* using log directory ‘/srv/hornik/tmp/CRAN_pretest/xvm.Rcheck’ * using R Under development (unstable) (2025-04-15 r88147) * 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 ‘xvm/DESCRIPTION’ ... OK * this is package ‘xvm’ version ‘0.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘BeiHao Li ’ New submission Possibly misspelled words in DESCRIPTION: GROMACS (7:190) RMSD (9:60) conformational (10:221) xpm (3:9, 7:116) xvg (2:64, 7:108) xvm (2:8, 7:14, 8:3, 9:8, 10:91) Found the following (possibly) invalid URLs: URL: https://github.com/RightSZ/xvm From: DESCRIPTION README.md Status: 404 Message: Not Found URL: https://github.com/RightSZ/xvm/issues From: DESCRIPTION Status: 404 Message: Not Found Found the following (possibly) invalid file URIs: URI: articles/xvg_file.html From: README.md URI: articles/xpm_file.html From: README.md The Title field starts with the package name. The Title field should be in title case. Current version is: ‘xvm: An R Package for Reading, Parsing, and Visualizing xvg and xpm Files’ In title case that is: ‘Xvm: An R Package for Reading, Parsing, and Visualizing Xvg and Xpm Files’ The Description field should not start with the package name, 'This package' or similar. * 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 ‘xvm’ can be installed ... [3s/3s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard files/directories found at top level: ‘LICENSE.md’ ‘docs’ * 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 ... [1s/1s] 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 ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] NOTE plot_xpm: no visible global function definition for ‘ggplot’ plot_xpm: no visible global function definition for ‘aes’ plot_xpm: no visible binding for global variable ‘x_actual’ plot_xpm: no visible binding for global variable ‘y_actual’ plot_xpm: no visible binding for global variable ‘value’ plot_xpm: no visible global function definition for ‘geom_raster’ plot_xpm: no visible global function definition for ‘geom_tile’ plot_xpm: no visible global function definition for ‘labs’ plot_xpm: no visible global function definition for ‘theme_bw’ plot_xpm: no visible global function definition for ‘theme’ plot_xpm: no visible global function definition for ‘element_text’ plot_xpm: no visible global function definition for ‘scale_x_continuous’ plot_xpm: no visible global function definition for ‘scale_y_continuous’ plot_xpm: no visible global function definition for ‘scale_fill_viridis_c’ plot_xpm: no visible global function definition for ‘coord_fixed’ plot_xpm: no visible binding for global variable ‘x_label’ plot_xpm: no visible binding for global variable ‘y_label’ plot_xpm_facet: no visible global function definition for ‘ggplot’ plot_xpm_facet: no visible global function definition for ‘geom_point’ plot_xpm_facet: no visible global function definition for ‘aes’ plot_xpm_facet: no visible binding for global variable ‘x_actual’ plot_xpm_facet: no visible binding for global variable ‘value’ plot_xpm_facet: no visible binding for global variable ‘color_var’ plot_xpm_facet: no visible global function definition for ‘scale_color_viridis_c’ plot_xpm_facet: no visible binding for global variable ‘y_actual’ plot_xpm_facet: no visible global function definition for ‘facet_wrap’ plot_xpm_facet: no visible global function definition for ‘labs’ plot_xpm_facet: no visible global function definition for ‘theme_bw’ plot_xpm_facet: no visible global function definition for ‘theme’ plot_xpm_facet: no visible global function definition for ‘element_rect’ plot_xpm_facet: no visible global function definition for ‘element_text’ plot_xpm_facet: no visible global function definition for ‘element_blank’ plot_xpm_facet: no visible global function definition for ‘geom_line’ plot_xpm_facet: no visible global function definition for ‘geom_ribbon’ plot_xpm_facet: no visible global function definition for ‘scale_fill_viridis_c’ plot_xpm_facet: no visible global function definition for ‘new_scale_fill’ plot_xvg: no visible global function definition for ‘setNames’ plot_xvg: no visible binding for global variable ‘.data’ Undefined global functions or variables: .data aes color_var coord_fixed element_blank element_rect element_text facet_wrap geom_line geom_point geom_raster geom_ribbon geom_tile ggplot labs new_scale_fill scale_color_viridis_c scale_fill_viridis_c scale_x_continuous scale_y_continuous setNames theme theme_bw value x_actual x_label y_actual y_label Consider adding importFrom("stats", "setNames") to your NAMESPACE file. * 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘ggpubr’ ‘stringr’ * checking package vignettes ... OK * checking re-building of vignette outputs ... [4s/4s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘xpm_file.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/xvm.Rcheck/vign_test/xvm/vignettes/xpm_file_files/figure-html/plot_single_xpm_file-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 13695 bytes Input file size = 13785 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11119 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11119 Output IDAT size = 11119 bytes (2576 bytes decrease) Output file size = 11197 bytes (2588 bytes = 18.77% decrease) Quitting from xpm_file.Rmd:119-123 [arrange_xpm_plots] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'ggpubr' --- Backtrace: ▆ 1. └─base::library(ggpubr) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'xpm_file.Rmd' failed with diagnostics: there is no package called 'ggpubr' --- failed re-building ‘xpm_file.Rmd’ --- re-building ‘xvg_file.Rmd’ using rmarkdown ** Processing: figures/plot_single_xvg_file-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 18599 bytes Input file size = 18701 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15720 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15720 Output IDAT size = 15720 bytes (2879 bytes decrease) Output file size = 15798 bytes (2903 bytes = 15.52% decrease) ** Processing: figures/plot_a_single_xvg_file-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 21533 bytes Input file size = 21635 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19888 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 19592 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 19592 Output IDAT size = 19592 bytes (1941 bytes decrease) Output file size = 19670 bytes (1965 bytes = 9.08% decrease) Quitting from xvg_file.Rmd:131-135 [arrange_xvg_plots] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'ggpubr' --- Backtrace: ▆ 1. └─base::library(ggpubr) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'xvg_file.Rmd' failed with diagnostics: there is no package called 'ggpubr' --- failed re-building ‘xvg_file.Rmd’ SUMMARY: processing the following files failed: ‘xpm_file.Rmd’ ‘xvg_file.Rmd’ Error: Vignette re-building failed. Execution halted * 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: 1 ERROR, 4 NOTEs