* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/sgdGMF.Rcheck’
* using R Under development (unstable) (2025-05-02 r88186)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (GCC) 15.1.0
    GNU Fortran (GCC) 15.1.0
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘sgdGMF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sgdGMF’ version ‘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 ‘sgdGMF’ can be installed ... [287s/214s] OK
* used C++ compiler: ‘g++-15 (GCC) 15.1.0’
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [33s/42s] 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 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 ... [11s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/14s]
 [12s/14s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(sgdGMF)
  Loading required package: ggplot2
  
  Attaching package: 'sgdGMF'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("sgdGMF")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 157 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-eigengap.R:15:3'): Rank selecion ───────────────────────────────
  Error in `while (tol >= 1) {
      j = ju
      yreg = lambdas[j:(j + 4)]
      xreg = (j + (-1:3))^(2/3)
      delta = 2 * abs(stats::cov(yreg, xreg))/stats::var(xreg)
      flag = which(-diff(lambdas) >= delta)
      ncomp = ifelse(length(flag) == 0, 0, utils::tail(flag[flag <= 
          maxcomp], 1))
      ju = ncomp + 1
      tol = abs(ju - j)
      iter = iter + 1
      if (iter > maxiter) 
          break
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─sgdGMF::sgdgmf.rank(data_pois$Y, family = poisson(), normalize = TRUE) at test-eigengap.R:15:3
   2.   └─sgdGMF:::eigengap.onatski(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 157 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [114s/147s] OK
* checking PDF version of manual ... [11s/13s] 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: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-MKL/sgdGMF.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 9:33.17, 530.00 + 36.21