.Rnw’
    
    --- re-building ‘twoACexamples.Rnw’ using Sweave
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    sensR
     --- call from context ---
    estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
    if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
    }
     --- R stacktrace ---
    where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
    where 2: twoAC(c(2, 2, 6))
    where 3: eval(expr, .GlobalEnv)
    where 4: eval(expr, .GlobalEnv)
    where 5: withVisible(eval(expr, .GlobalEnv))
    where 6: doTryCatch(return(expr), name, parentenv, handler)
    where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 8: tryCatchList(expr, classes, parentenv, handlers)
    where 9: 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))
    })
    where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
    where 11: evalFunc(ce, options)
    where 12: tryCatchList(expr, classes, parentenv, handlers)
    where 13: tryCatch(evalFunc(ce, options), finally = {
     cat("\n")
     sink()
    })
    where 14: driver$runcode(drobj, chunk, chunkopts)
    where 15: utils::Sweave(...)
    where 16: engine$weave(file, quiet = quiet, encoding = enc)
    where 17: doTryCatch(return(expr), name, parentenv, handler)
    where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 19: tryCatchList(expr, classes, parentenv, handlers)
    where 20: 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 21: tools:::.buildOneVignette("twoACexamples.Rnw", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sensR.Rcheck/vign_test/sensR",
     TRUE, FALSE, "twoACexamples", "UTF-8", "/home/hornik/tmp/scratch/RtmpImYe2X/file50ce239d235e.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (data, vcov = TRUE, warn = TRUE)
    {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
    }
    <bytecode: 0x559ae0db08e8>
    <environment: namespace:sensR>
     --- function search by body ---
    Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
    
    Error: processing vignette 'twoACexamples.Rnw' failed with diagnostics:
     chunk 2 (label = example1-1)
    Error in if (class(vcov) != "try-error") { : the condition has length > 1
    
    --- failed re-building ‘twoACexamples.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘twoACexamples.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.5-1
Check: examples
Result: ERROR
    Running examples in ‘sensR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: clm2twoAC
    > ### Title: Extract 2-AC coefficient table from a cumulative link model
    > ### Aliases: clm2twoAC
    > ### Keywords: models
    >
    > ### ** Examples
    >
    >
    > ## Example of a simple 2-AC model. First the conventional way:
    > twoAC(c(2, 2, 6))
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    sensR
     --- call from context ---
    estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
    if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
    }
     --- R stacktrace ---
    where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
    where 2: twoAC(c(2, 2, 6))
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (data, vcov = TRUE, warn = TRUE)
    {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
    }
    <bytecode: 0x9aa7ea0>
    <environment: namespace:sensR>
     --- function search by body ---
    Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(vcov) != "try-error") { : the condition has length > 1
    Calls: twoAC -> estimate.2AC
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.5-1
Check: tests
Result: ERROR
     Running ‘betabin.R’
     Comparing ‘betabin.Rout’ to ‘betabin.Rout.save’ ... OK
     Running ‘discrim.R’
     Comparing ‘discrim.Rout’ to ‘discrim.Rout.save’ ... OK
     Running ‘test-all.R’ [11s/13s]
     Running ‘testdouble.R’
     Running ‘twoAC.R’
    Running the tests in ‘tests/twoAC.R’ failed.
    Complete output:
     > library(sensR)
     >
     > ## Testing border line cases:
     > twoAC(c(5, 0, 15))
     Results for the 2-AC protocol with data c(5, 0, 15):
     Estimate Std. Error
     tau 0.0000 NA
     d.prime 0.9539 NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 2.287737 p-value = 0.022153
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 0, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 0, 15):
     Estimate Std. Error
     tau 0.0000 NA
     d.prime 0.9539 NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(0, 5, 15))
     Results for the 2-AC protocol with data c(0, 5, 15):
     Estimate Std. Error
     tau NA NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 4.560089 p-value = 5.1132e-06
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 15, 0))
     Results for the 2-AC protocol with data c(5, 15, 0):
     Estimate Std. Error
     tau NA NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = -2.632769 p-value = 0.0084692
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 0, 0))
     Results for the 2-AC protocol with data c(5, 0, 0):
     Estimate Std. Error
     tau 0 NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = -2.632769 p-value = 0.0084692
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(0, 0, 15))
     Results for the 2-AC protocol with data c(0, 0, 15):
     Estimate Std. Error
     tau 0 NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 4.560089 p-value = 5.1132e-06
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(0, 5, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(0, 5, 15):
     Estimate Std. Error
     tau NA NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(5, 15, 0), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 15, 0):
     Estimate Std. Error
     tau NA NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(5, 0, 0), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 0, 0):
     Estimate Std. Error
     tau 0 NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(0, 0, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(0, 0, 15):
     Estimate Std. Error
     tau 0 NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     >
     > ## Testing twoAC functions:
     > (fm1 <- twoAC(c(2, 2, 6)))
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     sensR
     --- call from context ---
     estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     --- R stacktrace ---
     where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     where 2: twoAC(c(2, 2, 6))
    
     --- value of length: 2 type: logical ---
     [1] TRUE TRUE
     --- function from context ---
     function (data, vcov = TRUE, warn = TRUE)
     {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
     }
     <bytecode: 0x942c748>
     <environment: namespace:sensR>
     --- function search by body ---
     Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(vcov) != "try-error") { : the condition has length > 1
     Calls: twoAC -> estimate.2AC
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.5-1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘methodology.Rnw’ using Sweave
    --- finished re-building ‘methodology.Rnw’
    
    --- re-building ‘twoACexamples.Rnw’ using Sweave
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    sensR
     --- call from context ---
    estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
    if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
    }
     --- R stacktrace ---
    where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
    where 2: twoAC(c(2, 2, 6))
    where 3: eval(expr, .GlobalEnv)
    where 4: eval(expr, .GlobalEnv)
    where 5: withVisible(eval(expr, .GlobalEnv))
    where 6: doTryCatch(return(expr), name, parentenv, handler)
    where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 8: tryCatchList(expr, classes, parentenv, handlers)
    where 9: 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))
    })
    where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
    where 11: evalFunc(ce, options)
    where 12: tryCatchList(expr, classes, parentenv, handlers)
    where 13: tryCatch(evalFunc(ce, options), finally = {
     cat("\n")
     sink()
    })
    where 14: driver$runcode(drobj, chunk, chunkopts)
    where 15: utils::Sweave(...)
    where 16: engine$weave(file, quiet = quiet, encoding = enc)
    where 17: doTryCatch(return(expr), name, parentenv, handler)
    where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 19: tryCatchList(expr, classes, parentenv, handlers)
    where 20: 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 21: tools:::.buildOneVignette("twoACexamples.Rnw", "/data/gannet/ripley/R/packages/tests-clang/sensR.Rcheck/vign_test/sensR",
     TRUE, FALSE, "twoACexamples", "UTF-8", "/tmp/RtmpEmtQAe/working_dir/RtmpxUonYZ/file2bfc6fbe2cd7.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (data, vcov = TRUE, warn = TRUE)
    {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
    }
    <bytecode: 0xab92a70>
    <environment: namespace:sensR>
     --- function search by body ---
    Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
    
    Error: processing vignette 'twoACexamples.Rnw' failed with diagnostics:
     chunk 2 (label = example1-1)
    Error in if (class(vcov) != "try-error") { : the condition has length > 1
    
