* using log directory 'd:/RCompile/CRANincoming/R-devel/networkUtils.Rcheck' * using R Under development (unstable) (2023-08-25 r85011 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.2.0 GNU Fortran (GCC) 12.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'networkUtils/DESCRIPTION' ... OK * this is package 'networkUtils' version '1.0.0.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Fanzhou Liang ' New submission Possibly misspelled words in DESCRIPTION: Almende (5:34) downloadnode (5:115) igraph (5:158) networkUtils (2:8, 5:71) networkgraph (5:99) visNetwork (5:59) The Title field is just the package name: provide a real title. * 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: notebook/.quarto These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. CRAN-pack does not know about notebook/.quarto * checking for portable file names ... WARNING Found the following files with non-portable file names: readme_img/Screenshot 2023-06-10 at 16.56.19.png readme_img/Screenshot 2023-06-10 at 17.23.15.png These are not fully portable file names. See section 'Package structure' in the 'Writing R Extensions' manual. * checking serialization versions ... OK * checking whether package 'networkUtils' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: 'change_log.json' 'notebook' 'pushGit.sh' 'readme_img' * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 ... WARNING '::' or ':::' imports not declared from: 'DiagrammeR' 'glue' 'rlang' 'spatstat.explore' 'spatstat.geom' 'stringr' Package in Depends field not imported from: 'igraph' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE mod_fileUploader_ui: warning in pickerInput(ns("pickEdgeSheet"), labe = "Select Edge Sheet", choices = NULL, selected = NULL, options = list(`live-search` = T)): partial argument match of 'labe' to 'label' mod_fileUploader_ui: warning in pickerInput(ns("pickNodeSheet"), labe = "Select Node Sheet", choices = NULL, selected = NULL, options = list(`live-search` = T)): partial argument match of 'labe' to 'label' add_vertex_sf: no visible global function definition for 'vertex_attr' add_vertex_sf: no visible global function definition for 'delete_vertex_attr' add_vertex_sf: no visible global function definition for 'vertex' add_vertex_sf: no visible global function definition for 'set_vertex_attr' add_vertex_sf: no visible global function definition for 'V' create_demo_graph: no visible global function definition for 'V' create_demo_graph: no visible global function definition for 'E' create_demo_graph: no visible global function definition for 'V<-' create_demo_graph: no visible global function definition for 'runif' create_demo_graph: no visible global function definition for 'E<-' mod_visNetInteraction_server : : no visible global function definition for 'edge_attr_names' mod_visNetInteraction_server : : no visible global function definition for 'vertex_attr_names' mod_visNetInteraction_server : : no visible global function definition for 'quantile' mod_visNetInteraction_server : : no visible global function definition for 'as_ids' mod_visNetInteraction_server : : no visible global function definition for 'E' mod_visNetInteraction_server : : no visible global function definition for 'V' mod_visNetInteraction_server : : no visible global function definition for '.inc' mod_visNetModification_server : : no visible global function definition for 'vertex_attr_names' mod_visNetModification_server : : no visible global function definition for 'V' mod_visNetModification_server : : no visible global function definition for 'V<-' mod_visNetModification_server : : no visible global function definition for 'edge_attr_names' mod_visNetModification_server : : no visible global function definition for 'E' mod_visNetModification_server : : no visible global function definition for 'E<-' mod_visNetModification_server : : : no visible global function definition for 'vertex_attr_names' mod_visNetModification_server : : : no visible global function definition for 'V' mod_visNetModification_server : : : no visible global function definition for 'V<-' mod_visNetModification_server : : : no visible global function definition for 'delete_vertex_attr' mod_visNetModification_server : : : no visible global function definition for 'edge_attr_names' mod_visNetModification_server : : : no visible global function definition for 'E' mod_visNetModification_server : : : no visible global function definition for 'E<-' mod_visNetModification_server : : : no visible global function definition for 'delete_edge_attr' mod_visNetModification_server : : : no visible global function definition for 'delete_graph_attr' modify_graph_i: no visible global function definition for 'E' modify_graph_i: no visible global function definition for 'edge' modify_graph_i: no visible global function definition for 'edge_attr' modify_graph_i: no visible global function definition for 'add_edges' modify_graph_i: no visible binding for global variable 'isNetwork_graphChange' pasteEdgeDetails: no visible global function definition for 'edge_attr' pasteNodeDetails: no visible global function definition for 