• using R version 4.3.0 alpha (2023-04-03 r84154)
  • using platform: x86_64-apple-darwin20 (64-bit)
  • R was compiled by
        Apple clang version 14.0.3 (clang-1403.0.22.14.1)
        GNU Fortran (GCC) 12.2.0
  • running under: macOS Ventura 13.3
  • using session charset: UTF-8
  • checking for file ‘ordinal/DESCRIPTION’ ... OK
  • checking extension type ... Package
  • this is package ‘ordinal’ version ‘2022.11-16’
  • 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 ‘ordinal’ can be installed ... [11s/14s] OK
  • used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
  • used SDK: ‘MacOSX11.3.sdk’
  • 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 R files for non-ASCII characters ... OK
  • checking R files for syntax errors ... OK
  • checking whether the package can be loaded ... [1s/2s] OK
  • checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
  • checking whether the package can be unloaded cleanly ... [1s/1s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
  • checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
  • checking loading without being on the library search path ... [1s/2s] 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 ... [14s/18s] OK
  • checking Rd files ... [1s/1s] OK
  • checking Rd metadata ... 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 LazyData ... OK
  • checking data for ASCII and uncompressed saves ... OK
  • checking line endings in C/C++/Fortran sources/headers ... OK
  • checking compiled code ... OK
  • checking sizes of PDF files under ‘inst/doc’ ... OK
  • checking installed files from ‘inst/doc’ ... OK
  • checking files in ‘vignettes’ ... OK
  • checking examples ... [6s/6s] OK
  • checking for unstated dependencies in ‘tests’ ... OK
  • checking tests ... [51s/58s] OK
      Running ‘anova.R’ [1s/1s]
      Running ‘clm.fit.R’ [1s/1s]
      Running ‘clm.formula.R’ [2s/2s]
      Running ‘clmm.R’ [3s/4s]
      Running ‘clmm.control.R’ [1s/2s]
      Running ‘clmm.formula.R’ [2s/2s]
      Running ‘clmm.methods.R’ [2s/2s]
      Running ‘confint.R’ [2s/2s]
      Running ‘nominal.test.R’ [3s/3s]
      Running ‘ranef.loading.R’ [2s/2s]
      Running ‘test-all.R’ [8s/9s]
      Running ‘test.clm.Theta.R’ [2s/2s]
      Running ‘test.clm.convergence.R’ [1s/1s]
      Running ‘test.clm.flex.link.R’ [4s/5s]
      Running ‘test.clm.model.matrix.R’ [2s/2s]
      Running ‘test.clm.predict.R’ [1s/2s]
      Running ‘test.clm.profile.R’ [1s/2s]
      Running ‘test.clm.single.anova.R’ [2s/2s]
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      Running ‘test.sign.R’ [2s/2s]
      Running ‘test0weights.R’ [2s/2s]
      Running ‘testAnova.clm2.R’ [2s/2s]
      Running ‘testCLM.R’ [2s/2s]
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes in ‘inst/doc’ ... OK
  • checking running R code from vignettes ... [8s/10s] OK
      ‘clm_article.Rnw’ using ‘UTF-8’... [4s/5s] OK
      ‘clmm2_tutorial.Rnw’ using ‘UTF-8’... [3s/5s] OK
  • checking re-building of vignette outputs ... [20s/24s] NOTE
    Error(s) in re-building vignettes:
    --- re-building ‘clm_article.Rnw’ using Sweave
    Changing to 'nlminb' optimizer for flexible link function
    Warning: (-1) Model failed to converge with max|grad| = 0.00567175 (tol = 1e-06)
    Warning: (1) Hessian is numerically singular: parameters are not uniquely determined
    In addition: Absolute convergence criterion was met, but relative criterion was not met
    Warning: (1) Hessian is numerically singular: parameters are not uniquely determined
    In addition: Absolute convergence criterion was met, but relative criterion was not met
    Warning: (1) Hessian is numerically singular: parameters are not uniquely determined
    In addition: Absolute convergence criterion was met, but relative criterion was not met
    Warning: (-2) Model failed to converge: degenerate Hessian with 1 negative eigenvalues
    In addition: maximum number of consecutive Newton modifications reached
    --- finished re-building 'clm_article.Rnw'

    --- re-building ‘clmm2_tutorial.Rnw’ using Sweave
    Error: processing vignette 'clmm2_tutorial.Rnw' failed with diagnostics:
    Running 'texi2dvi' on 'clmm2_tutorial.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `ntheorem.sty' not found.

    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)

    ! Emergency stop.
    <read *>
             
    l.15 ^^M
            
    ! ==> Fatal error occurred, no output PDF file produced!
    --- failed re-building ‘clmm2_tutorial.Rnw’

    SUMMARY: processing the following file failed:
      ‘clmm2_tutorial.Rnw’

    Error: Vignette re-building failed.
    Execution halted
  • checking PDF version of manual ... [5s/8s] OK
  • DONE
    Status: 1 NOTE
  • using check arguments '--no-clean-on-error '