    --- failed re-building ‘twoACexamples.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘twoACexamples.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.5-1
Check: examples
Result: ERROR
    Running examples in ‘sensR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: clm2twoAC
    > ### Title: Extract 2-AC coefficient table from a cumulative link model
    > ### Aliases: clm2twoAC
    > ### Keywords: models
    >
    > ### ** Examples
    >
    >
    > ## Example of a simple 2-AC model. First the conventional way:
    > twoAC(c(2, 2, 6))
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    sensR
     --- call from context ---
    estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
    if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
    }
     --- R stacktrace ---
    where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
    where 2: twoAC(c(2, 2, 6))
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (data, vcov = TRUE, warn = TRUE)
    {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
    }
    <bytecode: 0xafb0798>
    <environment: namespace:sensR>
     --- function search by body ---
    Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(vcov) != "try-error") { : the condition has length > 1
    Calls: twoAC -> estimate.2AC
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.5-1
Check: tests
Result: ERROR
     Running ‘betabin.R’ [4s/11s]
     Comparing ‘betabin.Rout’ to ‘betabin.Rout.save’ ... OK
     Running ‘discrim.R’
     Comparing ‘discrim.Rout’ to ‘discrim.Rout.save’ ... OK
     Running ‘test-all.R’ [11s/31s]
     Running ‘testdouble.R’
     Running ‘twoAC.R’ [4s/11s]
    Running the tests in ‘tests/twoAC.R’ failed.
    Complete output:
     > library(sensR)
     >
     > ## Testing border line cases:
     > twoAC(c(5, 0, 15))
     Results for the 2-AC protocol with data c(5, 0, 15):
     Estimate Std. Error
     tau 0.0000 NA
     d.prime 0.9539 NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 2.287737 p-value = 0.022153
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 0, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 0, 15):
     Estimate Std. Error
     tau 0.0000 NA
     d.prime 0.9539 NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(0, 5, 15))
     Results for the 2-AC protocol with data c(0, 5, 15):
     Estimate Std. Error
     tau NA NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 4.560089 p-value = 5.1132e-06
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 15, 0))
     Results for the 2-AC protocol with data c(5, 15, 0):
     Estimate Std. Error
     tau NA NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = -2.632769 p-value = 0.0084692
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(5, 0, 0))
     Results for the 2-AC protocol with data c(5, 0, 0):
     Estimate Std. Error
     tau 0 NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = -2.632769 p-value = 0.0084692
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(0, 0, 15))
     Results for the 2-AC protocol with data c(0, 0, 15):
     Estimate Std. Error
     tau 0 NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test:
     Likelihood root statistic = 4.560089 p-value = 5.1132e-06
     Alternative hypothesis: d-prime is different from 0
     > twoAC(c(0, 5, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(0, 5, 15):
     Estimate Std. Error
     tau NA NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(5, 15, 0), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 15, 0):
     Estimate Std. Error
     tau NA NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(5, 0, 0), stat = "Wald")
     Results for the 2-AC protocol with data c(5, 0, 0):
     Estimate Std. Error
     tau 0 NA
     d.prime -Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     > twoAC(c(0, 0, 15), stat = "Wald")
     Results for the 2-AC protocol with data c(0, 0, 15):
     Estimate Std. Error
     tau 0 NA
     d.prime Inf NA
    
     Use profile and confint methods to get confidence interval
    
     Significance test not available - try with the likelihood statistic
     >
     > ## Testing twoAC functions:
     > (fm1 <- twoAC(c(2, 2, 6)))
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     sensR
     --- call from context ---
     estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     --- R stacktrace ---
     where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     where 2: twoAC(c(2, 2, 6))
    
     --- value of length: 2 type: logical ---
     [1] TRUE TRUE
     --- function from context ---
     function (data, vcov = TRUE, warn = TRUE)
     {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
     }
     <bytecode: 0xa720438>
     <environment: namespace:sensR>
     --- function search by body ---
     Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(vcov) != "try-error") { : the condition has length > 1
     Calls: twoAC -> estimate.2AC
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.5-1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘methodology.Rnw’ using Sweave
    --- finished re-building ‘methodology.Rnw’
    
