* using log directory ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fastFGEE.Rcheck’
* using R version 4.6.1 Patched (2026-09-12 r90540)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-16 (Debian 16.2.0-1) 16.2.0
    GNU Fortran (Debian 16.2.0-1) 16.2.0
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-09-16 12:54:06 UTC
* checking for file ‘fastFGEE/DESCRIPTION’ ... OK
* this is package ‘fastFGEE’ version ‘0.2.0’
* 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 ‘fastFGEE’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/fastFGEE-00install.html' for details.
* used C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’
* 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 ... [3s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
* checking whether the package can be unloaded cleanly ... [3s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
* checking loading without being on the library search path ... [3s/4s] 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 ... [43s/60s] OK
* checking Rd files ... [0s/0s] 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 ... [3s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [24s/34s] ERROR
  Running ‘testthat.R’ [23s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fastFGEE)
  > 
  > test_check("fastFGEE")
  Saving _problems/test-dependency-and-registration-22.R
  Saving _problems/test-dependency-and-registration-53.R
  Saving _problems/test-dependency-and-registration-95.R
  Smoothing parameter tuning: fastkfold
  fold-specific beta provided
  fast k-fold cv list: 1 of 3
  fast k-fold cv list: 2 of 3
  fast k-fold cv list: 3 of 3
  Smoothing parameter tuning: fastkfold
  fold-specific beta provided
  fast k-fold cv list: 1 of 3
  fast k-fold cv list: 2 of 3
  fast k-fold cv list: 3 of 3
  Smoothing parameter tuning: fastkfold
  fold-specific beta provided
  fast k-fold cv list: 1 of 3
  fast k-fold cv list: 2 of 3
  fast k-fold cv list: 3 of 3
  Smoothing parameter tuning: fastkfold
  fold-specific beta provided
  fast k-fold cv list: 1 of 3
  fast k-fold cv list: 2 of 3
  fast k-fold cv list: 3 of 3
  [ FAIL 3 | WARN 2 | SKIP 6 | PASS 1969 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-fgee-integration.R:2:3', 'test-fgee-integration.R:71:3',
    'test-fgee-newfamilies.R:46:5', 'test-fgee-newfamilies.R:46:5',
    'test-fgee-newfamilies.R:98:3'
  • SuperGauss is installed, so the missing-package path cannot be exercised (1):
    'test-optional-deps.R:46:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dependency-and-registration.R:22:3'): archived numerical dependencies are absent from executable source ──
  Error in `.source_root()`: Could not locate the fastFGEE source tree for source-level tests.
  Backtrace:
      ▆
   1. └─fastFGEE (local) .source_root() at test-dependency-and-registration.R:22:3
  ── Error ('test-dependency-and-registration.R:53:3'): every Rcpp attribute export is registered ──
  Error in `.source_root()`: Could not locate the fastFGEE source tree for source-level tests.
  Backtrace:
      ▆
   1. └─fastFGEE (local) .source_root() at test-dependency-and-registration.R:53:3
  ── Error ('test-dependency-and-registration.R:95:3'): nuisance integration has one active definition per core wrapper ──
  Error in `.source_root()`: Could not locate the fastFGEE source tree for source-level tests.
  Backtrace:
      ▆
   1. └─fastFGEE (local) .source_root() at test-dependency-and-registration.R:95:3
  
  [ FAIL 3 | WARN 2 | SKIP 6 | PASS 1969 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [5s/6s] OK
* checking PDF version of manual ... [4s/6s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR