su: ignoring --preserve-environment, it's mutually exclusive with --login Attaching package: ‘shinydashboard’ The following object is masked from ‘package:graphics’: box Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Attaching package: ‘shinydashboardPlus’ The following objects are masked from ‘package:shinydashboard’: box, dashboardHeader, dashboardPage, dashboardSidebar, messageItem, notificationItem, taskItem The following object is masked from ‘package:graphics’: box Attaching package: ‘bs4Dash’ The following objects are masked from ‘package:shinydashboardPlus’: accordion, accordionItem, appButton, attachmentBlock, blockQuote, box, boxComment, boxDropdown, boxDropdownItem, boxLabel, boxPad, boxProfile, boxProfileItem, boxSidebar, carousel, carouselItem, controlbarItem, controlbarMenu, dashboardBadge, dashboardControlbar, dashboardFooter, dashboardHeader, dashboardPage, dashboardSidebar, dashboardUser, dashboardUserItem, descriptionBlock, dropdownDivider, loadingState, messageItem, notificationItem, productList, productListItem, progressBar, renderUser, skinSelector, socialBox, starBlock, taskItem, timelineBlock, timelineEnd, timelineItem, timelineItemMedia, timelineLabel, timelineStart, updateAccordion, updateBox, updateBoxSidebar, updateControlbar, updateControlbarMenu, updateSidebar, updateUserMessages, userBlock, userBox, userDescription, userList, userListItem, userMessage, userMessages, userOutput, userPost, userPostMedia, userPostTagItem, userPostTagItems The following objects are masked from ‘package:shinydashboard’: box, dashboardBody, dashboardHeader, dashboardPage, dashboardSidebar, dropdownMenu, dropdownMenuOutput, infoBox, infoBoxOutput, menuItem, menuItemOutput, menuSubItem, messageItem, notificationItem, renderInfoBox, renderMenu, renderValueBox, sidebarMenu, sidebarMenuOutput, sidebarUserPanel, tabBox, tabItem, tabItems, taskItem, updateTabItems, valueBox, valueBoxOutput The following objects are masked from ‘package:shiny’: actionButton, column, insertTab, tabsetPanel The following object is masked from ‘package:graphics’: box Listening on http://127.0.0.1:38577 Start*!~!#F Article table complete CUI table complete Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] <- 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Start*!~!#F Article table complete CUI table complete Start*!~!#F Article table complete CUI table complete Start*!~!#F Article table complete CUI table complete Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Warning: Error in db_query_fields.DBIConnection: Can't query fields. Caused by error: ! Failed to prepare query: ERROR: relation "CUIsearch_07032023_disorder_codi_cos_NA" does not exist LINE 2: FROM "CUIsearch_07032023_disorder_codi_cos_NA" AS "q01" ^ 147: 146: signalCondition 145: signal_abort 144: rlang::abort 143: cli_abort 142: value[[3L]] 141: tryCatchOne 140: tryCatchList 139: tryCatch 138: db_query_fields.DBIConnection 136: dbplyr_fallback 135: dbplyr_query_fields 133: tbl_sql 132: tbl.src_dbi 130: tbl.DBIConnection 129: tbl 128: dplyr::select 127: collect 126: %>% 123: [/srv/shiny-server/ONCE/app.R#306] 107: phecode_data 104: exprFunc 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$table_phecode 1: runApp Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Warning: Error in <-: length of 'dimnames' [2] not equal to array extent 125: colnames<- 124: genFindingTable 123: [/srv/shiny-server/ONCE/app.R#223] 107: allFinding_inter 104: exprFunc 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$table 1: runApp Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Warning: Error in <-: length of 'dimnames' [2] not equal to array extent 125: colnames<- 124: genFindingTable 123: [/srv/shiny-server/ONCE/app.R#223] 107: allFinding_inter 104: exprFunc 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$table 1: runApp Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Warning: Error in <-: length of 'dimnames' [2] not equal to array extent 125: colnames<- 124: genFindingTable 123: [/srv/shiny-server/ONCE/app.R#223] 107: allFinding_inter 104: exprFunc 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$table 1: runApp Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Warning: Error in <-: length of 'dimnames' [2] not equal to array extent 125: colnames<- 124: genFindingTable 123: [/srv/shiny-server/ONCE/app.R#223] 107: allFinding_inter 104: exprFunc 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$table 1: runApp Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Start*!~!#F Article table complete CUI table complete Joining with `by = join_by(title, clean_title, feature_id)` Joining with `by = join_by(rowid)` Joining with `by = join_by(cui, term, belong, cos_cui)` Warning: Setting row names on a tibble is deprecated. Joining with `by = join_by(Variable)` Warning in result$mgb_freq[is.na(result$mgb_freq)] = 1.2091114 * va_freq$word_freq[match(result$Variable, : number of items to replace is not a multiple of replacement length