* using log directory 'd:/RCompile/CRANincoming/R-devel/RDaggregator.Rcheck'
* using R version 4.5.0 alpha (2025-03-25 r88054 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 'RDaggregator/DESCRIPTION' ... OK
* this is package 'RDaggregator' version '1.0.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [11s] NOTE
Maintainer: 'Remy Dumas <remy.dumas84@gmail.com>'

New submission

License components with restrictions and base license permitting such:
  GPL (>= 3) + file LICENSE
File 'LICENSE':
  YEAR: 2025
  COPYRIGHT HOLDER: RDaggregator authors
  
  ---
  
  ## This file lists the copyright holders and licenses (if known) of the
  ## dataset (modified) in the RDaggregator package:
  ##
  ## Orphadata
  ## -----------
  ## Licensed under a Creative Commons Attribution 4.0 International (CC-BY-4.0)
  ## https://creativecommons.org/licenses/by/4.0/legalcode
  ##
  ## “Orphadata: Free access data from Orphanet. © INSERM 1999.
  ## Available on http://www.orphadata.org. Data version (XML data version).”

Possibly misspelled words in DESCRIPTION:
  Orphanet (7:71)

The Title field should be in title case. Current version is:
  'Data package for rare diseases in R'
In title case that is:
  'Data Package for Rare Diseases in R'

