* using log directory 'd:/RCompile/CRANincoming/R-devel/ILORA.Rcheck'
* using R Under development (unstable) (2024-07-28 r86931 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'ILORA/DESCRIPTION' ... OK
* this is package 'ILORA' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Ruqaiya Shaikh <ruqaiyashaikh41@gmail.com>'

New submission

Non-FOSS package license (MIT LICENSE)

Possibly misspelled words in DESCRIPTION:
  ILORA (2:40, 9:117)
* 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 ... WARNING
Found the following file with a non-portable file name:
  MIT LICENSE
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'ILORA' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ggplot2::last_plot' by 'plotly::last_plot' when loading 'ILORA'
See 'd:/RCompile/CRANincoming/R-devel/ILORA.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  MIT LICENSE
Standardizable: FALSE
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'MIT LICENSE'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... WARNING
Found the following file with non-ASCII characters:
  R/get_data.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function 'tools::showNonASCIIfile' can help in finding non-ASCII
characters in files.
* 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 ... WARNING
'::' or ':::' imports not declared from:
  'glue' 'lubridate' 'viridis'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [22s] NOTE
bar_plot: no visible binding for global variable 'invasion_status'
bar_plot: no visible binding for global variable 'acc_species_name'
calculate_market_metrics: no visible global function definition for
  'complete.cases'
calculate_mrt: no visible binding for global variable
  'first_record_year'
calculate_mrt: no visible binding for global variable 'mrt'
generate_palette: no visible global function definition for 'rainbow'
generate_palette: no visible global function definition for
  'heat.colors'
generate_palette: no visible global function definition for
  'terrain.colors'
generate_palette: no visible global function definition for
  'topo.colors'
generate_palette: no visible global function definition for 'cm.colors'
generate_palette: no visible global function definition for
  'colorRampPalette'
introduction_pathways_plot: no visible binding for global variable
  'introduction_pathways_reported'
introduction_pathways_plot: no visible binding for global variable
  'acc_species_name_int'
plot_first_record_year_histogram: no visible binding for global
  variable 'first_record_year'
plot_species_on_map: no visible global function definition for
  'na.omit'
plot_species_on_map: no visible binding for global variable 'longitude'
plot_species_on_map: no visible binding for global variable 'latitude'
plot_species_on_map: no visible binding for global variable
  'acc_species_name'
plot_species_on_map: no visible global function definition for
  'setNames'
plot_species_on_map: no visible binding for global variable
  'occurrence'
species_count_plot: no visible binding for global variable
  'growthhabit'
species_count_plot: no visible binding for global variable
  'acc_species_name_gen'
species_count_plot: no visible global function definition for 'reorder'
species_count_plot: no visible binding for global variable 'duration'
Undefined global functions or variables:
  acc_species_name acc_species_name_gen acc_species_name_int cm.colors
  colorRampPalette complete.cases duration first_record_year
  growthhabit heat.colors introduction_pathways_reported
  invasion_status latitude longitude mrt na.omit occurrence rainbow
  reorder setNames terrain.colors topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "colorRampPalette", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("stats", "complete.cases", "na.omit", "reorder", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'SpeciesDataPackage.Rd':
  '-package'
* checking Rd line widths ... NOTE
Rd file 'EDA.Rd':
  \examples lines wider than 100 characters:
     EDA("plot_species_on_map", species_name = "Quercus robur L.", palette = "inferno", opacity = 0.9, highlight = FALSE)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'calculate_mrt.Rd'
  'species'

Undocumented arguments in Rd file 'generate_palette.Rd'
  'n'

Undocumented arguments in Rd file 'get_data.Rd'
  'table_name'

