* using log directory ‘/srv/hornik/tmp/CRAN_pretest/DNMB.Rcheck’ * using R Under development (unstable) (2024-10-18 r87246) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘DNMB/DESCRIPTION’ ... OK * this is package ‘DNMB’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Jae-Yoon Sung ’ New submission Possibly misspelled words in DESCRIPTION: DNMB (3:29) ribosomal (8:253) The Title field should be in title case. Current version is: ‘Comprehensive genomics analysis for the Domestication of Non-Model Bacteria (DNMB)’ In title case that is: ‘Comprehensive Genomics Analysis for the Domestication of Non-Model Bacteria (DNMB)’ Size of tarball: 33989044 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 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 ‘DNMB’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘examples’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘Biostrings’ ‘ComplexHeatmap’ ‘Peptides’ ‘circlize’ ‘data.table’ ‘gtools’ ‘openxlsx’ ‘plyr’ ‘qdap’ ‘readr’ ‘reshape2’ ‘seqinr’ ‘stringr’ ‘tibble’ 'library' or 'require' calls not declared from: ‘Biostrings’ ‘ComplexHeatmap’ ‘circlize’ ‘dplyr’ ‘ggplot2’ ‘ggseqlogo’ ‘grid’ ‘gridExtra’ ‘openxlsx’ ‘plyr’ ‘readr’ ‘reshape2’ ‘seqinr’ ‘splitstackshape’ ‘stringr’ ‘tidyr’ 'library' or 'require' calls in package code: ‘Biostrings’ ‘ComplexHeatmap’ ‘circlize’ ‘dplyr’ ‘ggplot2’ ‘ggseqlogo’ ‘grid’ ‘gridExtra’ ‘openxlsx’ ‘plyr’ ‘readr’ ‘reshape2’ ‘seqinr’ ‘splitstackshape’ ‘stringr’ ‘tidyr’ 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 ... [4s/4s] NOTE CRISPR_array_extractor: no visible global function definition for ‘read_fwf’ CRISPR_array_extractor: no visible global function definition for ‘%>%’ CRISPR_array_extractor: no visible binding for global variable ‘.’ CRISPR_array_extractor : : no visible global function definition for ‘str_squish’ CRISPR_array_extractor: no visible binding for global variable ‘X1’ CRISPR_array_extractor: no visible global function definition for ‘mutate’ CRISPR_array_extractor: no visible binding for global variable ‘end’ CRISPR_array_extractor: no visible binding for global variable ‘values’ CRISPR_array_extractor: no visible binding for global variable ‘start’ CRISPR_array_extractor: no visible global function definition for ‘str_detect’ CRISPR_array_extractor: no visible binding for global variable ‘category’ CRISPR_array_extractor: no visible global function definition for ‘dcast’ CRISPR_array_extractor: no visible global function definition for ‘mutate_all’ CRISPR_array_extractor: no visible binding for global variable ‘region’ CRISPR_array_extractor: no visible binding for global variable ‘contig_length’ CRISPR_array_extractor: no visible global function definition for ‘str_sub’ CRISPR_array_extractor: no visible binding for global variable ‘repeat_start’ CRISPR_array_extractor: no visible binding for global variable ‘repeat_end’ CRISPR_array_extractor: no visible binding for global variable ‘CRISPR_table_1’ CRISPR_array_extractor: no visible global function definition for ‘rbind.fill’ CRISPR_array_extractor: no visible binding for global variable ‘rpt_unit_seq’ CRISPR_array_extractor: no visible global function definition for ‘mutate_at’ CRISPR_array_extractor : : no visible global function definition for ‘%>%’ CRISPR_array_extractor : : no visible global function definition for ‘setNames’ CRISPR_array_extractor: no visible global function definition for ‘setNames’ CRISPR_array_extractor: no visible binding for global variable ‘na_if’ CRISPR_array_extractor: no visible global function definition for ‘drop_na’ CRISPR_array_extractor: no visible binding for global variable ‘spacer’ CRISPR_array_extractor: no visible global function definition for ‘distinct’ CRISPR_array_extractor: no visible binding for global variable ‘N20’ CRISPR_array_extractor: no visible global function definition for ‘write.xlsx’ CRISPR_array_extractor: no visible global function definition for ‘write.table’ Codon_usage_calculator: no visible global function definition for ‘%>%’ Codon_usage_calculator: no visible binding for global variable ‘protein_id’ Codon_usage_calculator: no visible global function definition for ‘s2c’ Codon_usage_calculator: no visible global function definition for ‘mutate’ Codon_usage_calculator: no visible binding for global variable ‘eff’ Codon_usage_calculator: no visible global function definition for ‘group_by’ Codon_usage_calculator: no visible binding for global variable ‘AA’ Codon_usage_calculator: no visible global function definition for ‘reframe’ Codon_usage_calculator: no visible global function definition for ‘n’ Codon_usage_calculator: no visible global function definition for ‘ungroup’ Codon_usage_calculator: no visible global function definition for ‘select’ Codon_usage_calculator: no visible global function definition for ‘arrange’ Codon_usage_calculator: no visible binding for global variable ‘s2c’ Codon_usage_calculator: no visible global function definition for ‘top_n’ Codon_usage_calculator: no visible global function definition for ‘pull’ Codon_usage_calculator: no visible binding for global variable ‘aaa’ DNMB_table: no visible global function definition for ‘createWorkbook’ DNMB_table: no visible global function definition for ‘addWorksheet’ DNMB_table: no visible global function definition for ‘writeData’ DNMB_table: no visible global function definition for ‘saveWorkbook’ EggNOG_annotations: no visible global function definition for ‘bind_rows’ EggNOG_annotations: no visible global function definition for ‘%>%’ EggNOG_annotations: no visible global function definition for ‘mutate’ EggNOG_annotations: no visible binding for global variable ‘query’ EggNOG_annotations: no visible global function definition for ‘filter’ EggNOG_annotations: no visible global function definition for ‘str_detect’ EggNOG_annotations: no visible global function definition for ‘str_sub’ EggNOG_annotations: no visible binding for global variable ‘COG_category’ EggNOG_annotations: no visible global function definition for ‘case_when’ Figure_generator: no visible global function definition for ‘theme’ Figure_generator: no visible global function definition for ‘unit’ Figure_generator: no visible global function definition for ‘grid.grabExpr’ Figure_generator: no visible global function definition for ‘draw’ Figure_generator: no visible global function definition for ‘grid.arrange’ Figure_generator: no visible global function definition for ‘pdf’ Figure_generator: no visible global function definition for ‘grid.draw’ Figure_generator: no visible global function definition for ‘grid.text’ Figure_generator: no visible global function definition for ‘gpar’ Figure_generator: no visible global function definition for ‘dev.off’ Genbank_organizer: no visible global function definition for ‘read.csv’ Genbank_organizer: no visible global function definition for ‘separate’ Genbank_organizer: no visible binding for global variable ‘contig_1_definition’ Genbank_organizer: no visible global function definition for ‘na.omit’ Genbank_organizer: no visible binding for global variable ‘contig_1_seq_final_temp’ Genbank_organizer: no visible global function definition for ‘rbind.fill’ Genbank_organizer: no visible global function definition for ‘%>%’ Genbank_organizer: no visible global function definition for ‘mutate’ Genbank_organizer: no visible binding for global variable ‘top_strand’ Genbank_organizer: no visible global function definition for ‘str_extract’ Genbank_organizer: no visible global function definition for ‘setNames’ Genbank_organizer: no visible global function definition for ‘separate_rows’ Genbank_organizer: no visible binding for global variable ‘a’ Genbank_organizer: no visible global function definition for ‘rename_all’ Genbank_organizer: no visible binding for global variable ‘contig_final_1’ Genbank_organizer: no visible global function definition for ‘case_when’ Genbank_organizer: no visible binding for global variable ‘.’ Genbank_organizer: no visible binding for global variable ‘gene_number’ Genbank_organizer: no visible global function definition for ‘select’ Genbank_organizer: no visible binding for global variable ‘contig’ Genbank_organizer: no visible binding for global variable ‘contig_number’ Genbank_organizer: no visible global function definition for ‘everything’ Genbank_organizer: no visible binding for global variable ‘locus_tag’ Genbank_organizer: no visible binding for global variable ‘translation’ Genbank_organizer: no visible global function definition for ‘drop_na’ Genbank_organizer: no visible global function definition for ‘write.table’ InterProScan_annotations : : no visible global function definition for ‘read.csv’ InterProScan_annotations: no visible global function definition for ‘bind_rows’ InterProScan_annotations: no visible global function definition for ‘%>%’ InterProScan_annotations: no visible global function definition for ‘mutate’ InterProScan_annotations: no visible global function definition for ‘lead’ InterProScan_annotations: no visible binding for global variable ‘V3’ InterProScan_annotations: no visible binding for global variable ‘V1’ InterProScan_annotations: no visible binding for global variable ‘V14’ InterProScan_annotations: no visible binding for global variable ‘V2’ InterProScan_annotations: no visible binding for global variable ‘V15’ InterProScan_annotations: no visible global function definition for ‘filter’ InterProScan_annotations: no visible global function definition for ‘str_replace_all’ Promoter_prediction_to_genbank: no visible global function definition for ‘read.csv’ Promoter_prediction_to_genbank: no visible global function definition for ‘%>%’ Promoter_prediction_to_genbank: no visible global function definition for ‘mutate’ Promoter_prediction_to_genbank: no visible global function definition for ‘case_when’ Promoter_prediction_to_genbank: no visible global function definition for ‘str_pad’ Promoter_prediction_to_genbank: no visible global function definition for ‘write.table’ RBS_extractor: no visible global function definition for ‘%>%’ RBS_extractor: no visible binding for global variable ‘genbank_table’ RBS_extractor: no visible global function definition for ‘filter’ RBS_extractor: no visible binding for global variable ‘product’ RBS_extractor: no visible global function definition for ‘select’ RBS_extractor: no visible binding for global variable ‘rearranged_nt_seq’ RBS_extractor: no visible global function definition for ‘mutate’ RBS_extractor: no visible global function definition for ‘str_sub’ RBS_extractor: no visible global function definition for ‘vmatchPattern’ RBS_extractor: no visible binding for global variable ‘group’ RBS_extractor: no visible binding for global variable ‘start’ RBS_extractor: no visible binding for global variable ‘end’ RBS_extractor: no visible global function definition for ‘rbind.fill’ RBS_extractor: no visible binding for global variable ‘TR’ RBS_extractor: no visible binding for global variable ‘RBS_hit’ RBS_extractor: no visible binding for global variable ‘spacer’ RBS_extractor: no visible binding for global variable ‘ORFstart’ RBS_extractor: no visible binding for global variable ‘direction’ RBS_extractor: no visible binding for global variable ‘pull’ RBS_extractor: no visible binding for global variable ‘ORFmatch’ RBS_extractor: no visible global function definition for ‘make_col_scheme’ RBS_extractor: no visible global function definition for ‘ggseqlogo’ RBS_extractor: no visible global function definition for ‘theme_bw’ RBS_extractor: no visible global function definition for ‘theme’ RBS_extractor: no visible global function definition for ‘element_blank’ RBS_extractor: no visible global function definition for ‘element_text’ RBS_extractor: no visible global function definition for ‘ggplot’ RBS_extractor: no visible global function definition for ‘aes’ RBS_extractor: no visible global function definition for ‘geom_histogram’ RBS_extractor: no visible binding for global variable ‘..density..’ RBS_extractor: no visible global function definition for ‘scale_x_continuous’ RBS_extractor: no visible global function definition for ‘xlab’ RBS_extractor: no visible global function definition for ‘ylab’ RBS_extractor: no visible global function definition for ‘ggtitle’ RBS_extractor: no visible global function definition for ‘grid.arrange’ RBS_extractor: no visible global function definition for ‘ggsave’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘%>%’ codon_usage_tRNA_heatmap_generator: no visible binding for global variable ‘eff’ codon_usage_tRNA_heatmap_generator: no visible binding for global variable ‘freq’ codon_usage_tRNA_heatmap_generator: no visible binding for global variable ‘RSCU’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘group_by’ codon_usage_tRNA_heatmap_generator: no visible binding for global variable ‘Chemical_property’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘arrange’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘ungroup’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘pull’ codon_usage_tRNA_heatmap_generator: no visible binding for global variable ‘codon’ codon_usage_tRNA_heatmap_generator: no visible binding for global variable ‘codon_count’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘unit’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘rowAnnotation’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘anno_barplot’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘gpar’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘pdf’ codon_usage_tRNA_heatmap_generator: no visible global function definition for ‘dev.off’ gb_info: no visible global function definition for ‘fwf_widths’ gb_info: no visible global function definition for ‘%>%’ gb_info: no visible global function definition for ‘slice’ gb_info: no visible binding for global variable ‘.’ gb_info : : no visible global function definition for ‘str_squish’ gb_info: no visible global function definition for ‘mutate_all’ gb_info: no visible binding for global variable ‘X1’ gb_info: no visible global function definition for ‘group_by’ gb_info: no visible binding for global variable ‘X2’ gb_info: no visible global function definition for ‘mutate’ gb_info: no visible global function definition for ‘separate’ gb_info: no visible global function definition for ‘n’ genbank_fna_extractor: no visible global function definition for ‘read.csv’ genbank_fna_extractor: no visible global function definition for ‘separate’ genbank_fna_extractor: no visible binding for global variable ‘contig_1_seq_final_temp’ genbank_fna_extractor: no visible global function definition for ‘rbind.fill’ genbank_fna_extractor: no visible global function definition for ‘na.omit’ tRNA_anticodon_counter: no visible global function definition for ‘%>%’ tRNA_anticodon_counter: no visible binding for global variable ‘anticodon’ tRNA_anticodon_counter: no visible global function definition for ‘mutate’ tRNA_anticodon_counter: no visible binding for global variable ‘.’ tRNA_anticodon_counter: no visible global function definition for ‘str_extract’ tRNA_anticodon_counter: no visible binding for global variable ‘anticodon_location’ tRNA_anticodon_counter: no visible binding for global variable ‘start’ tRNA_anticodon_counter: no visible binding for global variable ‘nt_seq’ tRNA_anticodon_counter: no visible binding for global variable ‘anticodon_position’ tRNA_anticodon_counter: no visible binding for global variable ‘locus_tag’ tRNA_anticodon_counter: no visible binding for global variable ‘end’ tRNA_anticodon_counter: no visible binding for global variable ‘direction’ tRNA_anticodon_counter: no visible binding for global variable ‘product’ tRNA_anticodon_counter: no visible binding for global variable ‘tRNA_codon’ tRNA_anticodon_counter : : no visible global function definition for ‘s2c’ tRNA_anticodon_counter: no visible binding for global variable ‘AA’ tRNA_anticodon_counter: no visible global function definition for ‘n’ tRNA_anticodon_counter: no visible binding for global variable ‘s2c’ tRNA_anticodon_counter: no visible global function definition for ‘group_by’ tRNA_anticodon_counter: no visible global function definition for ‘top_n’ tRNA_anticodon_counter: no visible global function definition for ‘pull’ Undefined global functions or variables: %>% . ..density.. AA COG_category CRISPR_table_1 Chemical_property N20 ORFmatch ORFstart RBS_hit RSCU TR V1 V14 V15 V2 V3 X1 X2 a aaa addWorksheet aes anno_barplot anticodon anticodon_location anticodon_position arrange bind_rows case_when category codon codon_count contig contig_1_definition contig_1_seq_final_temp contig_final_1 contig_length contig_number createWorkbook dcast dev.off direction distinct draw drop_na eff element_blank element_text end everything filter freq fwf_widths genbank_table gene_number geom_histogram ggplot ggsave ggseqlogo ggtitle gpar grid.arrange grid.draw grid.grabExpr grid.text group group_by lead locus_tag make_col_scheme mutate mutate_all mutate_at n na.omit na_if nt_seq pdf product protein_id pull query rbind.fill read.csv read_fwf rearranged_nt_seq reframe region rename_all repeat_end repeat_start rowAnnotation rpt_unit_seq s2c saveWorkbook scale_x_continuous select separate separate_rows setNames slice spacer start str_detect str_extract str_pad str_replace_all str_squish str_sub tRNA_codon theme theme_bw top_n top_strand translation ungroup unit values vmatchPattern write.table write.xlsx writeData xlab ylab Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("stats", "end", "filter", "na.omit", "setNames", "start") importFrom("utils", "read.csv", "write.table") to your NAMESPACE file. Found the following assignments to the global environment: File ‘DNMB/R/CRISPR_array_extractor.R’: assign("CRISPR_by_spacer", CRISPR_by_spacer_dist, envir = .GlobalEnv) File ‘DNMB/R/Codon_usage_calculator.R’: assign("codon_usage", codon, envir = .GlobalEnv) File ‘DNMB/R/Count_tRNA_anticodon.R’: assign("tRNA_anticodon", tRNA_anticodon, envir = .GlobalEnv) assign("tRNA_distribution", tRNA_distribution, envir = .GlobalEnv) File ‘DNMB/R/DNMB_combiner.R’: assign("genbank_table", genbank_table, envir = .GlobalEnv) File ‘DNMB/R/EggNOG_organizer.R’: assign("EggNOG_table", eggNOG, envir = .GlobalEnv) File ‘DNMB/R/Genbank_fna_extractor.R’: assign("contig_length", contig_length, envir = .GlobalEnv) assign("genome_size", genome_size, envir = .GlobalEnv) assign(paste("contig", i, "seq", sep = "_"), toupper(get(paste("contig", i, "seq", "final", sep = "_"))), envir = .GlobalEnv) File ‘DNMB/R/Genbank_organizer.R’: assign("genbank_table", contig_final, envir = .GlobalEnv) File ‘DNMB/R/Genome_summary.R’: assign("Genome_summary", Genome_summary, envir = .GlobalEnv) File ‘DNMB/R/InterProScan_organizer.R’: assign("InterProScan_table", InterPro, envir = .GlobalEnv) File ‘DNMB/R/RBS_extractor.R’: assign("RBS_table", putative_RBS, envir = .GlobalEnv) assign("matched_RBS_table", putative_matched_RBS, envir = .GlobalEnv) assign("RBS_seqlogo", seqlogo_plot, envir = .GlobalEnv) assign("spacer_histogram", spacer_histogram, envir = .GlobalEnv) File ‘DNMB/R/codon_usage_tRNA_heatmap_generator.R’: assign("Codon_usage_tRNA_plot", my_heatmap, envir = .GlobalEnv) File ‘DNMB/R/run_DNMB.R’: assign("genbank_table", genbank_table, envir = .GlobalEnv) assign("genbank_table", genbank_table, envir = .GlobalEnv) * 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 ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'CRISPR_array_extractor.Rd' ‘save_output’ Documented arguments not in \usage in Rd file 'CRISPR_array_extractor.Rd': ‘df’ Undocumented arguments in Rd file 'Codon_usage_calculator.Rd' ‘target’ ‘save_output’ Documented arguments not in \usage in Rd file 'Codon_usage_calculator.Rd': ‘df’ Undocumented arguments in Rd file 'DNMB_table.Rd' ‘genbank_table’ ‘EggNOG_table’ ‘InterProScan_table’ ‘InterProScan_site’ ‘codon_usage’ ‘tRNA_anticodon’ ‘tRNA_distribution’ ‘RBS_table’ ‘CRISPR_by_spacer’ ‘save_dir’ Documented arguments not in \usage in Rd file 'DNMB_table.Rd': ‘gb_table’ ‘InterPro_search’ ‘InterPro_site’ ‘codon’ Documented arguments not in \usage in Rd file 'EggNOG_annotations.Rd': ‘df’ Undocumented arguments in Rd file 'Genbank_organizer.Rd' ‘save_output’ Documented arguments not in \usage in Rd file 'Genbank_organizer.Rd': ‘df’ Documented arguments not in \usage in Rd file 'InterProScan_annotations.Rd': ‘df’ Undocumented arguments in Rd file 'Promoter_prediction_to_genbank.Rd' ‘xlsx_dir’ ‘output_file’ Documented arguments not in \usage in Rd file 'Promoter_prediction_to_genbank.Rd': ‘df’ ‘EggNOG_dir’ ‘save_output’ Undocumented arguments in Rd file 'RBS_extractor.Rd' ‘save_plot’ Documented arguments not in \usage in Rd file 'RBS_extractor.Rd': ‘dependent’ Documented arguments not in \usage in Rd file 'genbank_fna_extractor.Rd': ‘df’ Documented arguments not in \usage in Rd file 'run_DNMB.Rd': ‘gb_table’ ‘InterPro_search’ ‘InterPro_site’ ‘codon’ Undocumented arguments in Rd file 'run_DNMB_combiner.Rd' ‘genbank_table’ ‘EggNOG_table’ ‘InterProScan_table’ Documented arguments not in \usage in Rd file 'run_DNMB_combiner.Rd': ‘gb_table’ ‘InterPro_search’ ‘InterPro_site’ ‘codon’ Undocumented arguments in Rd file 'tRNA_anticodon_counter.Rd' ‘target’ ‘save_output’ Documented arguments not in \usage in Rd file 'tRNA_anticodon_counter.Rd': ‘df’ ‘gb_dir’ 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 examples ... NONE * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 WARNINGs, 4 NOTEs