Size of tarball: 11150232 bytes
* 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 serialization versions ... OK
* checking whether package 'RDaggregator' can be installed ... OK
* 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.
  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'classifications.R' 'data-genes.R' 'data-pack.R' 'visualization.R'
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  'README.Rmd' 'data-raw'
* 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 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 ... [12s] NOTE
add_nomenclature_pack: no visible binding for global variable 'Name'
add_nomenclature_pack: no visible binding for global variable '.'
analyze_specifications: no visible global function definition for
  'any_of'
analyze_specifications: no visible binding for global variable
  'synonyms'
analyze_specifications: no visible binding for global variable
  'pref_symbol'
analyze_specifications: no visible binding for global variable
  'gene_id'
analyze_specifications: no visible binding for global variable 'HGNC'
analyze_specifications: no visible binding for global variable
  'association_status'
analyze_specifications: no visible binding for global variable
  'association_type'
analyze_specifications: no visible binding for global variable
  'orpha_code'
analyze_specifications: no visible binding for global variable
  'potential_codes'
analyze_specifications: no visible binding for global variable 'i'
analyze_specifications: no visible binding for global variable
  'new_code'
analyze_specifications: no visible binding for global variable
  'is_consistent'
apply_orpha_indent: no visible binding for global variable 'index'
apply_orpha_indent: no visible global function definition for 'any_of'
apply_orpha_indent: no visible binding for global variable 'n_indent'
assign_indent_index: no visible binding for global variable 'from'
assign_indent_index: no visible binding for global variable 'to'
assign_indent_index: no visible binding for global variable 'index'
check_orpha_gene_consistency: no visible global function definition for
  'any_of'
check_orpha_gene_consistency: no visible binding for global variable
  'orpha_code'
check_orpha_gene_consistency: no visible binding for global variable
  'i'
check_orpha_gene_consistency: no visible binding for global variable
  'is_consistent'
color_class_levels: no visible binding for global variable 'level'
complete_family: no visible binding for global variable 'to'
complete_family: no visible binding for global variable 'from'
default_dict: no visible binding for global variable 'default'
default_genes_version: no visible binding for global variable 'default'
default_pack_version: no visible binding for global variable 'default'
get_all_labels: no visible binding for global variable '.env'
get_children: no visible binding for global variable 'from'
get_children: no visible binding for global variable 'to'
get_classification_level: no visible binding for global variable
  'level'
get_descendants: no visible binding for global variable 'name'
get_descendants: no visible binding for global variable 'y'
get_label: no visible binding for global variable 'label'
get_lowest_groups: no visible binding for global variable '.env'
get_lowest_groups: no visible binding for global variable 'level'
get_parents: no visible binding for global variable 'to'
get_parents: no visible binding for global variable 'from'
get_siblings: no visible binding for global variable 'from'
get_siblings: no visible binding for global variable 'to'
get_type: no visible binding for global variable 'type'
group_by.orpha_df: no visible global function definition for ':='
group_by.orpha_df: no visible binding for global variable
  'all_ancestors'
group_by.orpha_df: no visible global function definition for 'all_of'
group_by.orpha_df: no visible binding for global variable '.rows'
horizontal_positions: no visible binding for global variable 'to'
horizontal_positions: no visible binding for global variable 'from'
horizontal_positions: no visible binding for global variable 'y'
horizontal_sizes: no visible binding for global variable 'to'
horizontal_sizes: no visible binding for global variable 'from'
horizontal_sizes: no visible binding for global variable 'y'
horizontal_sizes: no visible binding for global variable 'name'
interactive_plot: no visible binding for global variable 'name'
interactive_plot: no visible binding for global variable 'id'
interactive_plot: no visible binding for global variable 'color'
interactive_plot: no visible binding for global variable 'frame.color'
interactive_plot: no visible binding for global variable 'label.color'
load_associated_genes: no visible binding for global variable
  'location'
load_classifications: no visible binding for global variable 'location'
load_genes_synonyms: no visible binding for global variable 'location'
load_raw_nomenclature: no visible binding for global variable
  'location'
load_raw_redirections: no visible binding for global variable
  'location'
load_synonyms: no visible binding for global variable 'location'
merge_graphs: no visible binding for global variable 'from'
merge_graphs: no visible binding for global variable 'to'
minimize_graph: no visible binding for global variable 'from'
minimize_graph: no visible binding for global variable 'to'
minimize_graph: no visible binding for global variable 'to_rem'
mutate.grouped_orpha_df: no visible global function definition for
  'all_of'
mutate.grouped_orpha_df: no visible global function definition for
  'any_of'
process_genes : find_gene_synonyms: no visible binding for global
  variable 'n_syns'
process_genes : find_gene_synonyms: no visible binding for global
  variable 'synonyms'
process_genes: no visible binding for global variable 'reference'
process_genes: no visible binding for global variable 'OMIM'
process_genes: no visible binding for global variable 'Reactome'
process_genes: no visible binding for global variable 'SwissProt'
process_nomenclature : find_synonyms: no visible binding for global
  variable 'synonyms'
process_nomenclature : find_redirections: no visible binding for global
  variable 'to'
redirect_code: no visible binding for global variable 'redir_type'
redirect_code: no visible binding for global variable 'to'
save_genes_versions: no visible global function definition for
  'write.csv2'
save_pack_versions: no visible global function definition for
  'write.csv2'
specify_code: no visible global function definition for 'any_of'
specify_code: no visible binding for global variable 'orpha_code'
specify_code: no visible binding for global variable 'i'
specify_code: no visible binding for global variable 'new_code'
subtype_to_disorder: no visible binding for global variable 'level'
translate_orpha_concepts : t: no visible binding for global variable
  'label'
translate_orpha_concepts: no visible binding for global variable
  'location'
translate_orpha_concepts: no visible global function definition for
  'all_of'
vertical_positions: no visible binding for global variable 'from'
vertical_positions: no visible binding for global variable 'to'
Undefined global functions or variables:
  . .env .rows := HGNC Name OMIM Reactome SwissProt all_ancestors
  all_of any_of association_status association_type color default
  frame.color from gene_id i id index is_consistent label label.color
  level location n_indent n_syns name new_code orpha_code
  potential_codes pref_symbol redir_type reference synonyms to to_rem
  type write.csv2 y
Consider adding
  importFrom("utils", "write.csv2")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: get_all_labels.Rd:18-21: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  group_by.orpha_df.Rd: group_by
  layout_tree.Rd: plot.igraph
  orpha-genes.Rd: chop
  orpha_df.Rd: group_by
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [24s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                    user system elapsed
apply_orpha_indent 12.49   0.16   12.65
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [209s] OK
  Running 'testthat.R' [208s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [23s] OK
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... OK
* DONE
Status: 7 NOTEs