* using log directory 'd:/Rcompile/CRANpkg/local/4.6/openVA.Rcheck'
* using R Under development (unstable) (2025-04-16 r88149 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 ... [2s] 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 ... [1s] 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] NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
* checking S3 generic/method consistency ... WARNING
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... [8s] NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
* checking Rd \usage sections ... NOTE
OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... [8s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [26s] ERROR
  Running 'testthat.r' [25s]
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > library(testthat)
  > library(openVA)
  OpenJDK 64-Bit Server VM warning: The Windows job object has enabled multiple processor groups (2) but the UseAllWindowsProcessorGroups flag is off. Some processors might not be used.
  ────────────────────── Attaching packages for openVA 1.1.2 ─────────────────────
  ✔ InSilicoVA 1.4.0
  ✔ InterVA4   1.7.6
  ✔ InterVA5   1.1.3
  ✔ Tariff     1.0.5
  ── Optional packages (require manual installation if not attached) ─────────────
  × 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.
  ..........10% completed
  ..........20% completed
  ..........30% completed
  ..........40% completed
  ..........50% completed
  ..........60% completed
  ..........70% completed
  ..........80% completed
  ..........90% completed
  ..........100% completed
  .10% completed
  .20% completed
  .30% completed
  .40% completed
  .50% completed
  .60% completed
  .70% completed
  .80% completed
  .90% completed
  .100% completed
  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 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('tests.algorithm.r:24:3'): Insilico - ID and output correct ──────────
  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:
      ▆
   1. └─openVA::codeVA(...) at tests.algorithm.r:24:3
   2.   ├─base::do.call("insilico.train", pairlist(args)[[1]][-1])
   3.   └─InSilicoVA::insilico.train(...)
   4.     └─InSilicoVA::insilico.fit(...)
  ── Error ('tests.stackplot.r:22:1'): (code run outside of `test_that()`) ───────
  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:
      ▆
   1. └─openVA::codeVA(...) at tests.stackplot.r:22:1
   2.   ├─base::do.call("insilico.train", pairlist(args)[[1]][-1])
   3.   └─InSilicoVA::insilico.train(...)
   4.     └─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 ... [22s] OK
* checking HTML version of manual ... [3s] OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 5 NOTEs