* using log directory ‘/srv/hornik/tmp/CRAN_pretest/mvh.Rcheck’
* using R Under development (unstable) (2025-01-19 r87600)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.6 (1+b1)
    Debian flang-new version 19.1.6 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘mvh/DESCRIPTION’ ... OK
* this is package ‘mvh’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Thais Vasconcelos <tvasc@umich.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  Boyko (14:278)
  Herbarium (4:19)
  Vasconcelos (14:262)
  herbarium (14:143)

The Description field contains
  <https://doi.org/10.1101/2024.08.25.609600>
Please write DOIs as <doi:prefix/suffix>.

The Date field is over a month old.

This build time stamp is over a month old.
* 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 serialization versions ... OK
* checking whether package ‘mvh’ can be installed ... [3s/3s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] 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
Functions or methods with usage in Rd file 'create_directory.Rd' but not in code:
  ‘create_directory’

Codoc mismatches from Rd file 'download_specimen_images.Rd':
download_specimen_images
  Code: function(metadata, dir_name = file.path(tempdir(),
                 "my_virtual_collection"), resize = NULL, sleep = 2,
                 result_file_name = file.path(tempdir(),
                 "download_results"), timeout_limit = 300, verbose =
                 TRUE)
  Docs: function(metadata, dir_name = "my_virtual_collection", resize =
                 75, sleep = 2, result_file_name = "download_results",
                 timeout_limit = 300)
  Argument names in code not in docs:
    verbose
  Mismatches in argument default values:
    Name: 'dir_name' Code: file.path(tempdir(), "my_virtual_collection") Docs: "my_virtual_collection"
    Name: 'resize' Code: NULL Docs: 75
    Name: 'result_file_name' Code: file.path(tempdir(), "download_results") Docs: "download_results"

Codoc mismatches from Rd file 'search_specimen_metadata.Rd':
search_specimen_metadata
  Code: function(taxon_name = NULL, coordinates = NULL, buffer_distance
                 = NULL, limit = 500, verbose = TRUE, ...)
  Docs: function(taxon_name = NULL, coordinates = NULL, buffer_distance
                 = NULL, limit = 500, ...)
  Argument names in code not in docs:
    verbose
  Mismatches in argument names:
    Position: 5 Code: verbose Docs: ...

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs