############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GNOSIS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GNOSIS_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GNOSIS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘GNOSIS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GNOSIS’ version ‘1.4.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' NOTE Depends: includes the non-default packages: 'shiny', 'shinydashboard', 'shinydashboardPlus', 'dashboardthemes', 'shinyWidgets', 'shinymeta', 'tidyverse', 'operator.tools', 'maftools' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GNOSIS’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘shinydashboard::taskItem’ by ‘shinydashboardPlus::taskItem’ when loading ‘GNOSIS’ Warning: replacing previous import ‘shinydashboard::dashboardHeader’ by ‘shinydashboardPlus::dashboardHeader’ when loading ‘GNOSIS’ Warning: replacing previous import ‘shinydashboard::box’ by ‘shinydashboardPlus::box’ when loading ‘GNOSIS’ Warning: replacing previous import ‘shinydashboard::messageItem’ by ‘shinydashboardPlus::messageItem’ when loading ‘GNOSIS’ Warning: replacing previous import ‘shinydashboard::dashboardSidebar’ by ‘shinydashboardPlus::dashboardSidebar’ when loading ‘GNOSIS’ Warning: replacing previous import ‘shinydashboard::dashboardPage’ by ‘shinydashboardPlus::dashboardPage’ when loading ‘GNOSIS’ Warning: replacing previous import ‘shinyWidgets::progressBar’ by ‘shinydashboardPlus::progressBar’ when loading ‘GNOSIS’ Warning: replacing previous import ‘shinydashboard::notificationItem’ by ‘shinydashboardPlus::notificationItem’ when loading ‘GNOSIS’ Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘GNOSIS’ Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘GNOSIS’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/GNOSIS.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... 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 whether startup messages can be suppressed ... 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 ... NOTE Download_Server : : : no visible global function definition for ‘png’ Download_Server : : : no visible global function definition for ‘dev.off’ Download_Server : : : no visible global function definition for ‘svg’ Download_Server_1 : : : no visible global function definition for ‘png’ Download_Server_1 : : : no visible global function definition for ‘dev.off’ Download_Server_1 : : : no visible global function definition for ‘svg’ Download_Server_2 : : : no visible global function definition for ‘png’ Download_Server_2 : : : no visible global function definition for ‘dev.off’ Download_Server_2 : : : no visible global function definition for ‘svg’ Tab10_MAF_Plot_Summary_Server : : no visible global function definition for ‘mutate’ Tab10_MAF_Plot_Summary_Server : : no visible binding for global variable ‘PATIENT_ID’ Tab10_MAF_Plot_Summary_Server : : no visible global function definition for ‘ggplot’ Tab10_MAF_Plot_Summary_Server : : no visible global function definition for ‘theme_void’ Tab10_MAF_Plot_Summary_Server : : : no visible global function definition for ‘png’ Tab10_MAF_Plot_Summary_Server : : : no visible global function definition for ‘dev.off’ Tab10_MAF_Plot_Summary_Server : : : no visible global function definition for ‘svg’ Tab10_MAF_Plot_Summary_Server : : : no visible binding for global variable ‘Tab10_TT_Plot_Width’ Tab10_MAF_Plot_Summary_Server : : : no visible global function definition for ‘Tab10_Summary_Plot_Fraction’ Tab10_MAF_Text_Summary_Server : : no visible global function definition for ‘mutate’ Tab10_MAF_Text_Summary_Server : : no visible binding for global variable ‘PATIENT_ID’ Tab11_Log_Server : : no visible global function definition for ‘rename’ Tab11_Log_Server : : no visible binding for global variable ‘name’ Tab11_Log_Server : : no visible binding for global variable ‘timestamp’ Tab11_Log_Server : : no visible binding for global variable ‘value’ Tab11_Log_Server : : no visible binding for global variable ‘type’ Tab11_Log_Server : : no visible binding for global variable ‘binding’ Tab11_Log_Server : : no visible global function definition for ‘mutate’ Tab11_Log_Server : : no visible binding for global variable ‘Name’ Tab11_Log_Server : : no visible global function definition for ‘str_to_title’ Tab11_Log_Server : : no visible binding for global variable ‘Tab’ Tab11_Log_Server : : no visible binding for global variable ‘Timestamp’ Tab11_Log_Server : : no visible global function definition for ‘select’ Tab11_Log_Server : : no visible binding for global variable ‘Binding’ Tab11_Log_Server : : no visible binding for global variable ‘Value’ Tab11_Log_Server : : no visible global function definition for ‘arrange_at’ Tab11_Log_Server : : : no visible global function definition for ‘write.table’ Tab1_Input_Files_Manual_Server : : no visible global function definition for ‘read.delim’ Tab2_Exploratory_Tables_Server : : no visible global function definition for ‘as_tibble’ Tab2_Exploratory_Tables_Server : : no visible global function definition for ‘mutate’ Tab2_Exploratory_Tables_Server : : no visible global function definition for ‘:=’ Tab2_Exploratory_Tables_Server : : no visible binding for global variable ‘value’ Tab2_Exploratory_Tables_Server : : no visible global function definition for ‘select’ Tab3_CNACalc_Server : : no visible global function definition for ‘str_split’ Tab3_CNACalc_Server : : no visible binding for global variable ‘Hugo_Symbol’ Tab3_CNACalc_Server : : no visible global function definition for ‘select’ Tab3_CNACalc_Server : : no visible global function definition for ‘all_of’ Tab3_CNACalc_Server : : no visible global function definition for ‘mutate_if’ Tab3_Download_Server : : : no visible global function definition for ‘write.table’ Tab3_Factor_Levels_Server : : no visible global function definition for ‘mutate_at’ Tab3_Recode_Server : : no visible global function definition for ‘mutate’ Tab3_Subset_Server : : no visible global function definition for ‘mutate_at’ Tab4_Barplot_Server : : no visible global function definition for ‘ggplot’ Tab4_Barplot_Server : : no visible global function definition for ‘theme_void’ Tab4_Barplot_Server : : no visible global function definition for ‘aes’ Tab4_Barplot_Server : : no visible global function definition for ‘geom_bar’ Tab4_Barplot_Server : : no visible global function definition for ‘ggtitle’ Tab4_Barplot_Server : : no visible global function definition for ‘ylab’ Tab4_Barplot_Server : : no visible global function definition for ‘xlab’ Tab4_Barplot_Server : : no visible global function definition for ‘theme_bw’ Tab4_Barplot_Server : : no visible global function definition for ‘theme’ Tab4_Barplot_Server : : no visible global function definition for ‘element_text’ Tab4_Barplot_Server : : no visible global function definition for ‘labs’ Tab4_Barplot_Server : : no visible global function definition for ‘scale_x_discrete’ Tab4_BoxPlots_Server : : no visible global function definition for ‘ggplot’ Tab4_BoxPlots_Server : : no visible global function definition for ‘theme_void’ Tab4_BoxPlots_Server : : no visible global function definition for ‘aes’ Tab4_BoxPlots_Server : : no visible global function definition for ‘geom_boxplot’ Tab4_BoxPlots_Server : : no visible global function definition for ‘geom_jitter’ Tab4_BoxPlots_Server : : no visible global function definition for ‘ggtitle’ Tab4_BoxPlots_Server : : no visible global function definition for ‘ylab’ Tab4_BoxPlots_Server : : no visible global function definition for ‘xlab’ Tab4_BoxPlots_Server : : no visible global function definition for ‘theme_bw’ Tab4_BoxPlots_Server : : no visible global function definition for ‘theme’ Tab4_BoxPlots_Server : : no visible global function definition for ‘element_text’ Tab4_BoxPlots_Server : : no visible global function definition for ‘stat_summary’ Tab4_BoxPlots_Server : : no visible global function definition for ‘labs’ Tab4_BoxPlots_Server : : no visible global function definition for ‘scale_color_discrete’ Tab4_BoxPlots_Server : : no visible global function definition for ‘scale_x_discrete’ Tab4_Hist_Server : : no visible global function definition for ‘ggplot’ Tab4_Hist_Server : : no visible global function definition for ‘theme_void’ Tab4_Hist_Server : : no visible global function definition for ‘aes’ Tab4_Hist_Server : : no visible global function definition for ‘geom_histogram’ Tab4_Hist_Server : : no visible global function definition for ‘ggtitle’ Tab4_Hist_Server : : no visible global function definition for ‘ylab’ Tab4_Hist_Server : : no visible global function definition for ‘xlab’ Tab4_Hist_Server : : no visible global function definition for ‘scale_color_manual’ Tab4_Hist_Server : : no visible global function definition