Last updated on 2025-12-06 00:48:38 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4-1 | 13.10 | 541.78 | 554.88 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4-1 | 8.56 | 139.00 | 147.56 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.4-1 | 28.00 | 918.86 | 946.86 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.4-1 | 26.00 | 885.33 | 911.33 | OK | |
| r-devel-windows-x86_64 | 1.4-1 | 18.00 | 515.00 | 533.00 | OK | |
| r-patched-linux-x86_64 | 1.4-1 | 14.62 | 518.29 | 532.91 | OK | |
| r-release-linux-x86_64 | 1.4-1 | 12.81 | 521.57 | 534.38 | OK | |
| r-release-macos-arm64 | 1.4-1 | OK | ||||
| r-release-macos-x86_64 | 1.4-1 | 26.00 | 630.00 | 656.00 | OK | |
| r-release-windows-x86_64 | 1.4-1 | 18.00 | 518.00 | 536.00 | OK | |
| r-oldrel-macos-arm64 | 1.4-1 | OK | ||||
| r-oldrel-macos-x86_64 | 1.4-1 | 25.00 | 633.00 | 658.00 | OK | |
| r-oldrel-windows-x86_64 | 1.4-1 | 24.00 | 697.00 | 721.00 | OK |
Version: 1.4-1
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'Rsolnp', 'mmrm', 'knitr', 'rmarkdown', 'RBesT'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4-1
Check: examples
Result: ERROR
Running examples in ‘DoseFinding-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DoseFinding-package
> ### Title: DoseFinding: Planning and Analyzing Dose Finding Experiments
> ### Aliases: DoseFinding DoseFinding-package
> ### Keywords: internal
>
> ### ** Examples
>
>
> data(IBScovars)
>
> ## perform (model based) multiple contrast test
> ## define candidate dose-response shapes
> models <- Mods(linear = NULL, emax = 0.2, quadratic = -0.17,
+ doses = c(0, 1, 2, 3, 4))
> ## plot models
> plot(models)
> ## perform multiple contrast test
> test <- MCTtest(dose, resp, IBScovars, models=models,
+ addCovars = ~ gender)
>
> ## fit non-linear emax dose-response model
> fitemax <- fitMod(dose, resp, data=IBScovars, model="emax",
+ bnds = c(0.01,5))
> ## display fitted dose-effect curve
> plot(fitemax, CI=TRUE, plotData="meansCI")
>
> ## Calculate optimal designs for target dose (TD) estimation
> doses <- c(0, 10, 25, 50, 100, 150)
> fmodels <- Mods(linear = NULL, emax = 25, exponential = 85,
+ logistic = c(50, 10.8811),
+ doses = doses, placEff=0, maxEff=0.4)
> plot(fmodels, plotTD = TRUE, Delta = 0.2)
> weights <- rep(1/4, 4)
> desTD <- optDesign(fmodels, weights, Delta=0.2, designCrit="TD")
Error in callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd) :
Need suggested package Rsolnp for this calculation to use solnp optimizer
Calls: optDesign -> callOptim
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4-1
Check: tests
Result: ERROR
Running ‘testgFit.R’ [2s/2s]
Running ‘testplanMod.R’ [0s/0s]
Running ‘testsDesign.R’ [2s/2s]
Running ‘testsFitting.R’ [2s/2s]
Running ‘testsMCPMod.R’ [3s/4s]
Running ‘testsMCT.R’ [3s/4s]
Running ‘testsoptContr.R’ [1s/1s]
Running ‘testsplotDRMod.R’ [0s/0s]
Running ‘testssamplMod.R’ [2s/3s]
Running ‘testthat.R’ [64s/75s]
Running the tests in ‘tests/testsDesign.R’ failed.
Complete output:
> require("DoseFinding")
Loading required package: DoseFinding
> ## Some examples from the JASA paper (for validation)
> ########################################################################
> # Emax model p.1228 l. 5
> fMod <- Mods(emax = 25, doses = c(0,150), placEff=0, maxEff=0.4)
> fMod$emax[2] <- 0.6666667
> doses <- c(0, 18.75, 150)
> probs <- 1
> deswgts1 <- optDesign(fMod, probs, doses, Delta=0.2, designCrit = "TD",
+ optimizer="Nelder-Mead")
> deswgts2 <- optDesign(fMod, probs, doses, Delta=0.2, designCrit = "TD",
+ optimizer="nlminb")
> ## efficiency compared to standard design (last column)
> crt <- calcCrit(rep(1/6, 6), fMod, probs, c(0, 10, 25, 50, 100, 150),
+ Delta=0.2, designCrit = "TD")
> exp(deswgts1$crit - crt)
[1] 0.5099184
>
> # Paper p. 1228 l. 2
> fMod <- Mods(emax = 25, doses = c(0,150), placEff=0, maxEff=0.4)
> doses <- c(0, 18.75, 150)
> probs <- 1
> deswgts <- optDesign(fMod, probs, doses, Delta=0.2, designCrit = "TD")
Error in callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd) :
Need suggested package Rsolnp for this calculation to use solnp optimizer
Calls: optDesign -> callOptim
Execution halted
Running the tests in ‘tests/testsoptContr.R’ failed.
