- 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]
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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 '