* using log directory '/home/kingaa/projects/Rpkg/subplex/revdep/DAISIE.Rcheck'
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'DAISIE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DAISIE' version '4.2.0'
* 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 'DAISIE' can be installed ... [109s/132s] WARNING
Found the following significant warnings:
  Warning: Nonconforming tab character at (1) [-Wtabs]
  Warning: Unused variable ‘msg’ declared at (1) [-Wunused-variable]
  Warning: Unused dummy argument ‘neq’ at (1) [-Wunused-dummy-argument]
  Warning: Unused dummy argument ‘t’ at (1) [-Wunused-dummy-argument]
  Warning: Unused variable ‘ff1’ declared at (1) [-Wunused-variable]
  Warning: Unused variable ‘fff’ declared at (1) [-Wunused-variable]
See '/home/kingaa/projects/Rpkg/subplex/revdep/DAISIE.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 37.3Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
* 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 ... [38s/68s] NOTE
DAISIE_IW_pars: local variable ‘Kprime’ assigned but may not be used
DAISIE_IW_pars: local variable ‘ddep’ assigned but may not be used
DAISIE_KLdist: local variable ‘tp’ assigned but may not be used
DAISIE_ML1: local variable ‘max_idpars’ assigned but may not be used
DAISIE_SR_loglik: local variable ‘abstol’ assigned but may not be used
DAISIE_SR_loglik: local variable ‘reltol’ assigned but may not be used
DAISIE_SR_loglik_CS_M1: local variable ‘abstol’ assigned but may not be
  used
DAISIE_SR_loglik_CS_M1: local variable ‘reltol’ assigned but may not be
  used
DAISIE_extract_stt_median: local variable ‘time’ assigned but may not
  be used
DAISIE_format_CS_trait: local variable ‘number_type1_cols’ assigned but
  may not be used
DAISIE_format_CS_trait: local variable ‘prop_type2_pool’ assigned but
  may not be used
DAISIE_format_GW: local variable ‘row_index’ assigned but may not be
  used
DAISIE_loglik_IW: local variable ‘laa’ assigned but may not be used
DAISIE_loglik_IW: local variable ‘mu’ assigned but may not be used
DAISIE_loglik_rhs: local variable ‘rhs’ assigned but may not be used
DAISIE_loglik_rhs: local variable ‘xx3’ assigned but may not be used
DAISIE_loglik_rhs1: local variable ‘in4’ assigned but may not be used
DAISIE_loglik_rhs1: local variable ‘rhs’ assigned but may not be used
DAISIE_loglik_rhs2: local variable ‘rhs’ assigned but may not be used
DAISIE_loglik_rhs_time: local variable ‘ddep’ assigned but may not be
  used
DAISIE_loglik_rhs_time: local variable ‘xx3’ assigned but may not be
  used
DAISIE_loglik_rhs_time1: local variable ‘ddep’ assigned but may not be
  used
DAISIE_loglik_rhs_time2: local variable ‘ddep’ assigned but may not be
  used
DAISIE_numcol: local variable ‘lx’ assigned but may not be used
DAISIE_plot_extinction: local variable ‘ext_rate’ assigned but may not
  be used
DAISIE_plot_immigration: local variable ‘immig_rate’ assigned but may
  not be used
DAISIE_plot_input: local variable ‘geom_point_’ assigned but may not be
  used
DAISIE_plot_pc_rates: local variable ‘sims_plot’ assigned but may not
  be used
DAISIE_sim_core_trait_dep: local variable ‘num_immigrants_trait1’
  assigned but may not be used
DAISIE_sim_core_trait_dep: local variable ‘num_immigrants_trait2’
  assigned but may not be used
DAISIE_sim_core_trait_dep: local variable ‘num_spec_trait1’ assigned
  but may not be used
DAISIE_sim_core_trait_dep: local variable ‘num_spec_trait2’ assigned
  but may not be used
add_brt_table: local variable ‘brts’ assigned but may not be used
countspecies: local variable ‘N’ assigned but may not be used
countspeciestype1: local variable ‘N1’ assigned but may not be used
counttype1: local variable ‘N1’ assigned but may not be used
create_full_CS_stt: local variable ‘present’ assigned but may not be
  used
create_full_CS_stt_trait: local variable ‘present’ assigned but may not
  be used
nndivdep: local variable ‘nilm’ assigned but may not be used
shift_before_certain_brts: local variable ‘oldest_endemic’ assigned but
  may not be used
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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 ... [33s/52s] OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
DAISIE_sim        4.796  0.031   5.737
DAISIE_plot_input 3.896  0.100   6.093
DAISIE_SR_sim     3.318  0.005   6.003
DAISIE_numcol     2.677  0.022   5.385
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
 [105s/115s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [64s/63s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
