* using log directory 'd:/RCompile/CRANincoming/R-devel/MagellanNTK.Rcheck' * using R Under development (unstable) (2025-09-17 r88852 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 'MagellanNTK/DESCRIPTION' ... OK * this is package 'MagellanNTK' version '0.99.11' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [12s] NOTE Maintainer: 'Samuel Wieczorek ' New submission Possibly misspelled words in DESCRIPTION: DAPAR (21:51) MSPipelines (19:50) MagellanNTK (15:14, 19:30) Prostar (19:66, 22:13) Proteomics (22:22) ToolKit (15:47) proteomics (24:47) toolswith (17:56) Unknown, possibly misspelled, fields in DESCRIPTION: 'BiocViews' Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Found the following (possibly) invalid URLs: URL: http://www.bioconductor.org/packages/MagellanNTK (moved to https://www.bioconductor.org/packages/MagellanNTK) From: inst/CITATION Status: 301 Message: Moved Permanently URL: https://github.com/edyp-lab/Prostar.2.0 From: inst/doc/MagellanNTK.html Status: 404 Message: Not Found For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. Found the following (possibly) invalid DOIs: DOI: 10.1101/TODO From: inst/CITATION Status: 404 Message: Not Found DOI: 10.18129/B9.bioc.MagellanNTK From: inst/CITATION Status: 404 Message: Not Found The Description field should not start with the package name, 'This package' or similar. Size of tarball: 7167119 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 ... NOTE Found the following hidden files and directories: .nojekyll These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. CRAN-pack does not know about .nojekyll * checking for portable file names ... OK * checking whether package 'MagellanNTK' 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 ... OK * checking top-level files ... OK * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [24s] NOTE ActionOn_Child_Changed: no visible binding for global variable 'stepStatus' Build_SkippedInfoPanel: no visible binding for global variable 'stepStatus' Discover_Skipped_Steps: no visible binding for global variable 'stepStatus' GetMaxValidated_AllSteps: no visible binding for global variable 'stepStatus' GetMaxValidated_BeforePos: no visible binding for global variable 'stepStatus' GetStringStatus: no visible binding for global variable 'global' Insert_Dev_Sidebar: no visible global function definition for 'sidebarMenu' Insert_Dev_Sidebar: no visible global function definition for 'menuItem' Insert_Dev_Sidebar: no visible global function definition for 'menuSubItem' Insert_User_Sidebar: no visible global function definition for 'sidebarMenu' Insert_User_Sidebar: no visible global function definition for 'menuItem' Insert_User_Sidebar: no visible global function definition for 'menuSubItem' Save_Dataset_ui: no visible global function definition for 'downloadLink' ToggleState_Screens : : no visible binding for global variable 'stepStatus' chooseDir_server : : no visible global function definition for 'checkboxInput' chooseDir_server : : no visible global function definition for 'renderText' dataModal: no visible binding for global variable 'PrevNextBtnClass' download_btns: no visible binding for global variable 'actionBtnClass' download_btns_ui: no visible global function definition for 'downloadButton' download_dataset_server : : no visible binding for global variable 'actionBtnClass' find_funs: no visible global function definition for 'as_tibble' find_funs: no visible binding for global variable 'Priority' find_funs: no visible binding for global variable 'Package' find_funs: no visible global function definition for 'distinct' find_funs: no visible global function definition for 'tibble' is.validated: no visible binding for global variable 'stepStatus' launch_app: no visible binding for global variable 'dev_mode' loadapp_server : : : no visible global function definition for 'radioButtons' loadapp_server : : no visible global function definition for 'reactiveValuesToList' loadapp_server : : no visible global function definition for 'removeModal' mainapp_server : : no visible global function definition for 'updateSidebar' mainapp_server : : no visible global function definition for 'sidebarMenu' mainapp_server : : no visible global function definition for 'menuItem' mainapp_server : : no visible global function definition for 'menuSubItem' mainapp_server : : no visible global function definition for 'tabsetPanel' mainapp_server : : no visible global function definition for 'tabPanel' mainapp_ui: no visible binding for global variable 'PrevNextBtnClass' mainapp_ui: no visible global function definition for 'tabItems' mainapp_ui: no visible global function definition for 'tabItem' mdEditor_server : : no visible global function definition for 'isolate' mod_SweetAlert_server : : no visible binding for global variable 'actionBtnClass' mod_bsmodal_server : : no visible binding for global variable 'btn_success_color' mod_bug_report_server : : no visible global function definition for 'reactiveFileReader' mod_bug_report_server : : no visible global function definition for 'renderText' mod_bug_report_server : : no visible binding for global variable 'actionBtnClass' mod_bug_report_ui: no visible global function definition for 'verbatimTextOutput' mod_launch_magellan_server : : no visible global function definition for 'mod_open_demoDataset_server' mod_launch_magellan_ui: no visible global function definition for 'mod_open_demoDataset_ui' mod_launch_magellan_ui: no visible binding for global variable 'actionBtnClass' mod_load_workflow_server : : no visible global function definition for 'radioButtons' mod_load_workflow_server : : no visible global function definition for 'mod_insert_md_server' mod_load_workflow_server : : no visible global function definition for 'box' mod_load_workflow_server : : no visible global function definition for 'mod_insert_md_ui' mod_modalDialog_server : : no visible binding for global variable 'redBtnClass' mod_modalDialog_server : : no visible binding for global variable 'btn_css_style' mod_modalDialog_server : : no visible global function definition for 'removeModal' mod_modalDialog_server : : no visible global function definition for 'removeUI' mod_navbar_menu_ui: no visible global function definition for 'navbarPage' mod_navbar_menu_ui: no visible global function definition for 'navbarMenu' mod_navbar_menu_ui: no visible global function definition for 'tabPanel' mod_navbar_menu_ui: no visible global function definition for 'mod_open_demo_dataset_ui' nav : server: no visible binding for global variable 'lldata' nav : server: no visible binding for global variable 'dev_mode' nav_pipeline : server: no visible binding for global variable 'lldata' nav_pipeline : server: no visible binding for global variable 'dev_mode' nav_pipeline_server : : ActionOn_Data_Trigger: no visible binding for global variable 'stepStatus' nav_pipeline_server : : no visible binding for global variable 'stepStatus' nav_pipeline_server : : no visible global function definition for 'removeModal' nav_pipeline_server : : ResetPipeline: no visible binding for global variable 'stepStatus' nav_pipeline_ui: no visible global function definition for 'absolutePanel' nav_pipeline_ui: no visible binding for global variable 'tl_h_prev_icon' nav_pipeline_ui: no visible binding for global variable 'PrevNextBtnClass' nav_pipeline_ui: no visible binding for global variable 'btn_css_style' nav_pipeline_ui: no visible binding for global variable 'tl_h_next_icon' nav_process : server: no visible binding for global variable 'lldata' nav_process : server: no visible binding for global variable 'dev_mode' nav_process_server : : no visible binding for global variable 'stepStatus' nav_process_server : : no visible global function definition for 'removeModal' nav_process_server : : ResetProcess: no visible binding for global variable 'stepStatus' nav_process_server : : no visible global function definition for 'absolutePanel' nav_process_server : : no visible binding for global variable 'tl_h_prev_icon' nav_process_server : : no visible binding for global variable 'PrevNextBtnClass' nav_process_server : : no visible binding for global variable 'btn_css_style' nav_process_server : : no visible binding for global variable 'tl_h_next_icon' nav_process_ui: no visible binding for global variable 'tl_h_prev_icon' nav_process_ui: no visible binding for global variable 'PrevNextBtnClass' nav_process_ui: no visible binding for global variable 'btn_css_style' nav_process_ui: no visible binding for global variable 'tl_h_next_icon' nav_server : : no visible binding for global variable 'stepStatus' nav_server : : ActionOn_Data_Trigger: no visible binding for global variable 'stepStatus' nav_server : : no visible global function definition for 'removeModal' nav_server : : no visible global function definition for 'DisplayWholeUI' navbarPageWithInputs: no visible global function definition for 'navbarPage' navbarPageWithText: no visible global function definition for 'navbarPage' open_dataset_server : : no visible global function definition for 'fileInput' open_dataset_server : : no visible binding for global variable 'PrevNextBtnClass' open_dataset_server : : no visible global function definition for 'withProgress' open_dataset_server : : no visible global function definition for 'incProgress' open_dataset_server : : no visible global function definition for 'selectizeInput' open_workflow_server : : : no visible global function definition for 'stopApp' pipe_workflow_server : : no visible binding for global variable 'rv' pipe_workflow_server : : no visible global function definition for 'dl_ui' pipe_workflow_server : : no visible global function definition for 'dl_server' proc_workflow_server : : no visible binding for global variable 'rv' proc_workflow_server : : no visible global function definition for 'dl_ui' proc_workflow_server : : no visible global function definition for 'dl_server' process_layout: no visible global function definition for 'absolutePanel' runDirinputExample: no visible global function definition for 'titlePanel' runDirinputExample: no visible global function definition for 'shinyServer' runDirinputExample : : : no visible global function definition for 'stopApp' runDirinputExample : : no visible global function definition for 'renderText' shinyValue : : no visible binding for global variable 'input' timeline_pipeline_server : : no visible binding for global variable 'stepStatus' timeline_process_server : : no visible binding for global variable 'stepStatus' validity: no visible binding for global variable 'object' view_dataset_server : : no visible global function definition for 'renderPlot' view_dataset_ui: no visible global function definition for 'plotOutput' Undefined global functions or variables: DisplayWholeUI Package PrevNextBtnClass Priority absolutePanel actionBtnClass as_tibble box btn_css_style btn_success_color checkboxInput dev_mode distinct dl_server dl_ui downloadButton downloadLink fileInput global incProgress input isolate lldata menuItem menuSubItem mod_insert_md_server mod_insert_md_ui mod_open_demoDataset_server mod_open_demoDataset_ui mod_open_demo_dataset_ui navbarMenu navbarPage object plotOutput radioButtons reactiveFileReader reactiveValuesToList redBtnClass removeModal removeUI renderPlot renderText rv selectizeInput shinyServer sidebarMenu stepStatus stopApp tabItem tabItems tabPanel tabsetPanel tibble titlePanel tl_h_next_icon tl_h_prev_icon updateSidebar verbatimTextOutput withProgress Consider adding importFrom("graphics", "box") to your NAMESPACE file. Found the following calls to data() loading into the global environment: File 'MagellanNTK/R/core.R': data(lldata) File 'MagellanNTK/R/core_pipeline.R': data(lldata) File 'MagellanNTK/R/core_process.R': data(lldata) See section 'Good practice' in '?data'. * checking Rd files ... NOTE checkRd: (-1) GetMaxValidated_BeforePos.Rd:35-64: Lost braces 35 | Build_EncapsulateScreens_ui <- function(ns, id, config) { | ^ checkRd: (-1) GetMaxValidated_BeforePos.Rd:37-40: Lost braces 37 | if(rv.core$mode == 'dev'){ | ^ checkRd: (-1) GetMaxValidated_BeforePos.Rd:43-63: Lost braces 43 | renderUI({ | ^ checkRd: (-1) GetMaxValidated_BeforePos.Rd:45-61: Lost braces 45 | lapply(seq_len(len), function(i) { | ^ checkRd: (-1) GetMaxValidated_BeforePos.Rd:46-52: Lost braces 46 | if (i == 1) { | ^ checkRd: (-1) GetMaxValidated_BeforePos.Rd:52-60: Lost braces 52 | } else { | ^ checkRd: (-1) format_DT.Rd:50: Lost braces; missing escapes or markup? 50 | \item{hidden}{Default is reactive({NULL}),} | ^ checkRd: (-1) format_DT.Rd:60: Lost braces; missing escapes or markup? 60 | \item{hc_style}{Default is reactive({NULL}),} | ^ checkRd: (-1) format_DT.Rd:62: Lost braces; missing escapes or markup? 62 | \item{remoteReset}{Default is reactive({0}),} | ^ checkRd: (-1) insertCodeForExternalModules.Rd:172-190: Lost braces 172 | Get_Code_for_remoteReset2_observeEvents <- function(add.code = NULL) { | ^ checkRd: (-1) insertCodeForExternalModules.Rd:175-186: Lost braces 175 | observeEvent(req(remoteReset()), ignoreInit = FALSE, ignoreNULL = TRUE,{ | ^ checkRd: (-1) insertCodeForExternalModules.Rd:176-178: Lost braces 176 | lapply(names(rv.widgets), function(x){ | ^ checkRd: (-1) insertCodeForExternalModules.Rd:180-182: Lost braces 180 | lapply(names(rv.custom), function(x){ | ^ checkRd: (-1) insertCodeForExternalModules.Rd:201-219: Lost braces 201 | Get_Code_for_remoteReset_observeEvents <- function() { | ^ checkRd: (-1) insertCodeForExternalModules.Rd:204-214: Lost braces 204 | observeEvent(req(remoteReset() >=1), ignoreInit = TRUE, ignoreNULL = TRUE,{ | ^ checkRd: (-1) insertCodeForExternalModules.Rd:205-207: Lost braces 205 | lapply(names(rv.widgets), function(x){ | ^ checkRd: (-1) insertCodeForExternalModules.Rd:209-211: Lost braces 209 | lapply(names(rv.custom), function(x){ | ^ checkRd: (-1) mod_main_page.Rd:36: Lost braces; missing escapes or markup? 36 | \item{workflow.name}{= reactive({NULL}),} | ^ checkRd: (-1) mod_main_page.Rd:38: Lost braces; missing escapes or markup? 38 | \item{workflow.path}{= reactive({NULL}),} | ^ checkRd: (-1) nav.Rd:52: Lost braces; missing escapes or markup? 52 | \item{wholeReset}{= reactive({0}),} | ^ checkRd: (-1) nav_pipeline.Rd:52: Lost braces; missing escapes or markup? 52 | \item{wholeReset}{= reactive({0}),} | ^ * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [14s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK Running 'testthat.R' * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [14s] OK * checking PDF version of manual ... [24s] OK * checking HTML version of manual ... [17s] OK * DONE Status: 4 NOTEs