- using R version 4.4.0 Patched (2024-04-30 r86503)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.2.0-23) 13.2.0
GNU Fortran (Debian 13.2.0-23) 13.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘DoseFinding/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘DoseFinding’ version ‘1.1-1’
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: ‘RBesT’
- 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 serialization versions ... OK
- checking whether package ‘DoseFinding’ can be installed ... OK
See the install log for details.
- used C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
- checking package directory ... OK
- checking for future file timestamps ... 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [2s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
- checking loading without being on the library search path ... [1s/2s] 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 ... [34s/44s] OK
- checking Rd files ... [1s/1s] 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 ... [0s/0s] OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [10s/11s] ERROR
Running examples in ‘DoseFinding-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bMCTtest
> ### Title: Performs Bayesian multiple contrast test
> ### Aliases: bMCTtest
>
> ### ** Examples
>
>
> require(RBesT)
Loading required package: RBesT
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘RBesT’
>
> ###############################
> ## Normal outcome
> ###############################
>
> data(biom)
> ## define shapes for which to calculate optimal contrasts
> doses <- c(0, 0.05, 0.2, 0.6, 1)
> modlist <- Mods(emax = 0.05, linear = NULL, logistic = c(0.5, 0.1),
+ linInt = c(0, 1, 1, 1), doses = doses)
> ## specify an informative prior for placebo, weakly informative for other arms
> plc_prior <- mixnorm(inf = c(0.8, 0.4, 0.1), rob = c(0.2, 0.4, 10))
Error in mixnorm(inf = c(0.8, 0.4, 0.1), rob = c(0.2, 0.4, 10)) :
could not find function "mixnorm"
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [45s/48s] ERROR
Running ‘testgFit.R’ [2s/3s]
Running ‘testplanMod.R’ [0s/0s]
Running ‘testsDesign.R’ [4s/5s]
Running ‘testsFitting.R’ [2s/3s]
Running ‘testsMCPMod.R’ [4s/4s]
Running ‘testsMCT.R’ [5s/5s]
Running ‘testsoptContr.R’ [2s/2s]
Running ‘testsplotDRMod.R’ [0s/0s]
Running ‘testssampSize.R’ [0s/0s]
Running ‘testssamplMod.R’ [4s/4s]
Running ‘testthat.R’ [21s/21s]
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)
Loading required package: ggplot2
Loading required package: lattice
Loading required package: mvtnorm
> options(testthat.progress.max_fails = 100)
>
> Sys.unsetenv("R_TESTS")
> test_check("DoseFinding")
Running simulations
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[ FAIL 1 | WARN 10 | SKIP 12 | PASS 171 ]
══ Skipped tests (12) ══════════════════════════════════════════════════════════
• On CRAN (2): 'test-optContr.R:81:3', 'test-planMod.R:27:3'
• RBesT package not available (10): 'test-bMCTtest.R:57:3',
'test-bMCTtest.R:81:3', 'test-bMCTtest.R:103:3', 'test-bMCTtest.R:125:3',
'test-bMCTtest.R:147:3', 'test-bMCTtest.R:169:3', 'test-bMCTtest.R:189:3',
'test-bMCTtest.R:213:3', 'test-bMCTtest.R:228:3', 'test-bMCTtest.R:244:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bMCTtest.R:266:3'): 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"
[ FAIL 1 | WARN 10 | SKIP 12 | PASS 171 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [372s/475s] OK
- checking PDF version of manual ... [8s/10s] OK
- checking HTML version of manual ... [3s/4s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs, 1 NOTE