* using log directory ‘/srv/hornik/tmp/CRAN_pretest/MagellanNTK.Rcheck’ * using R Under development (unstable) (2025-09-16 r88844) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3+b1) Debian flang-new version 19.1.7 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘MagellanNTK/DESCRIPTION’ ... OK * this is package ‘MagellanNTK’ version ‘0.99.10’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] 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: 7180719 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 ... NOTE Found the following hidden files and directories: .nojekyll inst/www/sass/.sass_cache_keys These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. CRAN-pack does not know about .nojekyll inst/www/sass/.sass_cache_keys * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MagellanNTK’ can be installed ... [5s/5s] NOTE Found the following notes/warnings: Non-staged installation was used See ‘/srv/hornik/tmp/CRAN_pretest/MagellanNTK.Rcheck/00install.out’ for details. * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] 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 ... [11s/11s] 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’ GetPackageVersion: no visible global function definition for ‘installed.packages’ 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’ choose.dir.darwin: no visible global function definition for ‘tail’ chooseDir_server : : no visible global function definition for ‘checkboxInput’ chooseDir_server : : no visible global function definition for ‘renderText’ clipboard: no visible global function definition for ‘write.table’ dataModal: no visible binding for global variable ‘PrevNextBtnClass’ directoryInput: no visible global function definition for ‘packageVersion’ download_btns: no visible binding for global variable ‘actionBtnClass’ download_btns_server : : : no visible global function definition for ‘write.table’ 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 ‘help.search’ find_funs: no visible global function definition for ‘installed.packages’ 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 global function definition for ‘maintainer’ 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 ‘installed.packages’ 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 ‘sub_R25’ nav : server: no visible binding for global variable ‘dev_mode’ nav_pipeline : server: no visible binding for global variable ‘sub_R25’ 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 ‘sub_R25’ 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’ open_workflow_server : : no visible global function definition for ‘installed.packages’ 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 help.search incProgress input installed.packages isolate maintainer 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 packageVersion plotOutput radioButtons reactiveFileReader reactiveValuesToList redBtnClass removeModal removeUI renderPlot renderText rv selectizeInput shinyServer sidebarMenu stepStatus stopApp sub_R25 tabItem tabItems tabPanel tabsetPanel tail tibble titlePanel tl_h_next_icon tl_h_prev_icon updateSidebar verbatimTextOutput withProgress write.table Consider adding importFrom("graphics", "box") importFrom("utils", "help.search", "installed.packages", "maintainer", "packageVersion", "tail", "write.table") to your NAMESPACE file. Found the following calls to data() loading into the global environment: File ‘MagellanNTK/R/core.R’: data(sub_R25) File ‘MagellanNTK/R/core_pipeline.R’: data(sub_R25) File ‘MagellanNTK/R/core_process.R’: data(sub_R25) See section ‘Good practice’ in ‘?data’. * checking Rd files ... [0s/0s] 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 ... [0s/0s] WARNING Failed with error: 'there is no package called 'MultiAssayExperiment'' Error loading dataset 'sub_R25': Error in .requirePackage(package) : unable to load required package 'MultiAssayExperiment' The dataset(s) may use package(s) not declared in Depends/Imports. * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [1s/1s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [7s/7s] OK * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘foo.xlsx’ * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 6 NOTEs