* using log directory 'd:/RCompile/CRANincoming/R-devel/phylosem.Rcheck'
* using R Under development (unstable) (2023-08-21 r84998 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'phylosem/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phylosem' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'James Thorson <James.Thorson@noaa.gov>'

New submission

Possibly misspelled words in DESCRIPTION:
  Bijl (29:42)
  PCM (23:56, 26:68)
  Phylogenetic (3:8)
  SEM (24:33, 26:78)
  Thorson (24:62, 29:22)
  al (24:73)
  der (29:38)
  et (24:70)
  phylogenetic (23:22, 23:65, 27:14)
  submodels (27:84)
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'phylosem' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 12.2.0'
* checking installed package size ... OK
* 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 R 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 ... [17s] 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [86s] OK
* checking PDF version of manual ... [13s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE