* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/FREEtree.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 20.1.0-rc3
    flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘FREEtree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FREEtree’ version ‘0.1.0’
* package encoding: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FREEtree’ can be installed ... [49s/129s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/FREEtree-00install.html' for details.
* checking installed package size ... OK
* checking package 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 ... [16s/53s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/17s] OK
* checking whether the package can be unloaded cleanly ... [14s/36s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/47s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/26s] OK
* checking loading without being on the library search path ... [15s/31s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [63s/96s] OK
* checking Rd files ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [29s/36s] ERROR
Running examples in ‘FREEtree-Ex.R’ failed
The error most likely occurred in:

> ### Name: FREEtree
> ### Title: Initial FREEtree call which then calls actual FREEtree methods
> ###   depending on parameters being passed through.
> ### Aliases: FREEtree
> 
> ### ** Examples
> 
> #locate example data file
> dataf <- system.file("data/data.RData", package="FREEtree")
> mytree = FREEtree(data,fixed_regress=c("time","time2"), fixed_split=c("treatment"),
+                   var_select=paste("V",1:200,sep=""), minModuleSize = 5,
+                   cluster="patient", Fuzzy=TRUE, maxdepth_factor_select = 0.5,
+                   maxdepth_factor_screen = 0.04, minsize_multiplier = 5,
+                   alpha_screen = 0.2, alpha_select=0.2,alpha_predict=0.05)
Use FREEtree_time

Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
  convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Error in if (continue & (abs(newloglik - oldloglik[2]) < abstol)) { : 
  missing value where TRUE/FALSE needed
Calls: FREEtree -> FREEtree_time -> lmertree
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [45s/71s] ERROR
  Running ‘testthat.R’ [45s/71s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FREEtree)
  
  > 
  > test_check("FREEtree")
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_FREEtree.R:113:3'): FREEtree_time a5 estimation ────────────────
  Error in `if (continue & (abs(newloglik - oldloglik[2]) < abstol)) {
      if (newloglik > oldloglik[1]) 
          continue <- FALSE
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      â–†
   1. └─FREEtree::FREEtree(...) at test_FREEtree.R:113:3
   2.   └─FREEtree:::FREEtree_time(...)
   3.     └─glmertree::lmertree(...)
  ── Error ('test_FREEtree.R:230:3'): FREEtree_PC a0 estimation ──────────────────
  Error in `if (continue & (abs(newloglik - oldloglik[2]) < abstol)) {
      if (newloglik > oldloglik[1]) 
          continue <- FALSE
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      â–†
   1. └─FREEtree::FREEtree(...) at test_FREEtree.R:230:3
   2.   └─FREEtree:::FREEtree_PC(...)
   3.     └─glmertree::lmertree(...)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [7s/10s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 NOTE