* using log directory 'd:/RCompile/CRANincoming/R-devel/mappire.Rcheck'
* using R Under development (unstable) (2025-01-20 r87609 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 'mappire/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mappire' version '0.2.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Yanlin Liao <yanlin.liao@outlook.com>'

New submission

Non-FOSS package license (NA)

Possibly misspelled words in DESCRIPTION:
  allelic (3:60)
  polyploids (3:37)

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Yanlin",
                    family = "Liao",
                    role = c("aut", "cre"),
                    email = "yanlin.liao@outlook.com")
as necessary.

The Title field should be in title case. Current version is:
  'perform linkage analysis for polyploids using multi-allelic markers'
In title case that is:
  'Perform Linkage Analysis for Polyploids using Multi-Allelic Markers'
* 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 whether package 'mappire' 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 Description field: should contain one or more complete sentences.
Non-standard license specification:
  NA
Standardizable: FALSE
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'vignette'
* 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 ... WARNING
'::' or ':::' imports not declared from:
  'Deriv' 'colorspace' 'doParallel' 'doSNOW' 'foreach' 'gtools' 'metap'
  'plyr' 'stringi'
'library' or 'require' calls not declared from:
  'colorspace' 'combinat' 'doParallel' 'dplyr' 'foreach' 'ggplot2'
  'grid' 'randomcoloR' 'reshape2'
'library' or 'require' calls in package code:
  'colorspace' 'combinat' 'doParallel' 'dplyr' 'foreach' 'ggplot2'
  'grid' 'randomcoloR' 'reshape2'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [14s] NOTE
FindOrder: no visible binding for global variable 'fixed'
FindOrder: no visible binding for global variable 'phasing'
Find_IBD: no visible binding for global variable 'offspring_score_list'
Find_IBD: no visible binding for global variable 'Phase'
Find_IBD: no visible global function definition for 'png'
Find_IBD: no visible global function definition for 'dev.off'
Haplotype_linkage: no visible binding for global variable 'combs'
Haplotype_linkage: no visible binding for global variable
  'offspring_score_list1'
Haplotype_linkage: no visible global function definition for 'combn'
Haplotype_linkage: no visible global function definition for '%dopar%'
Haplotype_linkage: no visible binding for global variable 'i'
Haplotype_linkage : <anonymous>: no visible global function definition
  for 'complete.cases'
Haplotype_linkage_all: no visible binding for global variable
  'offspring_score_list1'
Haplotype_linkage_all: no visible global function definition for
  'combn'
Haplotype_linkage_all: no visible global function definition for
  '%dopar%'
Haplotype_linkage_all: no visible binding for global variable 'i'
Haplotype_linkage_all : <anonymous>: no visible global function
  definition for 'complete.cases'
Infer_offspring_inheritance : <anonymous>: no visible global function
  definition for 'complete.cases'
MarkerType_Overview: no visible global function definition for 'ggplot'
MarkerType_Overview: no visible global function definition for 'aes'
MarkerType_Overview: no visible binding for global variable 'Var1'
MarkerType_Overview: no visible binding for global variable 'Freq'
MarkerType_Overview: no visible global function definition for
  'geom_bar'
MarkerType_Overview: no visible global function definition for 'xlab'
MarkerType_Overview: no visible global function definition for 'ylab'
MarkerType_Overview: no visible global function definition for 'labs'
MarkerType_Overview: no visible global function definition for
  'ggtitle'
MarkerType_Overview: no visible global function definition for 'theme'
MarkerType_Overview: no visible global function definition for
  'element_text'
MarkerType_Overview: no visible global function definition for
  'element_blank'
MarkerType_Overview: no visible global function definition for
  'element_line'
MarkerType_Overview: no visible binding for global variable
  'MarkerType'
MarkerType_Overview: no visible binding for global variable 'Frequency'
MultiAllelic_Inheritance_simulator: no visible global function
  definition for 'read.table'
MultiAllelic_Inheritance_simulator: no visible global function
  definition for 'write.table'
Multi_allelic_simulator_rep: no visible binding for global variable
  'pair_1'
Multi_allelic_simulator_rep: no visible global function definition for
  'as.roman'
Multi_allelic_simulator_rep: no visible global function definition for
  'write.table'
bivalent_equation_generator: no visible global function definition for
  'combn'
bivalent_equation_generator: no visible global function definition for
  '%>%'
bivalent_equation_generator: no visible global function definition for
  'group_by'
bivalent_equation_generator: no visible global function definition for
  'summarise_at'
bivalent_equation_generator: no visible global function definition for
  'vars'
bivalent_equation_generator: no visible global function definition for
  'melt'
check_segregation: no visible binding for global variable
  'P1_gamete_diso'
check_segregation: no visible binding for global variable 'F1'
check_segregation : <anonymous>: no visible global function definition
  for 'complete.cases'
check_segregation : <anonymous>: no visible global function definition
  for 'pbinom'
check_segregation : <anonymous>: no visible global function definition
  for 'chisq.test'
create_bivalent_pairing: no visible global function definition for
  'permn'
create_gamete_disomic: no visible binding for global variable 'P1'
create_gamete_polysomic: no visible binding for global variable 'P1'
create_gamete_polysomic: no visible global function definition for
  'combn'
decide_MT: no visible binding for global variable 'P1'
disomic_equation_generator: no visible global function definition for
  'combn'
disomic_equation_generator : <anonymous>: no visible global function
  definition for 'melt'
filter_inheritance: no visible global function definition for 'abline'
find_possibility: no visible binding for global variable 'other_marker'
format_pairint_list: no visible binding for global variable
  'poly_total'
format_results: no visible binding for global variable 'poly_dosages'
found_probability: no visible binding for global variable 'F1'
found_probability: no visible binding for global variable 'i'
found_probability: no visible binding for global variable 'F1_ind'
generate_recombi_nonrecombi: no visible binding for global variable
  'tmp_P'
generate_recombi_nonrecombi: no visible binding for global variable
  'part1_hom1'
generate_recombi_nonrecombi: no visible binding for global variable
  'part1_hom2'
kronecker_string: no visible binding for global variable 'g_matrix_P1'
kronecker_string: no visible binding for global variable 'g_matrix_P2'
maximum_likelihood_estimator: no visible binding for global variable
  'maximum_equation'
maximum_likelihood_estimator: no visible global function definition for
  'optimize'
mphasing: no visible binding for global variable 'Linkage_all'
multiplot: no visible global function definition for 'grid.newpage'
multiplot: no visible global function definition for 'pushViewport'
multiplot: no visible global function definition for 'viewport'
multiplot: no visible global function definition for 'grid.layout'
obtain_color_IBD: no visible binding for global variable 'IBD'
obtain_color_IBD: no visible global function definition for
  'installed.packages'
obtain_color_IBD: no visible global function definition for
  'install.packages'
offspring_probability_estimator: no visible binding for global variable
  'offspring_score'
phasing_filter: no visible binding for global variable 'P_parents'
phasing_filter: no visible binding for global variable 'Q_parents'
phasing_filter: no visible binding for global variable 'tmp'
plot_IBD: no visible binding for global variable 'proba_res3'
plot_IBD: no visible binding for global variable 'individual'
plot_IBD: no visible global function definition for 'axis'
plot_IBD: no visible global function definition for 'symbols'
plot_IBD: no visible global function definition for 'rect'
plot_IBD: no visible global function definition for 'title'
plot_IBD: no visible global function definition for 'par'
plot_rf_comparison: no visible global function definition for 'ggplot'
plot_rf_comparison: no visible global function definition for 'aes'
plot_rf_comparison: no visible binding for global variable 'r'
plot_rf_comparison: no visible binding for global variable 'LOD'
plot_rf_comparison: no visible global function definition for
  'geom_point'
plot_rf_comparison: no visible global function definition for 'xlab'
plot_rf_comparison: no visible global function definition for 'ylab'
plot_rf_comparison: no visible global function definition for 'labs'
plot_rf_comparison: no visible global function definition for 'ggtitle'
plot_rf_comparison: no visible global function definition for 'theme'
plot_rf_comparison: no visible global function definition for
  'element_text'
plot_rf_comparison: no visible global function definition for
  'element_blank'
plot_rf_comparison: no visible global function definition for
  'element_line'
plot_rf_comparison: no visible binding for global variable
  'simulated_rf'
plot_rf_comparison: no visible binding for global variable
  'simulated_phasing_correct'
plot_rf_comparison: no visible global function definition for
  'geom_abline'
plot_rf_comparison: no visible global function definition for 'xlim'
plot_rf_comparison: no visible global function definition for 'ylim'
plot_rf_comparison: no visible global function definition for
  'element_rect'
plot_rf_comparison: no visible global function definition for 'png'
plot_rf_comparison: no visible global function definition for 'dev.off'
possible_gamete_parent: no visible global function definition for
  'combn'
prepare_pairwise_order: no visible binding for global variable
  'Linkage_all'
readDatfile: no visible global function definition for 'read.table'
recombination_estimate: no visible binding for global variable
  'Q_P2_equation'
recombination_estimate: no visible binding for global variable
  'offspring_probability_table'
recombination_estimate: no visible binding for global variable
  'marker_P'
recombination_estimate: no visible binding for global variable
  'marker_Q'
recombination_estimate : rf_MML: no visible global function definition
  for '%>%'
recombination_estimate : rf_MML: no visible global function definition
  for 'group_by'
recombination_estimate : rf_MML: no visible binding for global variable
  'gsub_probability'
recombination_estimate : rf_MML: no visible global function definition
  for 'summarise_at'
recombination_estimate : rf_MML: no visible global function definition
  for 'vars'
reconstruct_phasing: no visible binding for global variable 'P1_all'
reconstruct_phasing: no visible binding for global variable 'P1_list'
reconstruct_phasing: no visible binding for global variable
  'Linkage_all'
results_evaluation: no visible binding for global variable
  'Linkage_res'
seg_pro_NEW: no visible binding for global variable 'offspring_temp'
seg_pro_NEW: no visible global function definition for 'complete.cases'
significant_marker: no visible binding for global variable
  'start_marker'
significant_marker: no visible binding for global variable
  'other_marker'
simplify_equation: no visible binding for global variable
  'tetraploid_equation'
simplify_equation: no visible binding for global variable 'a_parents'
simplify_equation: no visible binding for global variable 'combs_b_P1'
simplify_equation: no visible binding for global variable 'z'
unique_hap: no visible binding for global variable 'a_parents'
unique_hap: no visible binding for global variable 'combs_b_P1'
Undefined global functions or variables:
  %>% %dopar% F1 F1_ind Freq Frequency IBD LOD Linkage_all Linkage_res
  MarkerType P1 P1_all P1_gamete_diso P1_list P_parents Phase
  Q_P2_equation Q_parents Var1 a_parents abline aes as.roman axis
  chisq.test combn combs combs_b_P1 complete.cases dev.off
  element_blank element_line element_rect element_text fixed
  g_matrix_P1 g_matrix_P2 geom_abline geom_bar geom_point ggplot
  ggtitle grid.layout grid.newpage group_by gsub_probability i
  individual install.packages installed.packages labs marker_P marker_Q
  maximum_equation melt offspring_probability_table offspring_score
  offspring_score_list offspring_score_list1 offspring_temp optimize
  other_marker pair_1 par part1_hom1 part1_hom2 pbinom permn phasing
  png poly_dosages poly_total proba_res3 pushViewport r read.table rect
  simulated_phasing_correct simulated_rf start_marker summarise_at
  symbols tetraploid_equation theme title tmp tmp_P vars viewport
  write.table xlab xlim ylab ylim z
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "axis", "par", "rect", "symbols",
             "title")
  importFrom("stats", "chisq.test", "complete.cases", "optimize",
             "pbinom")
  importFrom("utils", "as.roman", "combn", "install.packages",
             "installed.packages", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: Multi_allelic_simulator_rep.Rd:39-41: Dropping empty section \value
prepare_Rd: check_segregation.Rd:35-37: Dropping empty section \value
prepare_Rd: estimated_phasing.Rd:15-17: Dropping empty section \value
prepare_Rd: plot_rf_comparison.Rd:14-16: Dropping empty section \value
prepare_Rd: simulated_phasing.Rd:17-19: Dropping empty section \value
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'FindOrder' 'Find_IBD' 'Haplotype_linkage_all' 'Linkage_all'
  'Linkage_res' 'MT' 'Phase' 'all_equations' 'code_converter'
  'combine_res' 'dsg_table' 'evaluated_res' 'filter_inheritance'
  'find_possibility' 'genfile' 'kronecker_string'
  'linkagelist_to_linkage' 'map' 'mapfile' 'mphasing'
  'obtain_color_IBD' 'offspring_score_list' 'phasing_filter' 'plot_IBD'
  'poly' 'pool_linkage' 'prepare_pairwise_order' 'prepare_phasing_list'
  'recombination_estimate' 'reconstruct_phasing' 'res_IBD'
  'run.PedigreeSim' 'significant_marker' 'simulated_phasing_gametes'
Undocumented data sets:
  'Linkage_all' 'Linkage_res' 'MT' 'Phase' 'all_equations' 'dsg_table'
  'evaluated_res' 'genfile' 'map' 'mapfile' 'offspring_score_list'
  'poly' 'res_IBD'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in Rd file 'recombination_estimator.Rd' but not in code:
  'recombination_estimator'

Codoc mismatches from Rd file 'Haplotype_linkage.Rd':
Haplotype_linkage
  Code: function(Mrk_P = combs[c, ][1], Mrk_Q = combs[c, ][2],
                 offspring_score_list = offspring_score_list1, poly,
                 MT, cores, all_equations, pairing)
  Docs: function(Mrk_P = combs[c, ][1], Mrk_Q = combs[c, ][2],
                 offspring_score_list = offspring_score_list1, poly,
                 cores, all_equations, pairing)
  Argument names in code not in docs:
    MT
  Mismatches in argument names:
    Position: 5 Code: MT Docs: cores
    Position: 6 Code: cores Docs: all_equations
    Position: 7 Code: all_equations Docs: pairing

Codoc mismatches from Rd file 'results_evaluation.Rd':
results_evaluation
  Code: function(result = Linkage_res$output, genfile = genfile,
                 mapfile = mapfile, plot = TRUE, figurename, ploidy)
  Docs: function(result = Linkage_res$output, genfile = genfile,
                 mapfile = mapfile, plot = TRUE, filename)
  Argument names in code not in docs:
    figurename ploidy
  Argument names in docs not in code:
    filename
  Mismatches in argument names:
    Position: 5 Code: figurename Docs: filename

Codoc mismatches from Rd file 'sharing_identification.Rd':
sharing_identification
  Code: function(mrk, ploidy)
  Docs: function(mrk)
  Argument names in code not in docs:
    ploidy

Codoc mismatches from Rd file 'simulated_phasing.Rd':
simulated_phasing
  Code: function(genfile, mrk1, mrk2, ploidy)
  Docs: function(genfile, mrk1, mrk2)
  Argument names in code not in docs:
    ploidy

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'create_gamete_disomic.Rd'
  'ploidy'

Undocumented arguments in Rd file 'create_gamete_polysomic.Rd'
  'ploidy'

Undocumented arguments in Rd file 'found_probability.Rd'
  'ploidy'

Undocumented arguments in Rd file 'multiplot.Rd'
  '...'

Undocumented arguments in Rd file 'readDatfile.Rd'
  '...'

Undocumented arguments in Rd file 'unique_hap.Rd'
  'hap_mrkP' 'hap_mrkQ'
Documented arguments not in \usage in Rd file 'unique_hap.Rd':
  'pair_comb'

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 ... NOTE
Argument items with no description in Rd file 'MarkerType_Overview.Rd':
  'poly'
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                           old_size new_size compress
  Linkage_all.rda              25Kb     13Kb    bzip2
  Phase.rda                   121Kb     26Kb       xz
  all_equations.rda           119Kb     21Kb       xz
  dsg_table.rda                12Kb      3Kb       xz
  genfile.rda                  15Kb      8Kb       xz
  offspring_score_list.rda     41Kb     16Kb    bzip2
  poly.rda                     15Kb      8Kb    bzip2
  res_IBD.rda                 174Kb     53Kb       xz
* checking examples ... NONE
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... OK
* checking for code which exercises the package ... WARNING
No examples, no tests, no vignettes
* DONE
Status: 6 WARNINGs, 6 NOTEs