* using log directory ‘/srv/hornik/tmp/CRAN/r3PG.Rcheck’
* using R Under development (unstable) (2023-09-17 r85158)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (13)
    GNU Fortran (Debian 13.2.0-3) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘r3PG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘r3PG’ version ‘0.1.6’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘Volodymyr Trotsiuk <volodymyr.trotsiuk@wsl.ch>’

License components with restrictions and base license permitting such:
  GPL-3 + file LICENSE

Found the following (possibly) invalid URLs:
  URL: http://www.repostatus.org/#active (moved to https://www.repostatus.org/#active)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://cran.r-project.org/web/packages/r3PG/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://github.com/trotsiuk/r3PG/blob/master/data-raw/ (moved to https://github.com/trotsiuk/r3PG/tree/master/data-raw)
    From: README.md
    Status: 301
    Message: Moved Permanently
  The canonical URL of the CRAN page for a package is 
    https://CRAN.R-project.org/package=pkgname
  For content that is 'Moved Permanently', please change http to https,
  add trailing slashes, or replace the old by the new URL.

Found the following (possibly) invalid file URI:
  URI: volodymyr.trotsiuk@wsl.ch
    From: README.md
* 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 ‘r3PG’ can be installed ... [18s/18s] OK
* used C compiler: ‘Debian clang version 16.0.6 (15)’
* used Fortran compiler: ‘GNU Fortran (Debian 13.2.0-3) 13.2.0’
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Invalid license file pointers: LICENSE
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘development’
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    r3PG 0.1.6
    ### Bug fixed
    - replace real(kind=8) with real(kind=kind(0.0d0)) in the more modern source files #97
    ### New function and data sets
    ### Major changes
    ### Minor changes
    - re-structuring the repository and moving the files to the main directory #95
    - adding GitHub CI
  Cannot process chunk/lines:
    r3PG 0.1.5
    ### Bug fixed
    - update of the `r3pg_ll` function in the vignette #89. There were wrong default parameters used.
    - new mcmc run for the vignette.
    ### New function and data sets
    ### Major changes
    - constrain the `frost_days` to the maximum days in month `prepare_climate` #68. Additionaly, in the main Fortran program f_frost is now calculated using the number of days per month (not standard 30 days as in original program). Consequently this lead to the deviation in the output of biomass to the third digit (see tests).
    ### Minor changes
    - improved checks for the climate data (whether within hard ranges) #90
  Cannot process chunk/lines:
    r3PG 0.1.4
    ### Bug fixed
    - minor bug fixes for the `prepare_input.R`, `prepare_climate.R`, `prepare_sizeDist.R` #69
    - ensuring that thinning values are withing plausible range `prepare_thinning.R` #75
    - correct ordering of species in `prepare_thinning.R` #70
    - insuring that the cumulative volume is not decreasing `md_3PG.f95` #63
    - likelihood function in the vignette contained wrong error values `r3pg_ll` #54
    - adjusting the vignette for the new `multidplyr` version #47
    ### New function and data sets
    - `get_parameters` Gets parameters sets for species from published studies
    - `param.db` Data.frame containing all parameters from the literature review.
    - `prepare_site` to check whether the site data are within the plausible range #73.
    - `prepare_species` to check whether the species data are within the plausible range #73.
    ### Minor changes
    - adding the LICENSE
    - renaming and exporting the `param.default`, `var.default` and `sizedist.default` internal data
* checking R 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 ... [2s/2s] 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 ... WARNING
Variables with usage in documentation object 'd_climate' but not in code:
  ‘d_climate’

Variables with usage in documentation object 'd_parameters' but not in code:
  ‘d_parameters’

Variables with usage in documentation object 'd_site' but not in code:
  ‘d_site’

Variables with usage in documentation object 'd_sizeDist' but not in code:
  ‘d_sizeDist’

Variables with usage in documentation object 'd_species' but not in code:
  ‘d_species’

Variables with usage in documentation object 'd_thinning' but not in code:
  ‘d_thinning’

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... 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 ... [0s/0s] ERROR
Running examples in ‘r3PG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prepare_climate
> ### Title: Subsets or replicate a climate data
> ### Aliases: prepare_climate
> 
> ### ** Examples
> 
> # sub-setting climate data
> prepare_climate( climate = d_climate, from = '2003-04', to = '2010-11')
Error: object 'd_climate' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] ERROR
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("r3PG")
  Loading required package: r3PG
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-basic.R:7:5'): basic model run ─────────────────────────────────
  Error in `eval(code, test_env)`: object 'd_thinning' not found
  Backtrace:
      ▆
   1. └─r3PG::run_3PG(...) at test-basic.R:7:4
  ── Error ('test-vba.R:7:3'): Evergreen 3-PGpjs check ───────────────────────────
  Error in `eval(code, test_env)`: object 'd_site' not found
  Backtrace:
      ▆
   1. └─r3PG::run_3PG(...) at test-vba.R:7:2
   2.   └─r3PG::prepare_input(...)
   3.     └─r3PG::prepare_site(site = site)
   4.       └─base::data.frame(site)
  ── Error ('test-vba.R:22:3'): Evergreen 3-PGmix check ──────────────────────────
  Error in `eval(code, test_env)`: object 'd_site' not found
  Backtrace:
      ▆
   1. └─r3PG::run_3PG(...) at test-vba.R:22:2
   2.   └─r3PG::prepare_input(...)
   3.     └─r3PG::prepare_site(site = site)
   4.       └─base::data.frame(site)
  ── Error ('test-vba.R:38:3'): Broadleaf 3-PGpjs check ──────────────────────────
  Error in `eval(code, test_env)`: object 'd_site' not found
  Backtrace:
      ▆
   1. └─r3PG::run_3PG(...) at test-vba.R:38:2
   2.   └─r3PG::prepare_input(...)
   3.     └─r3PG::prepare_site(site = site)
   4.       └─base::data.frame(site)
  ── Error ('test-vba.R:53:3'): Broadleaf 3-PGmix check ──────────────────────────
  Error in `eval(code, test_env)`: object 'd_site' not found
  Backtrace:
      ▆
   1. └─r3PG::run_3PG(...) at test-vba.R:53:2
   2.   └─r3PG::prepare_input(...)
   3.     └─r3PG::prepare_site(site = site)
   4.       └─base::data.frame(site)
  ── Error ('test-vba.R:69:3'): Mixtures 3-PGmix check ───────────────────────────
  Error in `eval(code, test_env)`: object 'd_thinning' not found
  Backtrace:
      ▆
   1. └─r3PG::run_3PG(...) at test-vba.R:69:2
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [0s/0s] 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: 2 ERRORs, 2 WARNINGs, 3 NOTEs