* using log directory 'd:/Rcompile/CRANpkg/local/4.4/openVA.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'openVA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'openVA' version '1.1.2'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'openVA' can be installed ... OK
* checking installed package size ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s] OK
* checking whether the package can be unloaded cleanly ... [2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s] OK
* checking loading without being on the library search path ... [2s] OK
* checking whether startup messages can be suppressed ... [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 ... [10s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [11s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [36s] ERROR
Running 'testthat.r' [35s]
Running the tests in 'tests/testthat.r' failed.
Complete output:
> library(testthat)
> library(openVA)
笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏 Attaching packages for openVA 1.1.2 笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏笏
笨� InSilicoVA 1.4.0
笨� InterVA4 1.7.6
笨� InterVA5 1.1.3
笨� Tariff 1.0.5
笏笏 Optional packages (require manual installation if not attached) 笏笏笏笏笏笏笏笏笏笏笏笏笏
ﾃ� nbc4va
If you need to use these methods, you may need to load or install the packages: nbc4va.
>
> test_check("openVA")
InSilicoVA Sampler Initiated, 200 Iterations to Sample
Error in .jcall(obj, "[D", "Fit", dimensions.j, probbase.j, probbase_order.j, :
java.awt.HeadlessException:
The application does not have desktop access,
but this program performed an operation which requires it.
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100% completed
Start re-sampling for significant Tariff cells
Calculating ranks
InSilicoVA Sampler Initiated, 200 Iterations to Sample
Error in .jcall(obj, "[D", "Fit", dimensions.j, probbase.j, probbase_order.j, :
java.awt.HeadlessException:
The application does not have desktop access,
but this program performed an operation which requires it.
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 246 ]
笊絶武 Failed tests 笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武笊絶武
笏笏 Error ('tests.algorithm.r:24:3'): Insilico - ID and output correct 笏笏笏笏笏笏笏笏笏笏
Error in `insilico.fit(data = data, isNumeric = isNumeric, updateCondProb = updateCondProb,
keepProbbase.level = keepProbbase.level, CondProb = CondProb,
CondProbNum = CondProbNum, datacheck = FALSE, datacheck.missing = FALSE,
warning.write = FALSE, external.sep = FALSE, Nsim = Nsim,
thin = thin, burnin = burnin, auto.length = auto.length,
conv.csmf = conv.csmf, jump.scale = jump.scale, levels.prior = levels.prior,
levels.strength = levels.strength, trunc.min = trunc.min,
trunc.max = trunc.max, subpop = subpop, java_option = java_option,
seed = seed, phy.code = phy.code, phy.cat = phy.cat, phy.unknown = phy.unknown,
phy.external = phy.external, phy.debias = phy.debias, exclude.impossible.cause = FALSE,
indiv.CI = indiv.CI, impossible.combination = impossible.combination,
customization.dev = TRUE, Probbase_by_symp.dev = FALSE, probbase.dev = probbase.touse,
table.dev = table.alpha, table.num.dev = table.num, gstable.dev = colnames(probbase.touse),
nlevel.dev = 15)`:
Backtrace:
笆�
1. 笏披楳openVA::codeVA(...) at tests.algorithm.r:24:3
2. 笏懌楳base::do.call("insilico.train", pairlist(args)[[1]][-1])
3. 笏披楳InSilicoVA::insilico.train(...)
4. 笏披楳InSilicoVA::insilico.fit(...)
笏笏 Error ('tests.stackplot.r:22:1'): (code run outside of `test_that()`) 笏笏笏笏笏笏笏
Error in `insilico.fit(data = data, isNumeric = isNumeric, updateCondProb = updateCondProb,
keepProbbase.level = keepProbbase.level, CondProb = CondProb,
CondProbNum = CondProbNum, datacheck = FALSE, datacheck.missing = FALSE,
warning.write = FALSE, external.sep = FALSE, Nsim = Nsim,
thin = thin, burnin = burnin, auto.length = auto.length,
conv.csmf = conv.csmf, jump.scale = jump.scale, levels.prior = levels.prior,
levels.strength = levels.strength, trunc.min = trunc.min,
trunc.max = trunc.max, subpop = subpop, java_option = java_option,
seed = seed, phy.code = phy.code, phy.cat = phy.cat, phy.unknown = phy.unknown,
phy.external = phy.external, phy.debias = phy.debias, exclude.impossible.cause = FALSE,
indiv.CI = indiv.CI, impossible.combination = impossible.combination,
customization.dev = TRUE, Probbase_by_symp.dev = FALSE, probbase.dev = probbase.touse,
table.dev = table.alpha, table.num.dev = table.num, gstable.dev = colnames(probbase.touse),
nlevel.dev = 15)`:
Backtrace:
笆�
1. 笏披楳openVA::codeVA(...) at tests.stackplot.r:22:1
2. 笏懌楳base::do.call("insilico.train", pairlist(args)[[1]][-1])
3. 笏披楳InSilicoVA::insilico.train(...)
4. 笏披楳InSilicoVA::insilico.fit(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 246 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s] OK
* checking PDF version of manual ... [17s] OK
* checking HTML version of manual ... [3s] OK
* DONE
Status: 1 ERROR