* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/gllvm.Rcheck’
* using R Under development (unstable) (2026-06-29 r90198)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-06-29 12:13:16 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘gllvm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gllvm’ version ‘2.0.11’
* 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 ‘gllvm’ can be installed ... [16m/83m] OK
* used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
* 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 whether startup messages can be suppressed ... 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 ... [82s/82s] 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 R/sysdata.rda ... 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 ... [15s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [13m/14m]
 [13m/14m] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gllvm)
  Loading required package: TMB
  
  Attaching package: 'gllvm'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("gllvm")
  Saving _problems/test-fitgllvm-114.R
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 126 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-fitgllvm.R:114:3'): concurrent ordination models work ──────────
  Error in `FAstart(eta = mu, family = family, y = y, num.lv = num.lv, num.lv.c = num.lv.c, lv.X = lv.X, phis = phi, num.RR = num.RR, zeta = zeta, zeta.struc = zeta.struc, link = link, maxit = maxit, max.iter = max.iter, disp.group = disp.group, randomB = randomB, method = method, Ntrials = Ntrials, ZINB.phi = ZINB.phi, start.optimizer = start.optimizer, start.optim.method = start.optim.method, Power = Power)`: Calculating starting values failed. Try centering and scaling your predictors, a smaller 'num.lv.c' value, or change 'starting.val' to 'zero' or 'random'.
  Backtrace:
      ▆
   1. └─gllvm::gllvm(y, X, num.lv.c = 2, family = "poisson", seed = 999) at test-fitgllvm.R:114:3
   2.   └─gllvm:::gllvm.iter(...)
   3.     ├─base::do.call(gllvm.TMB, args)
   4.     └─gllvm (local) `<fn>`(...)
   5.       └─gllvm:::start_values_gllvm_TMB(...)
   6.         └─gllvm:::FAstart(...)
  
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 126 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [217s/218s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘vignette1.Rmd’ using rmarkdown
--- finished re-building ‘vignette1.Rmd’

--- re-building ‘vignette10.Rmd’ using rmarkdown
--- finished re-building ‘vignette10.Rmd’

--- re-building ‘vignette2.rmd’ using rmarkdown
--- finished re-building ‘vignette2.rmd’

--- re-building ‘vignette3.rmd’ using rmarkdown

Quitting from vignette3.rmd:193-199 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `FAstart()`:
! Calculating starting values failed. Maybe too many latent variables. Try smaller 'num.lv' value or change 'starting.val' to 'zero' or 'random'.
---
Backtrace:
    ▆
 1. └─gllvm::gllvm(y = spider$abund, family = poisson(), num.lv = 2)
 2.   └─gllvm:::gllvm.iter(...)
 3.     ├─base::do.call(gllvm.TMB, args)
 4.     └─gllvm (local) `<fn>`(...)
 5.       └─gllvm:::start_values_gllvm_TMB(...)
 6.         └─gllvm:::FAstart(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette3.rmd' failed with diagnostics:
Calculating starting values failed. Maybe too many latent variables. Try smaller 'num.lv' value or change 'starting.val' to 'zero' or 'random'.
--- failed re-building ‘vignette3.rmd’

--- re-building ‘vignette4.rmd’ using rmarkdown
--- finished re-building ‘vignette4.rmd’

--- re-building ‘vignette5.Rmd’ using rmarkdown
--- finished re-building ‘vignette5.Rmd’

--- re-building ‘vignette6.Rmd’ using rmarkdown
--- finished re-building ‘vignette6.Rmd’

--- re-building ‘vignette7.Rmd’ using rmarkdown
--- finished re-building ‘vignette7.Rmd’

--- re-building ‘vignette8.Rmd’ using rmarkdown
--- finished re-building ‘vignette8.Rmd’

--- re-building ‘vignette9.Rmd’ using rmarkdown
--- finished re-building ‘vignette9.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette3.rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... 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
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/gllvm.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:42:54, 2081.22 + 84.44