* using log directory 'd:/Rcompile/CRANpkg/local/4.6/litteR.Rcheck'
* using R Under development (unstable) (2025-09-03 r88788 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'litteR/DESCRIPTION' ... OK
* this is package 'litteR' version '1.0.1'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'litteR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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] OK
* checking whether the package can be loaded with stated dependencies ... [2s] OK
* checking whether the package can be unloaded cleanly ... [2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [2s] OK
* checking loading without being on the library search path ... [2s] OK
* checking whether startup messages can be suppressed ... [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 ... [6s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [3s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [3s] ERROR
  Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(litteR)
  
  litteR version: 1.0.1
  Type create_litter_project() to create a new project.
  Type vignette("litteR-manual") to open the user manual.
  Open the data file and check the presence of essential column names
  (see manual, Section 4.2).
  Open the settings file and check the settings.
  Type litter() to start litteR.
  > 
  > test_check("litteR")
  2025-09-04 14:29:50 [INFO] Check if required metadata columns 'location_code' and 'date' exist.
  2025-09-04 14:29:50 [INFO] All required columns are available
  2025-09-04 14:29:50 [INFO] Check if optional columns are available.
  2025-09-04 14:29:50 [INFO] No optional columns found.
  2025-09-04 14:29:50 [INFO] Checking date format
  2025-09-04 14:29:50 [INFO] All dates are OSPAR compliant (dd/mm/YYYY)
  2025-09-04 14:29:50 [INFO] Checking consistency of dates
  2025-09-04 14:29:50 [INFO] Dates are consistent. All dates are dd/mm/YYYY
  2025-09-04 14:29:50 [INFO] Check if all litter types in the type file are present in the data file
  2025-09-04 14:29:50 [WARN] The following types in the type file are missing in the data file: 'p: b [2]'
  2025-09-04 14:29:50 [INFO] Select only litter data
  2025-09-04 14:29:50 [WARN] The following columns will be excluded from analysis:'dummy'
  2025-09-04 14:29:50 [INFO] Check for empty cells
  2025-09-04 14:29:50 [INFO] No empty cells found
  2025-09-04 14:29:50 [INFO] Check that litter counts are numbers
  2025-09-04 14:29:50 [INFO] Only numbers found
  2025-09-04 14:29:50 [INFO] Check that litter counts are nonnegative numbers
  2025-09-04 14:29:50 [INFO] No negative numbers found
  2025-09-04 14:29:50 [INFO] Check that litter counts are natural numbers
  2025-09-04 14:29:50 [INFO] Only natural numbers found
  2025-09-04 14:29:50 [INFO] Check if not all litter counts in a single survey (record) are zero
  2025-09-04 14:29:50 [INFO] No records found with only zero-counts
  2025-09-04 14:29:50 [INFO] Check for duplicated records
  2025-09-04 14:29:50 [INFO] No duplicated records found
  2025-09-04 14:29:50 [INFO] No records with the same location_code/date found
  2025-09-04 14:29:50 [INFO] Checking extension of 'test.xyz' (should be 'csv')
  2025-09-04 14:29:50 [ERROR] file 'test.xyz' should have 'csv' as extension.
  2025-09-04 14:29:50 [INFO] Check if required metadata columns 'location_code' and 'date' exist.
  2025-09-04 14:29:50 [INFO] All required columns are available
  2025-09-04 14:29:50 [INFO] Check if optional columns are available.
  2025-09-04 14:29:50 [INFO] No optional columns found.
  2025-09-04 14:29:50 [INFO] Checking date format
  2025-09-04 14:29:50 [INFO] All dates are OSPAR compliant (dd/mm/YYYY)
  2025-09-04 14:29:50 [INFO] Checking consistency of dates
  2025-09-04 14:29:50 [INFO] Dates are consistent. All dates are dd/mm/YYYY
  2025-09-04 14:29:50 [INFO] Check if all litter types in the type file are present in the data file
  2025-09-04 14:29:50 [INFO] All litter types are present
  2025-09-04 14:29:50 [INFO] Select only litter data
  2025-09-04 14:29:50 [INFO] Check for empty cells
  2025-09-04 14:29:50 [ERROR] The following data column(s) contain(s) empty cells:p: a [1]
  2025-09-04 14:29:50 [INFO] Check if required metadata columns 'location_code' and 'date' exist.
  2025-09-04 14:29:50 [INFO] All required columns are available
  2025-09-04 14:29:50 [INFO] Check if optional columns are available.
  2025-09-04 14:29:50 [INFO] No optional columns found.
  2025-09-04 14:29:50 [INFO] Checking date format
  2025-09-04 14:29:50 [INFO] All dates are OSPAR compliant (dd/mm/YYYY)
  2025-09-04 14:29:50 [INFO] Checking consistency of dates
  2025-09-04 14:29:50 [INFO] Dates are consistent. All dates are dd/mm/YYYY
  2025-09-04 14:29:50 [INFO] Check if all litter types in the type file are present in the data file
  2025-09-04 14:29:50 [INFO] All litter types are present
  2025-09-04 14:29:50 [INFO] Select only litter data
  2025-09-04 14:29:50 [INFO] Check for empty cells
  2025-09-04 14:29:50 [INFO] No empty cells found
  2025-09-04 14:29:50 [INFO] Check that litter counts are numbers
  2025-09-04 14:29:50 [INFO] Only numbers found
  2025-09-04 14:29:50 [INFO] Check that litter counts are nonnegative numbers
  2025-09-04 14:29:50 [INFO] No negative numbers found
  2025-09-04 14:29:50 [INFO] Check that litter counts are natural numbers
  2025-09-04 14:29:50 [INFO] Only natural numbers found
  2025-09-04 14:29:50 [INFO] Check if not all litter counts in a single survey (record) are zero
  2025-09-04 14:29:50 [INFO] No records found with only zero-counts
  2025-09-04 14:29:50 [INFO] Check for duplicated records
  2025-09-04 14:29:50 [WARN] The following records are duplicated: 2 and 3. Only the first record of each duplicate will be retained.
  2025-09-04 14:29:50 [INFO] No records with the same location_code/date found
  2025-09-04 14:29:50 [INFO] Check if required metadata columns 'location_code' and 'date' exist.
  2025-09-04 14:29:50 [INFO] All required columns are available
  2025-09-04 14:29:50 [INFO] Check if optional columns are available.
  2025-09-04 14:29:50 [INFO] No optional columns found.
  2025-09-04 14:29:50 [INFO] Checking date format
  2025-09-04 14:29:50 [INFO] All dates are OSPAR compliant (dd/mm/YYYY)
  2025-09-04 14:29:50 [INFO] Checking consistency of dates
  2025-09-04 14:29:50 [INFO] Dates are consistent. All dates are dd/mm/YYYY
  2025-09-04 14:29:50 [INFO] Check if all litter types in the type file are present in the data file
  2025-09-04 14:29:50 [INFO] All litter types are present
  2025-09-04 14:29:50 [INFO] Select only litter data
  2025-09-04 14:29:50 [INFO] Check for empty cells
  2025-09-04 14:29:50 [INFO] No empty cells found
  2025-09-04 14:29:50 [INFO] Check that litter counts are numbers
  2025-09-04 14:29:50 [INFO] Only numbers found
  2025-09-04 14:29:50 [INFO] Check that litter counts are nonnegative numbers
  2025-09-04 14:29:50 [INFO] No negative numbers found
  2025-09-04 14:29:50 [INFO] Check that litter counts are natural numbers
  2025-09-04 14:29:50 [INFO] Only natural numbers found
  2025-09-04 14:29:50 [INFO] Check if not all litter counts in a single survey (record) are zero
  2025-09-04 14:29:50 [INFO] No records found with only zero-counts
  2025-09-04 14:29:50 [INFO] Check for duplicated records
  2025-09-04 14:29:50 [INFO] No duplicated records found
  2025-09-04 14:29:50 [WARN] The following records have different counts for the same `location_code` and `date`:2 and 3. All these records will be retained in the analysis.
  2025-09-04 14:29:50 [INFO] Check if required metadata columns 'location_code' and 'date' exist.
  2025-09-04 14:29:50 [INFO] All required columns are available
  2025-09-04 14:29:50 [INFO] Check if optional columns are available.
  2025-09-04 14:29:50 [INFO] No optional columns found.
  2025-09-04 14:29:50 [INFO] Checking date format
  2025-09-04 14:29:50 [INFO] All dates are ISO 8601 compliant (YYYY-mm-dd)
  2025-09-04 14:29:50 [INFO] Checking consistency of dates
  2025-09-04 14:29:50 [INFO] Dates are consistent. All dates are YYYY-mm-dd
  2025-09-04 14:29:50 [INFO] Check if all litter types in the type file are present in the data file
  2025-09-04 14:29:50 [WARN] The following types in the type file are missing in the data file: 'plastic: yokes [1]'
  2025-09-04 14:29:50 [INFO] Select only litter data
  2025-09-04 14:29:50 [ERROR] No columns with litter data found. See the type file for valid litter types.
  2025-09-04 14:29:50 [INFO] Check if required metadata columns 'location_code' and 'date' exist.
  2025-09-04 14:29:50 [INFO] All required columns are available
  2025-09-04 14:29:50 [INFO] Check if optional columns are available.
  2025-09-04 14:29:50 [INFO] No optional columns found.
  2025-09-04 14:29:50 [INFO] Checking date format
  2025-09-04 14:29:50 [INFO] All dates are ISO 8601 compliant (YYYY-mm-dd)
  2025-09-04 14:29:50 [INFO] Checking consistency of dates
  2025-09-04 14:29:50 [INFO] Dates are consistent. All dates are YYYY-mm-dd
  2025-09-04 14:29:50 [INFO] Check if all litter types in the type file are present in the data file
  2025-09-04 14:29:50 [INFO] All litter types are present
  2025-09-04 14:29:50 [INFO] Select only litter data
  2025-09-04 14:29:50 [INFO] Check for empty cells
  2025-09-04 14:29:50 [INFO] No empty cells found
  2025-09-04 14:29:50 [INFO] Check that litter counts are numbers
  2025-09-04 14:29:50 [INFO] Only numbers found
  2025-09-04 14:29:50 [INFO] Check that litter counts are nonnegative numbers
  2025-09-04 14:29:50 [INFO] No negative numbers found
  2025-09-04 14:29:50 [INFO] Check that litter counts are natural numbers
  2025-09-04 14:29:50 [WARN] Non-natural numbers (i.e., numbers that are not in 0, 1, 2, ...) found in columns:'plastic: yokes [1]'. Please, verify if these numbers are correct.These columns will be included in the analysis.
  2025-09-04 14:29:50 [INFO] Check if not all litter counts in a single survey (record) are zero
  2025-09-04 14:29:50 [INFO] No records found with only zero-counts
  2025-09-04 14:29:50 [INFO] Check for duplicated records
  2025-09-04 14:29:50 [INFO] No duplicated records found
  2025-09-04 14:29:50 [INFO] No records with the same location_code/date found
  2025-09-04 14:29:50 [INFO] Check if required metadata columns 'location_code' and 'date' exist.
  2025-09-04 14:29:50 [INFO] All required columns are available
  2025-09-04 14:29:50 [INFO] Check if optional columns are available.
  2025-09-04 14:29:50 [INFO] No optional columns found.
  2025-09-04 14:29:50 [INFO] Checking date format
  2025-09-04 14:29:50 [INFO] All dates are ISO 8601 compliant (YYYY-mm-dd)
  2025-09-04 14:29:50 [INFO] Checking consistency of dates
  2025-09-04 14:29:50 [INFO] Dates are consistent. All dates are YYYY-mm-dd
  2025-09-04 14:29:50 [INFO] Check if all litter types in the type file are present in the data file
  2025-09-04 14:29:50 [INFO] All litter types are present
  2025-09-04 14:29:50 [INFO] Select only litter data
  2025-09-04 14:29:50 [INFO] Check for empty cells
  2025-09-04 14:29:50 [INFO] No empty cells found
  2025-09-04 14:29:50 [INFO] Check that litter counts are numbers
  2025-09-04 14:29:50 [ERROR] The following data column(s) contain(s) text: 'plastic: yokes [1]'. Please correct your data file.
  2025-09-04 14:29:50 [INFO] Check if required metadata columns 'location_code' and 'date' exist.
  2025-09-04 14:29:50 [INFO] All required columns are available
  2025-09-04 14:29:50 [INFO] Check if optional columns are available.
  2025-09-04 14:29:50 [INFO] No optional columns found.
  2025-09-04 14:29:50 [INFO] Checking date format
  2025-09-04 14:29:50 [INFO] All dates are ISO 8601 compliant (YYYY-mm-dd)
  2025-09-04 14:29:50 [INFO] Checking consistency of dates
  2025-09-04 14:29:50 [INFO] Dates are consistent. All dates are YYYY-mm-dd
  2025-09-04 14:29:50 [INFO] Check if all litter types in the type file are present in the data file
  2025-09-04 14:29:50 [INFO] All litter types are present
  2025-09-04 14:29:50 [INFO] Select only litter data
  2025-09-04 14:29:50 [INFO] Check for empty cells
  2025-09-04 14:29:50 [ERROR] The following data column(s) contain(s) empty cells:plastic: yokes [1]
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 71 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-counts.R:3:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-stats.R:59:5'): Wilcoxon is correct ──────────────────────────
  p_value(wl) not equal to wr$p.value.
  1/1 mismatches
  [1] 0.00185 - 0.00224 == -0.000389
  ── Failure ('test-stats.R:60:5'): Wilcoxon is correct ──────────────────────────
  test_statistic(wl) not equivalent to wr$statistic.
  1/1 mismatches
  [1] 53.5 - 33.5 == 20
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 71 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [7s] OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... [6s] OK
* DONE
Status: 1 ERROR