Undocumented arguments in Rd file 'plot_species_on_map.Rd'
  'opacity'
Documented arguments not in \usage in Rd file 'plot_species_on_map.Rd':
  'dot_opacity'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
Files named as vignettes but with no recognized vignette engine:
   'vignettes/README.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ... ERROR
Running examples in 'ILORA-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EDA
> ### Title: Exploratory Data Analysis Function
> ### Aliases: EDA
> 
> ### ** Examples
> 
> # Call the bar_plot function
> EDA("bar_plot")
Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
	Is the server running on that host and accepting TCP/IP connections?
connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
	Is the server running on that host and accepting TCP/IP connections?
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [59s] ERROR
  Running 'testthat.R' [59s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(ILORA)
  Warning message:
  replacing previous import 'ggplot2::last_plot' by 'plotly::last_plot' when loading 'ILORA' 
  > 
  > test_check("ILORA")
  [ FAIL 13 | WARN 0 | SKIP 1 | PASS 9 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-get_data.R:97:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-get_data.R:26:3'): get_data returns a data frame for valid inputs ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::get_data(...) at test-get_data.R:26:3
   2.   ├─DBI::dbConnect(...)
   3.   └─RPostgres::dbConnect(...)
   4.     └─RPostgres (local) .local(drv, ...)
   5.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:33:3'): get_data returns NULL for invalid species ───
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::get_data(...) at test-get_data.R:33:3
   2.   ├─DBI::dbConnect(...)
   3.   └─RPostgres::dbConnect(...)
   4.     └─RPostgres (local) .local(drv, ...)
   5.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:49:3'): get_species_details retrieves correct details for a single species ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::get_species_details(species_name) at test-get_data.R:49:3
   2.   ├─DBI::dbConnect(...)
   3.   └─RPostgres::dbConnect(...)
   4.     └─RPostgres (local) .local(drv, ...)
   5.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:69:3'): get_species_details retrieves correct details for multiple species ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::get_species_details(species_names) at test-get_data.R:69:3
   2.   ├─DBI::dbConnect(...)
   3.   └─RPostgres::dbConnect(...)
   4.     └─RPostgres (local) .local(drv, ...)
   5.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:91:3'): get_species_details handles invalid input types ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
       ▆
    1. ├─testthat::expect_error(get_species_details(123), "species_name should be character or list of characters") at test-get_data.R:91:3
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─ILORA::get_species_details(123)
    8.   ├─DBI::dbConnect(...)
    9.   └─RPostgres::dbConnect(...)
   10.     └─RPostgres (local) .local(drv, ...)
   11.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:115:3'): plot_species_on_map creates a plot for given species ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::plot_species_on_map(species_names) at test-get_data.R:115:3
   2.   └─ILORA::get_data(species_names, c("longitude", "latitude"))
   3.     ├─DBI::dbConnect(...)
   4.     └─RPostgres::dbConnect(...)
   5.       └─RPostgres (local) .local(drv, ...)
   6.         └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:123:3'): plot_species_on_map handles custom colors ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::plot_species_on_map(species_names, custom_colors = custom_colors) at test-get_data.R:123:3
   2.   └─ILORA::get_data(species_names, c("longitude", "latitude"))
   3.     ├─DBI::dbConnect(...)
   4.     └─RPostgres::dbConnect(...)
   5.       └─RPostgres (local) .local(drv, ...)
   6.         └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:130:3'): plot_species_on_map returns error for invalid custom colors input ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-get_data.R:130:3
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─ILORA::plot_species_on_map(species_names, custom_colors = custom_colors)
    8.   └─ILORA::get_data(species_names, c("longitude", "latitude"))
    9.     ├─DBI::dbConnect(...)
   10.     └─RPostgres::dbConnect(...)
   11.       └─RPostgres (local) .local(drv, ...)
   12.         └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:136:3'): bar_plot creates a plot ────────────────────
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::bar_plot() at test-get_data.R:136:3
   2.   ├─DBI::dbConnect(...)
   3.   └─RPostgres::dbConnect(...)
   4.     └─RPostgres (local) .local(drv, ...)
   5.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:142:3'): bar_plot has correct title and labels ──────
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::bar_plot() at test-get_data.R:142:3
   2.   ├─DBI::dbConnect(...)
   3.   └─RPostgres::dbConnect(...)
   4.     └─RPostgres (local) .local(drv, ...)
   5.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:150:3'): species_count_plot creates ggplot objects ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::species_count_plot() at test-get_data.R:150:3
   2.   ├─DBI::dbConnect(...)
   3.   └─RPostgres::dbConnect(...)
   4.     └─RPostgres (local) .local(drv, ...)
   5.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:157:3'): species_count_plot has correct titles and labels ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::species_count_plot() at test-get_data.R:157:3
   2.   ├─DBI::dbConnect(...)
   3.   └─RPostgres::dbConnect(...)
   4.     └─RPostgres (local) .local(drv, ...)
   5.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  ── Error ('test-get_data.R:173:3'): introduction_pathways_plot creates a Plotly pie chart ──
  Error: connection to server at "localhost" (::1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  connection to server at "localhost" (127.0.0.1), port 5432 failed: Connection refused (0x0000274D/10061)
  	Is the server running on that host and accepting TCP/IP connections?
  
  Backtrace:
      ▆
   1. └─ILORA::introduction_pathways_plot() at test-get_data.R:173:3
   2.   ├─DBI::dbConnect(...)
   3.   └─RPostgres::dbConnect(...)
   4.     └─RPostgres (local) .local(drv, ...)
   5.       └─RPostgres:::connection_create(names(opts), as.vector(opts), check_interrupts)
  
  [ FAIL 13 | WARN 0 | SKIP 1 | PASS 9 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [15s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs, 5 WARNINGs, 7 NOTEs