for ‘scale_fill_manual’ Tab4_Hist_Server : : no visible global function definition for ‘theme_bw’ Tab4_Hist_Server : : no visible global function definition for ‘theme’ Tab4_Hist_Server : : no visible global function definition for ‘element_text’ Tab4_Hist_Server : : no visible global function definition for ‘scale_fill_discrete’ Tab4_Hist_Server : : no visible global function definition for ‘scale_color_discrete’ Tab4_Hist_Server : : no visible binding for global variable ‘value’ Tab4_Hist_Server : : no visible global function definition for ‘facet_wrap’ Tab4_Hist_Server : : no visible global function definition for ‘guides’ Tab4_Hist_Server : : : no visible global function definition for ‘png’ Tab4_Hist_Server : : : no visible global function definition for ‘dev.off’ Tab4_Hist_Server : : : no visible global function definition for ‘svg’ Tab4_Hist_Server : : no visible global function definition for ‘geom_density’ Tab4_Hist_Server : : no visible global function definition for ‘xlim’ Tab4_Hist_Server : : no visible global function definition for ‘colorRampPalette’ Tab4_Hist_Server : : no visible binding for global variable ‘x’ Tab4_Hist_Server : : no visible binding for global variable ‘y’ Tab4_Hist_Server : : no visible global function definition for ‘geom_line’ Tab4_Hist_Server : : no visible global function definition for ‘geom_ribbon’ Tab4_Hist_Server : : no visible binding for global variable ‘quant’ Tab4_Hist_Server : : no visible global function definition for ‘scale_x_continuous’ Tab4_Hist_Server : : no visible global function definition for ‘unit’ Tab4_Hist_Server : : no visible binding for global variable ‘..density..’ Tab4_Scatterplot_Server : : no visible global function definition for ‘ggplot’ Tab4_Scatterplot_Server : : no visible global function definition for ‘theme_void’ Tab4_Scatterplot_Server : : no visible global function definition for ‘geom_point’ Tab4_Scatterplot_Server : : no visible global function definition for ‘aes’ Tab4_Scatterplot_Server : : no visible global function definition for ‘ggtitle’ Tab4_Scatterplot_Server : : no visible global function definition for ‘ylab’ Tab4_Scatterplot_Server : : no visible global function definition for ‘xlab’ Tab4_Scatterplot_Server : : no visible global function definition for ‘theme_bw’ Tab4_Scatterplot_Server : : no visible global function definition for ‘theme’ Tab4_Scatterplot_Server : : no visible global function definition for ‘element_text’ Tab4_Scatterplot_Server : : no visible global function definition for ‘scale_colour_discrete’ Tab5_KM_Plot_Quart_Server : : no visible global function definition for ‘ggplot’ Tab5_KM_Plot_Quart_Server : : no visible global function definition for ‘theme_void’ Tab5_KM_Plot_Quart_Server : : no visible global function definition for ‘theme_bw’ Tab5_KM_Plot_Quart_Server : : no visible global function definition for ‘theme’ Tab5_KM_Plot_Quart_Server : : no visible global function definition for ‘element_text’ Tab5_KM_Plot_Server : : no visible global function definition for ‘ggplot’ Tab5_KM_Plot_Server : : no visible global function definition for ‘theme_void’ Tab5_KM_Plot_Server : : no visible global function definition for ‘theme_bw’ Tab5_KM_Plot_Server : : no visible global function definition for ‘theme’ Tab5_KM_Plot_Server : : no visible global function definition for ‘element_text’ Tab5_KM_Plot_Treatment_Server : : no visible global function definition for ‘ggplot’ Tab5_KM_Plot_Treatment_Server : : no visible global function definition for ‘theme_void’ Tab5_KM_Plot_Treatment_Server : : no visible global function definition for ‘theme_bw’ Tab5_KM_Plot_Treatment_Server : : no visible global function definition for ‘theme’ Tab5_KM_Plot_Treatment_Server : : no visible global function definition for ‘element_text’ Tab5_KM_Plot_Treatment_Server : : : no visible global function definition for ‘png’ Tab5_KM_Plot_Treatment_Server : : : no visible global function definition for ‘dev.off’ Tab5_KM_Plot_Treatment_Server : : : no visible global function definition for ‘svg’ Tab6_ANOVA_Server : : no visible global function definition for ‘group_by’ Tab6_ANOVA_Server : : no visible global function definition for ‘select’ Tab6_ANOVA_Server : : no visible binding for global variable ‘Adj_Pval’ Tab6_Chi_Square_Server : : no visible global function definition for ‘select’ Tab6_Chi_Square_Server : : no visible binding for