* using log directory 'd:/RCompile/CRANincoming/R-devel/occTest.Rcheck'
* using R Under development (unstable) (2023-09-13 r85142 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'occTest/DESCRIPTION' ... OK
* this is package 'occTest' version '0.1.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... WARNING
Maintainer: 'Josep M Serra-Diaz <pep.agroparistech@gmail.com>'

New submission

Package was archived on CRAN

Insufficient package version (submitted: 0.1.1, existing: 0.1.1)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2023-04-03 as issues were not corrected
    in time.

Suggests or Enhances not in mainstream repositories:
  originr, parallelsugar
Availability using Additional_repositories specification:
  originr         yes   https://pepbioalerts.github.io/drat
  parallelsugar   yes   https://pepbioalerts.github.io/drat

Reading CITATION file fails with
  there is no package called 'CoordinateCleaner'
when package is not installed.

The Date field is not in ISO 8601 yyyy-mm-dd format.

Size of tarball: 6636171 bytes
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  'originr', 'parallelsugar'
* 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 'occTest' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Warning: replacing previous import 'stats::filter' by 'dplyr::filter' when loading 'occTest'
See 'd:/RCompile/CRANincoming/R-devel/occTest.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... 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 R files for non-ASCII characters ... OK
* 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 whether startup messages can be suppressed ... 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 ... [45s] NOTE
centroid_assessment_BIEN: no visible binding for global variable
  'countryISO3'
centroid_assessment_BIEN: no visible binding for global variable
  'state_province'
centroid_assessment_BIEN: no visible binding for global variable
  'county_parish'
centroid_assessment_BIEN: no visible binding for global variable
  'countryBIEN'
centroid_assessment_BIEN: no visible binding for global variable
  'county'
centroid_assessment_BIEN: no visible binding for global variable
  'cent_ID'
centroid_assessment_BIEN: no visible binding for global variable
  'centroid_distance'
centroid_assessment_BIEN: no visible binding for global variable
  'dist_max'
centroid_assessment_BIEN: no visible binding for global variable
  'country'
envOutliers: no visible binding for global variable 'pr_ab'
occFilter: no visible binding for global variable 'phase'
Undefined global functions or variables:
  cent_ID centroid_distance country countryBIEN countryISO3 county
  county_parish dist_max phase pr_ab state_province
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Unknown package 'flexsdm' in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in documentation object 'centroidDetection':
  '.c.field'

Documented arguments not in \usage in documentation object '.cc_urb_occTest':
  'a'

Documented arguments not in \usage in documentation object '.ne_download_occTest':
  'desetdir'

Documented arguments not in \usage in documentation object 'mcp_test':
  'myPres' 'myEnv' 'checkPairs' 'pvalSet' 'verbose'

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' ... OK
* checking examples ... [12s] ERROR
Running examples in 'occTest-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findEnvOutliers
> ### Title: Find outlying occurrence data in environmental space
> ### Aliases: findEnvOutliers
> 
> ### ** Examples
> 
> myPres=read.csv(system.file('extdata/SpeciesCSVs/Camissonia_tanacetifolia.csv',
+                             package='occOutliers'))
Warning in file(file, "rt") :
  file("") only supports open = "w+" and open = "w+b": using the former
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  no lines available in input
Calls: read.csv -> read.table
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [15s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 4 NOTEs