Complete output:
> ## commented out for time (and dependency reasons)
> require("DoseFinding")
Loading required package: DoseFinding
> if(!(require("quadprog") & require("Rsolnp")))
+ stop("need packages quadprog and Rsolnp to run these tests")
Loading required package: quadprog
Loading required package: Rsolnp
Error: need packages quadprog and Rsolnp to run these tests
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'Rsolnp'
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> ## Note: Files in this directory are old test cases that accumulated
> ## historically over time, many of them commented out for time reasons
> ## (and unorganized due to lack of anything close to testthat at the
> ## time of creation). The testthat sub-directory now contains a
> ## selected subset of these tests (with some additions) that have been
> ## brought in the testthat format.
>
> library(testthat)
> library(DoseFinding)
>
> test_check("DoseFinding")
Loading required package: multcomp
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS
Attaching package: 'TH.data'
The following object is masked from 'package:MASS':
geyser
Message: Need bounds in "bnds" for nonlinear models, using default bounds from "defBnds".
Message: Need bounds in "bnds" for nonlinear models, using default bounds from "defBnds".
Message: Need bounds in "bnds" for nonlinear models, using default bounds from "defBnds".
Loading required package: RBesT
Loading required package: RBesT
Loading required package: RBesT
Loading required package: RBesT
Loading required package: RBesT
Loading required package: RBesT
Loading required package: RBesT
Saving _problems/test-bMCTtest-272.R
Message: Need bounds in "bnds" for nonlinear models, using default bounds from "defBnds".
Message: Need bounds in "bnds" for nonlinear models, using default bounds from "defBnds".
Saving _problems/test-optDesign-50.R
Saving _problems/test-optDesign-72.R
Saving _problems/test-optDesign-80.R
Saving _problems/test-optDesign-92.R
Saving _problems/test-optDesign-102.R
Saving _problems/test-optDesign-115.R
Saving _problems/test-optDesign-128.R
Saving _problems/test-optDesign-144.R
Saving _problems/test-optDesign-175.R
Saving _problems/test-optDesign-181.R
Saving _problems/test-optDesign-257.R
Message: Need bounds in "bnds" for nonlinear models, using default bounds from "defBnds".
Message: Need bounds in "bnds" for nonlinear models, using default bounds from "defBnds".
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upper limit for sample size is raised
[ FAIL 12 | WARN 7 | SKIP 17 | PASS 557 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-bMCTtest.R:210:3', 'test-bMCTtest.R:228:3',
'test-bMCTtest.R:247:3', 'test-optContr.R:79:3', 'test-planMod.R:25:3',
'test-powMCTInterim.R:133:3', 'test-powMCTInterim.R:163:3',
'test-sampSize.R:20:3', 'test-sampSize.R:36:3', 'test-sampSize.R:52:3'
• RBesT package not available (7): 'test-bMCTtest.R:55:3',
'test-bMCTtest.R:79:3', 'test-bMCTtest.R:101:3', 'test-bMCTtest.R:123:3',
'test-bMCTtest.R:145:3', 'test-bMCTtest.R:167:3', 'test-bMCTtest.R:186:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bMCTtest.R:272:3'): Error message for incorrect prior arguments ──
Error in `mixnorm(inf = c(0.8, 0.4, 0.1), rob = c(0.2, 0.4, 10))`: could not find function "mixnorm"
── Error ('test-optDesign.R:50:3'): the emax model (table 2, line 2) gives the same results ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(fMod, probs, doses, Delta = 0.2, designCrit = "TD") at test-optDesign.R:50:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:72:3'): the exponential model (table 3, line 1) gives the same results ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(fMod, probs, doses, Delta = 0.2, designCrit = "TD") at test-optDesign.R:72:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:80:3'): the logistic model (table 4, line 7) gives the same results ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(fMod, probs, doses, Delta = 0.05, designCrit = "TD") at test-optDesign.R:80:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:92:3'): the logistic model (table 4, line 1) gives the same results ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(fMod, probs, doses, Delta = 0.2, designCrit = "TD") at test-optDesign.R:92:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:101:3'): the beta model (table 5, line 5) gives the same results ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(...) at test-optDesign.R:101:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:115:3'): the beta model (table 5, line 10) gives the same results ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(fMod, probs, doses, Delta = 0.1, designCrit = "TD") at test-optDesign.R:115:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:128:3'): the beta model (table 5, line 1) gives the same results ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(fMod, probs, doses, Delta = 0.2, designCrit = "TD") at test-optDesign.R:128:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:144:3'): standardized Dopt and Dopt&TD criteria work ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(...) at test-optDesign.R:144:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:174:3'): feasible starting values are used when on boundary ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(...) at test-optDesign.R:174:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:181:3'): there are no instabilities for numerical gradients ──
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(mm, probs = 1, designCrit = "TD", Delta = 0.5) at test-optDesign.R:181:3
2. └─DoseFinding:::callOptim(...)
── Error ('test-optDesign.R:257:1'): (code run outside of `test_that()`) ───────
Error in `callOptim(objFunc, optimizer, nD, control, lowbnd, uppbnd)`: Need suggested package Rsolnp for this calculation to use solnp optimizer
Backtrace:
▆
1. └─DoseFinding::optDesign(models, probs = 1) at test-optDesign.R:257:1
2. └─DoseFinding:::callOptim(...)
[ FAIL 12 | WARN 7 | SKIP 17 | PASS 557 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4-1
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4-1
Check: HTML version of manual
Result: NOTE
Skipping checking math rendering: package 'V8' unavailable
Flavor: r-devel-linux-x86_64-debian-gcc