'vertex_attr' plotPPPdensity: no visible global function definition for 'par' plotPPPdensity: no visible global function definition for 'colorRampPalette' search_idx: no visible binding for global variable 'name' search_idx: no visible global function definition for 'make_empty_graph' search_idx: no visible global function definition for 'V' search_idx: no visible global function definition for 'E' search_idx: no visible global function definition for '.inc' simpleNetworkUtilApp_server: no visible binding for global variable 'graph' Undefined global functions or variables: .inc E E<- V V<- add_edges as_ids colorRampPalette delete_edge_attr delete_graph_attr delete_vertex_attr edge edge_attr edge_attr_names graph isNetwork_graphChange make_empty_graph name par quantile runif set_vertex_attr vertex vertex_attr vertex_attr_names Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "par") importFrom("stats", "quantile", "runif") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'mod_visNetModification_ui' 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 documentation object 'mod_fileUploader_ui' '...' Documented arguments not in \usage in documentation object 'mod_fileUploader_ui': 'input' 'output' 'session' Undocumented arguments in documentation object 'mod_visNetInteraction_server' 'show_hidden' Documented arguments not in \usage in documentation object 'mod_visNetInteraction_ui': 'input' 'output' 'session' Undocumented arguments in documentation object 'mod_visNetModification_server' 'dev' 'hard_delete' 'NodeAttrTooltip' 'EdgeAttrTooltip' 'debug' Undocumented arguments in documentation object 'modify_graph_i' 'visNetwork_graphChange' 'hard_delete' Documented arguments not in \usage in documentation object 'modify_graph_i': 'visNetwork_graphChage' Undocumented arguments in documentation object 'pasteDetails' '...' Documented arguments not in \usage in documentation object 'simpleNetworkUtilApp_server': 'graph' 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 ... ERROR Running examples in 'networkUtils-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: pasteDetails > ### Title: pasteDetails > ### Aliases: pasteDetails pasteNodeDetails pasteEdgeDetails > > ### ** Examples > > # example code > > # paste normal object > nL = list( + id = 1, + object = "Apple", + category = "Fruit", + size = 24.22 + ) > x_html = pasteDetails(nL) > cat(x_paste) Error: object 'x_paste' not found Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... ERROR Running 'testthat.R' Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(networkUtils) Loading required package: igraph Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > > test_check("networkUtils") Loading required package: shiny [ FAIL 3 | WARN 0 | SKIP 1 | PASS 18 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-golem-recommended.R:72:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-mod_visNet.R:1:1'): (code run outside of `test_that()`) ──────── Error in `module(childScope$input, childScope$output, childScope, ...)`: argument "graph_rct" is missing, with no default Backtrace: ▆ 1. └─shiny::testServer(...) at test-mod_visNet.R:1:0 2. ├─shiny:::withMockContext(session, rlang::exec(app, !!!args)) 3. │ ├─shiny::isolate(...) 4. │ │ ├─shiny::..stacktraceoff..(...) 5. │ │ └─ctx$run(...) 6. │ │ ├─promises::with_promise_domain(...) 7. │ │ │ └─domain$wrapSync(expr) 8. │ │ ├─shiny::withReactiveDomain(...) 9. │ │ │ └─promises::with_promise_domain(...) 10. │ │ │ └─domain$wrapSync(expr) 11. │ │ │ └─base::force(expr) 12. │ │ └─env$runWith(self, func) 13. │ │ └─shiny (local) contextFunc() 14. │ │ └─shiny::..stacktraceon..(expr) 15. │ ├─shiny::withReactiveDomain(...) 16. │ │ └─promises::with_promise_domain(...) 17. │ │ └─domain$wrapSync(expr) 18. │ │ └─base::force(expr) 19. │ └─withr::with_options(...) 20. │ └─base::force(code) 21. ├─rlang::exec(app, !!!args) 22. └─networkUtils (local) ``(id = "proxy1") 23. └─shiny::moduleServer(...) 24. ├─session$setReturned(callModule(module, id, session = session)) 25. └─shiny::callModule(module, id, session = session) 26. ├─shiny::withReactiveDomain(...) 27. │ └─promises::with_promise_domain(...) 28. │ └─domain$wrapSync(expr) 29. │ └─base::force(expr) 30. └─networkUtils (local) module(childScope$input, childScope$output, childScope, ...) 31. └─networkUtils::mod_visNetModification_server(...) 32. ├─base::stopifnot(is.reactive(igraphObj)) 33. └─shiny::is.reactive(igraphObj) ── Error ('test-mod_visNetworkRead.R:1:1'): (code run outside of `test_that()`) ── Error in `eval(code, test_env)`: object 'mod_visNetworkRead_server' not found Backtrace: ▆ 1. └─shiny::testServer(...) at test-mod_visNetworkRead.R:1:0 2. └─shiny:::isModuleServer(app) ── Error ('test-mod_visNetworkWrite.R:1:1'): (code run outside of `test_that()`) ── Error in `eval(code, test_env)`: object 'mod_visNetworkWrite_server' not found Backtrace: ▆ 1. └─shiny::testServer(...) at test-mod_visNetworkWrite.R:1:0 2. └─shiny:::isModuleServer(app) [ FAIL 3 | WARN 0 | SKIP 1 | PASS 18 ] Error: Test failures Execution halted * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 2 ERRORs, 4 WARNINGs, 4 NOTEs