* using log directory ‘/srv/hornik/tmp/CRAN/BioCro.Rcheck’
* using R Under development (unstable) (2024-04-18 r86444)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘BioCro/DESCRIPTION’ ... OK
* this is package ‘BioCro’ version ‘3.1.1’
* checking CRAN incoming feasibility ... [5s/35s] NOTE
Maintainer: ‘Justin M. McGrath <jmcgrath@illinois.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  Lochocki (9:14)
  al (9:26)
  et (9:23)
  modularity (6:22)

Found the following (possibly) invalid URLs:
  URL: https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.268715
    From: inst/doc/thick_layer_absorption.html
    Status: 404
    Message: Not Found

Size of tarball: 20844066 bytes
* 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 ‘BioCro’ can be installed ... [65s/65s] WARNING
Found the following significant warnings:
  module_library/AuxBioCro.cpp:1090:21: warning: variable length arrays are a C99 feature [-Wvla-extension]
  module_library/CanAC.cpp:69:31: warning: variable length arrays are a C99 feature [-Wvla-extension]
  module_library/CanAC.cpp:72:26: warning: variable length arrays are a C99 feature [-Wvla-extension]
  module_library/c3CanAC.cpp:70:31: warning: variable length arrays are a C99 feature [-Wvla-extension]
  module_library/c3CanAC.cpp:73:26: warning: variable length arrays are a C99 feature [-Wvla-extension]
  module_library/multilayer_canopy_properties.cpp:125:31: warning: variable length arrays are a C99 feature [-Wvla-extension]
  module_library/multilayer_canopy_properties.cpp:129:26: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/srv/hornik/tmp/CRAN/BioCro.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 17.0.6 (5)’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘inc’
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] OK
* checking Rd files ... [0s/0s] 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 ... [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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [31s/31s] OK
  Running ‘testthat.R’ [30s/30s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [109s/109s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 3 NOTEs