global variable ‘Adj_Pval’ Tab6_FE_Server : : no visible global function definition for ‘select’ Tab6_FE_Server : : no visible binding for global variable ‘Adj_Pval’ Tab6_FE_Sim_Server : : no visible global function definition for ‘select’ Tab6_FE_Sim_Server : : no visible binding for global variable ‘Adj_Pval’ Tab6_KW_Server : : no visible global function definition for ‘select’ Tab6_KW_Server : : no visible binding for global variable ‘Adj_Pval’ Tab7_Multi_Cox_Server : : no visible global function definition for ‘select’ Tab7_Multi_Cox_Server : : no visible global function definition for ‘ggplot’ Tab7_Multi_Cox_Server : : no visible global function definition for ‘theme_void’ Tab7_Uni_Cox_Server : : no visible global function definition for ‘select’ Tab7_Uni_Cox_Server : : no visible binding for global variable ‘Adj_LRT’ Tab7_Uni_Cox_Server : : no visible binding for global variable ‘Adj_Wald’ Tab7_Uni_Cox_Server : : no visible binding for global variable ‘Adj_Logrank’ Tab8_Adjusted_Survival_Curves_Server : : no visible global function definition for ‘mutate’ Tab8_Adjusted_Survival_Curves_Server : : no visible global function definition for ‘:=’ Tab8_Adjusted_Survival_Curves_Server : : no visible global function definition for ‘select’ Tab8_Adjusted_Survival_Curves_Server : : no visible global function definition for ‘theme_bw’ Tab8_Adjusted_Survival_Curves_Server : : no visible global function definition for ‘theme’ Tab8_Adjusted_Survival_Curves_Server : : no visible global function definition for ‘element_text’ Tab8_Adjusted_Survival_Curves_Server : : no visible global function definition for ‘ggplot’ Tab8_Adjusted_Survival_Curves_Server : : no visible global function definition for ‘theme_void’ Tab9_RPST_Ctree_Server : : no visible binding for global variable ‘.’ Tab9_RPST_Ctree_Server : : no visible global function definition for ‘ggplot’ Tab9_RPST_Ctree_Server : : no visible global function definition for ‘theme_void’ Tab9_RPST_Ctree_Server : : no visible global function definition for ‘mutate’ Tab9_RPST_Ctree_Server : : no visible global function definition for ‘select’ Tab9_RPST_Ctree_Server : : no visible binding for global variable ‘Time’ Tab9_RPST_Ctree_Server : : no visible binding for global variable ‘Node’ Tab9_RPST_Ctree_Server : : no visible binding for global variable ‘Cen’ Tab9_RPST_Ctree_Server : : no visible global function definition for ‘theme_bw’ Tab9_RPST_Ctree_Server : : no visible global function definition for ‘theme’ Tab9_RPST_Ctree_Server : : no visible global function definition for ‘element_text’ Tab9_RPST_Rpart_Server : : no visible binding for global variable ‘.’ Tab9_RPST_Rpart_Server : : no visible global function definition for ‘ggplot’ Tab9_RPST_Rpart_Server : : no visible global function definition for ‘theme_void’ Tab9_RPST_Rpart_Server : : no visible global function definition for ‘mutate’ Tab9_RPST_Rpart_Server : : no visible global function definition for ‘select’ Tab9_RPST_Rpart_Server : : no visible binding for global variable ‘Time’ Tab9_RPST_Rpart_Server : : no visible binding for global variable ‘Node’ Tab9_RPST_Rpart_Server : : no visible binding for global variable ‘Cen’ Tab9_RPST_Rpart_Server : : no visible global function definition for ‘theme_bw’ Tab9_RPST_Rpart_Server : : no visible global function definition for ‘theme’ Tab9_RPST_Rpart_Server : : no visible global function definition for ‘element_text’ Undefined global functions or variables: . ..density.. := Adj_LRT Adj_Logrank Adj_Pval Adj_Wald Binding Cen Hugo_Symbol Name Node PATIENT_ID Tab Tab10_Summary_Plot_Fraction Tab10_TT_Plot_Width Time Timestamp Value aes all_of arrange_at as_tibble binding colorRampPalette dev.off element_text facet_wrap geom_bar geom_boxplot geom_density geom_histogram geom_jitter geom_line geom_point geom_ribbon ggplot ggtitle group_by guides labs mutate mutate_at mutate_if name png quant read.delim rename scale_color_discrete scale_color_manual scale_colour_discrete scale_fill_discrete scale_fill_manual scale_x_continuous scale_x_discrete select stat_summary str_split str_to_title svg theme theme_bw theme_void timestamp type unit value write.table x xlab xlim y ylab Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "png", "svg") importFrom("utils", "read.delim", "timestamp", "write.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/GNOSIS.Rcheck/00check.log’ for details.