* using log directory ‘/srv/hornik/tmp/CRAN_pretest/archipelago.Rcheck’ * using R Under development (unstable) (2025-02-28 r87848) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘archipelago/DESCRIPTION’ ... OK * this is package ‘archipelago’ version ‘0.0.1.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/3s] NOTE Maintainer: ‘Dylan Lawless ’ New submission Version contains large components (0.0.1.9000) Non-FOSS package license (`use_mit_license()`, `use_gpl3_license()` or friends to pick a license) Possibly misspelled words in DESCRIPTION: VSAT (8:73, 8:195, 8:774) customizability (8:626) The Title field starts with the package name. The Title field should be in title case. Current version is: ‘Archipelago plot method for illustration of variant set association test statistics’ In title case that is: ‘Archipelago Plot Method for Illustration of Variant Set Association Test Statistics’ The Description field should not start with the package name, 'This package' or similar. Size of tarball: 5976530 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 whether package ‘archipelago’ can be installed ... [1s/1s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: `use_mit_license()`, `use_gpl3_license()` or friends to pick a license Standardizable: FALSE * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘cran-comments.md’ ‘docs’ ‘revdep’ ‘validation’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * 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 'library' or 'require' calls not declared from: ‘dplyr’ ‘ggplot2’ 'library' or 'require' calls in package code: ‘dplyr’ ‘ggplot2’ 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 ... [2s/2s] NOTE archipelago_plot: no visible global function definition for ‘%>%’ archipelago_plot: no visible binding for global variable ‘quantile’ archipelago_plot: no visible global function definition for ‘group_by’ archipelago_plot: no visible binding for global variable ‘CHR’ archipelago_plot: no visible global function definition for ‘summarise’ archipelago_plot: no visible binding for global variable ‘BP’ archipelago_plot: no visible global function definition for ‘ungroup’ archipelago_plot: no visible binding for global variable ‘width’ archipelago_plot: no visible global function definition for ‘pull’ archipelago_plot: no visible global function definition for ‘arrange’ archipelago_plot: no visible global function definition for ‘mutate’ archipelago_plot: no visible binding for global variable ‘new_pos_in_chr’ archipelago_plot: no visible binding for global variable ‘CHR_order’ archipelago_plot: no visible global function definition for ‘bind_rows’ archipelago_plot: no visible global function definition for ‘aggregate’ archipelago_plot: no visible global function definition for ‘filter’ archipelago_plot: no visible binding for global variable ‘metric’ archipelago_plot: no visible binding for global variable ‘pos’ archipelago_plot: no visible binding for global variable ‘set_ID’ archipelago_plot: no visible global function definition for ‘left_join’ archipelago_plot: no visible global function definition for ‘ggplot’ archipelago_plot: no visible global function definition for ‘geom_point’ archipelago_plot: no visible global function definition for ‘aes’ archipelago_plot: no visible binding for global variable ‘P’ archipelago_plot: no visible global function definition for ‘ylab’ archipelago_plot: no visible global function definition for ‘geom_hline’ archipelago_plot: no visible global function definition for ‘theme_bw’ archipelago_plot: no visible global function definition for ‘ggtitle’ archipelago_plot: no visible global function definition for ‘theme’ archipelago_plot: no visible global function definition for ‘element_blank’ archipelago_plot: no visible global function definition for ‘element_line’ archipelago_plot: no visible global function definition for ‘margin’ archipelago_plot: no visible global function definition for ‘guides’ archipelago_plot: no visible global function definition for ‘ggsave’ archipelago_plot: no visible binding for global variable ‘color_group’ archipelago_plot: no visible binding for global variable ‘color_condition’ archipelago_plot: no visible global function definition for ‘geom_segment’ archipelago_plot: no visible binding for global variable ‘pos_variant_set’ archipelago_plot: no visible binding for global variable ‘pos_variant’ archipelago_plot: no visible binding for global variable ‘P_variant_set’ archipelago_plot: no visible binding for global variable ‘P_variant’ archipelago_plot: no visible global function definition for ‘scale_color_manual’ archipelago_plot: no visible global function definition for ‘scale_x_continuous’ archipelago_plot: no visible global function definition for ‘xlab’ archipelago_plot: no visible global function definition for ‘geom_text’ Undefined global functions or variables: %>% BP CHR CHR_order P P_variant P_variant_set aes aggregate arrange bind_rows color_condition color_group element_blank element_line filter geom_hline geom_point geom_segment geom_text ggplot ggsave ggtitle group_by guides left_join margin metric mutate new_pos_in_chr pos pos_variant pos_variant_set pull quantile scale_color_manual scale_x_continuous set_ID summarise theme theme_bw ungroup width xlab ylab Consider adding importFrom("stats", "aggregate", "filter", "quantile") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'archipelago_plot.Rd': \usage lines wider than 90 characters: "Variant Set Association Test\nwith individual variant contributions\nand contributions for significant VSAT", These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘df2’ ‘vsat_pval’ Undocumented data sets: ‘df2’ ‘vsat_pval’ 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 ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'archipelago_plot.Rd' ‘crit_val_VSAT’ ‘crit_val_single_variant’ Documented arguments not in \usage in Rd file 'archipelago_plot.Rd': ‘crit_val’ 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 contents of ‘data’ directory ... WARNING Files not of a type allowed in a ‘data’ directory: ‘archipelago_plot.pdf’ ‘archipelago_vsat_raw_plot.pdf’ Please use e.g. ‘inst/extdata’ for non-R data files * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [0s/0s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [2s/2s] OK Running ‘testthat.R’ [1s/1s] * 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: 5 WARNINGs, 5 NOTEs