    --- re-building ‘twoACexamples.Rnw’ using Sweave
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    sensR
     --- call from context ---
    estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
     --- call from argument ---
    if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
    }
     --- R stacktrace ---
    where 1: estimate.2AC(data = data, vcov = TRUE, warn = FALSE)
    where 2: twoAC(c(2, 2, 6))
    where 3: eval(expr, .GlobalEnv)
    where 4: eval(expr, .GlobalEnv)
    where 5: withVisible(eval(expr, .GlobalEnv))
    where 6: doTryCatch(return(expr), name, parentenv, handler)
    where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 8: tryCatchList(expr, classes, parentenv, handlers)
    where 9: 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))
    })
    where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
    where 11: evalFunc(ce, options)
    where 12: tryCatchList(expr, classes, parentenv, handlers)
    where 13: tryCatch(evalFunc(ce, options), finally = {
     cat("\n")
     sink()
    })
    where 14: driver$runcode(drobj, chunk, chunkopts)
    where 15: utils::Sweave(...)
    where 16: engine$weave(file, quiet = quiet, encoding = enc)
    where 17: doTryCatch(return(expr), name, parentenv, handler)
    where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 19: tryCatchList(expr, classes, parentenv, handlers)
    where 20: 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 21: tools:::.buildOneVignette("twoACexamples.Rnw", "/data/gannet/ripley/R/packages/tests-devel/sensR.Rcheck/vign_test/sensR",
     TRUE, FALSE, "twoACexamples", "UTF-8", "/tmp/RtmpRPq9Yj/working_dir/RtmpR4PFRM/file37bd3142bb82.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (data, vcov = TRUE, warn = TRUE)
    {
     vcov <- as.logical(vcov)
     stopifnot(is.logical(vcov))
     nll <- function(par) {
     tau <- par[1]
     d.prime <- par[2]
     p1 <- pnorm(-tau, d.prime, sqrt(2))
     p12 <- pnorm(tau, d.prime, sqrt(2))
     prob <- c(p1, p12 - p1, 1 - p12)
     prob[prob <= 0] <- 1
     -sum(data * log(prob))
     }
     x <- data
     if (x[1] > 0 && x[2] == 0 && x[3] == 0) {
     tau <- 0
     d.prime <- -Inf
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] == 0) {
     tau <- NA
     d.prime <- NA
     }
     else if (x[1] == 0 && x[2] == 0 && x[3] > 0) {
     tau <- 0
     d.prime <- Inf
     }
     else if (x[1] > 0 && x[2] > 0 && x[3] == 0) {
     d.prime <- -Inf
     tau <- NA
     }
     else if (x[1] == 0 && x[2] > 0 && x[3] > 0) {
     d.prime <- Inf
     tau <- NA
     }
     else {
     prob <- data/sum(data)
     gamma <- cumsum(prob)[-3]
     z <- qnorm(gamma) * sqrt(2)
     tau <- (z[2] - z[1])/2
     d.prime <- -z[1] - tau
     }
     prob <- data/sum(data)
     prob[prob <= 0] <- 1
     logLikMax <- sum(data * log(prob))
     coef <- matrix(NA, 2, 2, dimnames = list(c("tau", "d.prime"),
     c("Estimate", "Std. Error")))
     coef[, 1] <- c(tau, d.prime)
     res <- list(coefficients = coef, data = data, logLik = logLikMax)
     if (vcov) {
     makeWarn <- TRUE
     if (all(is.finite(coef[, 1])) && tau > 0) {
     makeWarn <- FALSE
     hess <- hessian(nll, x = c(tau, d.prime), method = "Richardson",
     method.args = list())
     vcov <- try(solve(hess), silent = TRUE)
     if (class(vcov) != "try-error") {
     makeWarn <- TRUE
     res$coefficients[, 2] <- sqrt(diag(vcov))
     res$vcov <- vcov
     }
     }
     if (warn && makeWarn)
     warning("vcov and standard errors are not available",
     call. = FALSE)
     }
     return(res)
    }
    <bytecode: 0xac180a0>
    <environment: namespace:sensR>
     --- function search by body ---
    Function estimate.2AC in namespace sensR has this body.
     ----------- END OF FAILURE REPORT --------------
    
    Error: processing vignette 'twoACexamples.Rnw' failed with diagnostics:
     chunk 2 (label = example1-1)
    Error in if (class(vcov) != "try-error") { : the condition has length > 1
    
    --- failed re-building ‘twoACexamples.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘twoACexamples.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc