* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sars.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘sars/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sars’ version ‘1.3.7’
* 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 ‘sars’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/sars-00install.html' for details.
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [22s/27s] OK
* checking Rd files ... [1s/1s] 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [42s/47s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [43s/47s] ERROR
  Running ‘testthat.R’ [43s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sars)
  > 
  > test_check("sars")
  
   Now attempting to fit the 20 SAR models: 
  
  ──  multi_sars ────────────────────────────────────────────── multi-model SAR ──
  → power    : ✔
  → powerR   : ✔
  → epm1     : ✔
  → epm2     : ✔
  → p1       : ✔
  → p2       : ✔
  → loga     : ✔
  → koba     : ✔
  → monod    : ✔
  → negexpo  : ✔
  → chapman  : ✔
  → weibull3 : ✔
  → asymp    : ✔
  → ratio    : ✔
  → gompertz : ✔
  → weibull4 : ✔
  → betap    : ✔
  → logistic : ✔
  → heleg    : ✔
  → linear   : ✔
  
  Model fitting completed - all models succesfully fitted. Now undertaking model validation checks. Additional models  will be excluded if necessary:
  
  16 remaining models used to construct the multi SAR:
   Power, PowerR, Extended Power model 2, Persistence function 1, Persistence function 2, Logarithmic, Kobayashi, Monod, Negative exponential, Chapman Richards, Cumulative Weibull 3 par., Rational function, Gompertz, Beta-P cumulative, Logistic(Standard), Heleg(Logistic) 
  ────────────────────────────────────────────────────────────────────────────────
  
   Now attempting to fit the 20 SAR models: 
  
  ──  multi_sars ────────────────────────────────────────────── multi-model SAR ──
  → power    : ✔
  → powerR   : ✔
  → epm1     : ✔
  → epm2     : ✔
  → p1       : ✔
  → p2       : ✔
  → loga     : ✔
  → koba     : ✔
  → monod    : ✔
  → negexpo  : ✔
  → chapman  : Warning: could not compute parameters statistics
  → weibull3 : ✔
  → asymp    : ✔
  → ratio    : Warning: could not compute parameters statistics
  → gompertz : ✔
  → weibull4 : Warning: could not compute parameters statistics
  → betap    : Warning: could not compute parameters statistics
  → logistic : ✔
  → heleg    : ✔
  → linear   : ✔
  
  No model validation checks selected
  
  20 remaining models used to construct the multi SAR:
   Power, PowerR, Extended Power model 1, Extended Power model 2, Persistence function 1, Persistence function 2, Logarithmic, Kobayashi, Monod, Negative exponential, Chapman Richards, Cumulative Weibull 3 par., Asymptotic regression, Rational function, Gompertz, Cumulative Weibull 4 par., Beta-P cumulative, Logistic(Standard), Heleg(Logistic), Linear model 
  ────────────────────────────────────────────────────────────────────────────────
  
   Now attempting to fit the 2 SAR models: 
  
  ──  multi_sars ────────────────────────────────────────────── multi-model SAR ──
  → linear : ✔
  → power  : ✔
  
   Now attempting to fit the 3 SAR models: 
  
  ──  multi_sars ────────────────────────────────────────────── multi-model SAR ──
  → power : ✔
  → koba  : ✔
  → ratio : ✔
  [ FAIL 2 | WARN 0 | SKIP 20 | PASS 147 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test_crit_method.R:5:3', 'test_crit_method.R:96:3',
    'test_grid_start.R:4:3', 'test_indiv_CIs.R:5:3', 'test_logistic.R:5:3',
    'test_multi.R:4:3', 'test_multi.R:30:3', 'test_multi.R:45:3',
    'test_multi.R:76:3', 'test_multi.R:89:3', 'test_p2.R:4:3',
    'test_pred.R:27:3', 'test_shape.R:4:3', 'test_thresholds.R:5:3',
    'test_thresholds.R:72:3', 'test_thresholds.R:94:3',
    'test_thresholds.R:133:3', 'test_warnings.R:5:3', 'test_weibull3.R:4:3',
    'test_weibull3.R:15:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_lin_pow.R:37:3'): lin_pow returns warning for all identical species ──
  Error in `grepl(as.character(pattern), x, ignore.case, FALSE, perl, fixed, 
      useBytes, FALSE)`: NA in coercion to bool
  Backtrace:
      â–†
   1. └─testthat::expect_warning(...) at test_lin_pow.R:37:3
   2.   └─testthat:::compare_messages(...)
   3.     └─base::grepl(regexp, messages, ...)
  ── Error ('test_power.R:40:3'): sar_power returns warning for all identical species ──
  Error in `grepl(as.character(pattern), x, ignore.case, FALSE, perl, fixed, 
      useBytes, FALSE)`: NA in coercion to bool
  Backtrace:
      â–†
   1. └─testthat::expect_warning(...) at test_power.R:40:3
   2.   └─testthat:::compare_messages(...)
   3.     └─base::grepl(regexp, messages, ...)
  
  [ FAIL 2 | WARN 0 | SKIP 20 | PASS 147 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [30s/43s] OK
* checking PDF version of manual ... [6s/7s] OK
* checking HTML version of manual ... [2s/3s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR