* using log directory ‘/srv/hornik/tmp/CRAN/gadget3.Rcheck’
* using R Under development (unstable) (2024-07-01 r86857)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1)
    Debian flang-new version 18.1.8 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘gadget3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gadget3’ version ‘0.12-0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/8s] Note_to_CRAN_maintainers
Maintainer: ‘Jamie Lentin <lentinj@shuttlethread.com>’
* 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 ‘gadget3’ can be installed ... [3s/3s] 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 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 ... [8s/8s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  run_tmb.Rd: MakeADFun
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [29s/29s] OK
  Running ‘test-aab_env.R’ [0s/0s]
  Running ‘test-action_age.R’ [1s/1s]
  Running ‘test-action_grow.R’ [1s/1s]
  Running ‘test-action_mature.R’ [1s/1s]
  Running ‘test-action_migrate.R’ [1s/1s]
  Running ‘test-action_naturalmortality.R’ [0s/0s]
  Running ‘test-action_predate-catchability.R’ [2s/2s]
  Running ‘test-action_predate-numberfleet.R’ [1s/1s]
  Running ‘test-action_predate.R’ [1s/1s]
  Running ‘test-action_renewal.R’ [1s/1s]
  Running ‘test-action_report.R’ [1s/1s]
  Running ‘test-action_spawn-multipleoutputs.R’ [1s/1s]
  Running ‘test-action_spawn.R’ [1s/1s]
  Running ‘test-action_tagging.R’ [1s/1s]
  Running ‘test-action_time.R’ [0s/0s]
  Running ‘test-eval.R’ [0s/0s]
  Running ‘test-formula_utils.R’ [0s/0s]
  Running ‘test-init_val.R’ [1s/1s]
  Running ‘test-likelihood_bounds.R’ [1s/1s]
  Running ‘test-likelihood_data.R’ [1s/1s]
  Running ‘test-likelihood_distribution-surveyindices.R’ [1s/1s]
  Running ‘test-likelihood_distribution.R’ [4s/4s]
  Running ‘test-likelihood_random.R’ [0s/0s]
  Running ‘test-likelihood_tagging_ckmr.R’ [1s/1s]
  Running ‘test-likelihood_understocking.R’ [0s/0s]
  Running ‘test-params.R’ [0s/0s]
  Running ‘test-run.R’ [0s/0s]
  Running ‘test-run_r.R’ [1s/1s]
  Running ‘test-run_tmb-reporting_enabled.R’ [0s/0s]
  Running ‘test-run_tmb.R’ [1s/1s]
  Running ‘test-step.R’ [1s/1s]
  Running ‘test-stock.R’ [0s/0s]
  Running ‘test-stock_age.R’ [0s/0s]
  Running ‘test-stock_areas.R’ [1s/1s]
  Running ‘test-stock_tag.R’ [0s/0s]
  Running ‘test-stock_time.R’ [0s/0s]
  Running ‘test-suitability.R’ [1s/1s]
  Running ‘test-timedata.R’ [0s/0s]
  Running ‘test-timevariable.R’ [0s/0s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [22s/22s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE