* using log directory 'd:/RCompile/CRANincoming/R-devel/DRUGSENS.Rcheck'
* using R Under development (unstable) (2025-01-09 r87552 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'DRUGSENS/DESCRIPTION' ... OK
* this is package 'DRUGSENS' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Flavio Lombardo <flavio.lombardo@unibas.ch>'

New submission

Possibly misspelled words in DESCRIPTION:
  QuPath (15:54)
  QuPath's (4:27)

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid URLs:
  URL: %22https://git.scicore.unibas.ch/ovca-research/DRUGSENS/issues%22
    From: README.md
    Message: Invalid URI scheme
  URL: https://git.scicore.unibas.ch/ovca-research/DRUGSENS/issues (moved to https://git.scicore.unibas.ch/ovca-research/DRUGSENS/-/issues)
    From: DESCRIPTION
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.

The Title field should be in title case. Current version is:
  'Allows users to automatically analyze QuPath™'s output data from imaging analysis. In addition, it will automatically extract metadata from the QuPath's data.'
In title case that is:
  'Allows Users to Automatically Analyze QuPath™'s Output Data from Imaging Analysis. in Addition, it will Automatically Extract Metadata from the QuPath's Data.'

The Description field should not start with the package name,
  'This package' or similar.
* checking package namespace information ... OK
* checking package dependencies ... INFO
Vignette dependency required without any vignettes: 'knitr'
* 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 'DRUGSENS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'testthat'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'assets'
* 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
data_binding: no visible binding for global variable
  'list_of_relabeling'
get_QC_plots: no visible binding for global variable
  'marker_positivity_ratio'
get_QC_plots: no visible binding for global variable
  'marker_positivity'
get_QC_plots: no visible binding for global variable 'x'
get_QC_plots: no visible binding for global variable 'y'
get_QC_plots_parsed_merged_data: no visible binding for global variable
  'Name'
process_file: no visible global function definition for 'read.csv'
process_file: no visible binding for global variable
  'list_of_relabeling'
Undefined global functions or variables:
  Name list_of_relabeling marker_positivity marker_positivity_ratio
  read.csv x y
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'make_count_dataframe.Rd':
  \examples lines wider than 100 characters:
     bind_data <- data_binding(path_to_the_projects_folder = system.file("extdata/to_merge/", package = "DRUGSENS"), files_extension_to_look ... [TRUNCATED]

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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 5 NOTEs