Back to Mac ARM64 build report for BioC 3.18
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This page was generated on 2024-04-18 11:32:11 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 877/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GNOSIS 1.0.0  (landing page)
Lydia King
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/GNOSIS
git_branch: RELEASE_3_18
git_last_commit: e38823a
git_last_commit_date: 2023-10-24 11:52:23 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for GNOSIS on kjohnson1


To the developers/maintainers of the GNOSIS package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GNOSIS
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GNOSIS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GNOSIS_1.0.0.tar.gz
StartedAt: 2024-04-17 15:24:35 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 15:31:36 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 420.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GNOSIS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GNOSIS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GNOSIS_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/GNOSIS.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GNOSIS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GNOSIS’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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 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 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 : <anonymous> : <anonymous>: no visible global function
  definition for ‘png’
Download_Server : <anonymous> : <anonymous>: no visible global function
  definition for ‘dev.off’
Download_Server : <anonymous> : <anonymous>: no visible global function
  definition for ‘svg’
Download_Server_1 : <anonymous> : <anonymous>: no visible global
  function definition for ‘png’
Download_Server_1 : <anonymous> : <anonymous>: no visible global
  function definition for ‘dev.off’
Download_Server_1 : <anonymous> : <anonymous>: no visible global
  function definition for ‘svg’
Download_Server_2 : <anonymous> : <anonymous>: no visible global
  function definition for ‘png’
Download_Server_2 : <anonymous> : <anonymous>: no visible global
  function definition for ‘dev.off’
Download_Server_2 : <anonymous> : <anonymous>: no visible global
  function definition for ‘svg’
Tab10_MAF_Plot_Summary_Server : <anonymous>: no visible global function
  definition for ‘mutate’
Tab10_MAF_Plot_Summary_Server : <anonymous>: no visible binding for
  global variable ‘PATIENT_ID’
Tab10_MAF_Plot_Summary_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab10_MAF_Plot_Summary_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab10_MAF_Plot_Summary_Server : <anonymous> : <anonymous>: no visible
  global function definition for ‘png’
Tab10_MAF_Plot_Summary_Server : <anonymous> : <anonymous>: no visible
  global function definition for ‘dev.off’
Tab10_MAF_Plot_Summary_Server : <anonymous> : <anonymous>: no visible
  global function definition for ‘svg’
Tab10_MAF_Plot_Summary_Server : <anonymous> : <anonymous>: no visible
  binding for global variable ‘Tab10_TT_Plot_Width’
Tab10_MAF_Plot_Summary_Server : <anonymous> : <anonymous>: no visible
  global function definition for ‘Tab10_Summary_Plot_Fraction’
Tab10_MAF_Text_Summary_Server : <anonymous>: no visible global function
  definition for ‘mutate’
Tab10_MAF_Text_Summary_Server : <anonymous>: no visible binding for
  global variable ‘PATIENT_ID’
Tab11_Log_Server : <anonymous>: no visible global function definition
  for ‘rename’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘name’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘timestamp’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘value’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘type’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘binding’
Tab11_Log_Server : <anonymous>: no visible global function definition
  for ‘mutate’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘Name’
Tab11_Log_Server : <anonymous>: no visible global function definition
  for ‘str_to_title’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘Tab’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘Timestamp’
Tab11_Log_Server : <anonymous>: no visible global function definition
  for ‘select’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘Binding’
Tab11_Log_Server : <anonymous>: no visible binding for global variable
  ‘Value’
Tab11_Log_Server : <anonymous>: no visible global function definition
  for ‘arrange_at’
Tab11_Log_Server : <anonymous> : <anonymous>: no visible global
  function definition for ‘write.table’
Tab1_Input_Files_Manual_Server : <anonymous>: no visible global
  function definition for ‘read.delim’
Tab2_Exploratory_Tables_Server : <anonymous>: no visible global
  function definition for ‘as_tibble’
Tab2_Exploratory_Tables_Server : <anonymous>: no visible global
  function definition for ‘mutate’
Tab2_Exploratory_Tables_Server : <anonymous>: no visible global
  function definition for ‘:=’
Tab2_Exploratory_Tables_Server : <anonymous>: no visible binding for
  global variable ‘value’
Tab2_Exploratory_Tables_Server : <anonymous>: no visible global
  function definition for ‘select’
Tab3_CNACalc_Server : <anonymous>: no visible global function
  definition for ‘str_split’
Tab3_CNACalc_Server : <anonymous>: no visible binding for global
  variable ‘Hugo_Symbol’
Tab3_CNACalc_Server : <anonymous>: no visible global function
  definition for ‘select’
Tab3_CNACalc_Server : <anonymous>: no visible global function
  definition for ‘all_of’
Tab3_CNACalc_Server : <anonymous>: no visible global function
  definition for ‘mutate_if’
Tab3_Download_Server : <anonymous> : <anonymous>: no visible global
  function definition for ‘write.table’
Tab3_Factor_Levels_Server : <anonymous>: no visible global function
  definition for ‘mutate_at’
Tab3_Recode_Server : <anonymous>: no visible global function definition
  for ‘mutate’
Tab3_Subset_Server : <anonymous>: no visible global function definition
  for ‘mutate_at’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘aes’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘geom_bar’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘ggtitle’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘ylab’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘xlab’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘theme_bw’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘theme’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘element_text’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘labs’
Tab4_Barplot_Server : <anonymous>: no visible global function
  definition for ‘scale_x_discrete’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘aes’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘geom_boxplot’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘geom_jitter’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘ggtitle’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘ylab’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘xlab’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘theme_bw’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘theme’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘element_text’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘stat_summary’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘labs’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘scale_color_discrete’
Tab4_BoxPlots_Server : <anonymous>: no visible global function
  definition for ‘scale_x_discrete’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘ggplot’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘theme_void’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘aes’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘geom_histogram’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘ggtitle’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘ylab’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘xlab’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘scale_color_manual’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘scale_fill_manual’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘theme_bw’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘theme’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘element_text’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘scale_fill_discrete’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘scale_color_discrete’
Tab4_Hist_Server : <anonymous>: no visible binding for global variable
  ‘value’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘facet_wrap’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘guides’
Tab4_Hist_Server : <anonymous> : <anonymous>: no visible global
  function definition for ‘png’
Tab4_Hist_Server : <anonymous> : <anonymous>: no visible global
  function definition for ‘dev.off’
Tab4_Hist_Server : <anonymous> : <anonymous>: no visible global
  function definition for ‘svg’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘geom_density’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘xlim’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘colorRampPalette’
Tab4_Hist_Server : <anonymous>: no visible binding for global variable
  ‘x’
Tab4_Hist_Server : <anonymous>: no visible binding for global variable
  ‘y’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘geom_line’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘geom_ribbon’
Tab4_Hist_Server : <anonymous>: no visible binding for global variable
  ‘quant’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘scale_x_continuous’
Tab4_Hist_Server : <anonymous>: no visible global function definition
  for ‘unit’
Tab4_Hist_Server : <anonymous>: no visible binding for global variable
  ‘..density..’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘geom_point’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘aes’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘ggtitle’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘ylab’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘xlab’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘theme_bw’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘theme’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘element_text’
Tab4_Scatterplot_Server : <anonymous>: no visible global function
  definition for ‘scale_colour_discrete’
Tab5_KM_Plot_Quart_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab5_KM_Plot_Quart_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab5_KM_Plot_Quart_Server : <anonymous>: no visible global function
  definition for ‘theme_bw’
Tab5_KM_Plot_Quart_Server : <anonymous>: no visible global function
  definition for ‘theme’
Tab5_KM_Plot_Quart_Server : <anonymous>: no visible global function
  definition for ‘element_text’
Tab5_KM_Plot_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab5_KM_Plot_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab5_KM_Plot_Server : <anonymous>: no visible global function
  definition for ‘theme_bw’
Tab5_KM_Plot_Server : <anonymous>: no visible global function
  definition for ‘theme’
Tab5_KM_Plot_Server : <anonymous>: no visible global function
  definition for ‘element_text’
Tab5_KM_Plot_Treatment_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab5_KM_Plot_Treatment_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab5_KM_Plot_Treatment_Server : <anonymous>: no visible global function
  definition for ‘theme_bw’
Tab5_KM_Plot_Treatment_Server : <anonymous>: no visible global function
  definition for ‘theme’
Tab5_KM_Plot_Treatment_Server : <anonymous>: no visible global function
  definition for ‘element_text’
Tab5_KM_Plot_Treatment_Server : <anonymous> : <anonymous>: no visible
  global function definition for ‘png’
Tab5_KM_Plot_Treatment_Server : <anonymous> : <anonymous>: no visible
  global function definition for ‘dev.off’
Tab5_KM_Plot_Treatment_Server : <anonymous> : <anonymous>: no visible
  global function definition for ‘svg’
Tab6_ANOVA_Server : <anonymous>: no visible global function definition
  for ‘group_by’
Tab6_ANOVA_Server : <anonymous>: no visible global function definition
  for ‘select’
Tab6_ANOVA_Server : <anonymous>: no visible binding for global variable
  ‘Adj_Pval’
Tab6_Chi_Square_Server : <anonymous>: no visible global function
  definition for ‘select’
Tab6_Chi_Square_Server : <anonymous>: no visible binding for global
  variable ‘Adj_Pval’
Tab6_FE_Server : <anonymous>: no visible global function definition for
  ‘select’
Tab6_FE_Server : <anonymous>: no visible binding for global variable
  ‘Adj_Pval’
Tab6_FE_Sim_Server : <anonymous>: no visible global function definition
  for ‘select’
Tab6_FE_Sim_Server : <anonymous>: no visible binding for global
  variable ‘Adj_Pval’
Tab6_KW_Server : <anonymous>: no visible global function definition for
  ‘select’
Tab6_KW_Server : <anonymous>: no visible binding for global variable
  ‘Adj_Pval’
Tab7_Multi_Cox_Server : <anonymous>: no visible global function
  definition for ‘select’
Tab7_Multi_Cox_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab7_Multi_Cox_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab7_Uni_Cox_Server : <anonymous>: no visible global function
  definition for ‘select’
Tab7_Uni_Cox_Server : <anonymous>: no visible binding for global
  variable ‘Adj_LRT’
Tab7_Uni_Cox_Server : <anonymous>: no visible binding for global
  variable ‘Adj_Wald’
Tab7_Uni_Cox_Server : <anonymous>: no visible binding for global
  variable ‘Adj_Logrank’
Tab8_Adjusted_Survival_Curves_Server : <anonymous>: no visible global
  function definition for ‘mutate’
Tab8_Adjusted_Survival_Curves_Server : <anonymous>: no visible global
  function definition for ‘:=’
Tab8_Adjusted_Survival_Curves_Server : <anonymous>: no visible global
  function definition for ‘select’
Tab8_Adjusted_Survival_Curves_Server : <anonymous>: no visible global
  function definition for ‘theme_bw’
Tab8_Adjusted_Survival_Curves_Server : <anonymous>: no visible global
  function definition for ‘theme’
Tab8_Adjusted_Survival_Curves_Server : <anonymous>: no visible global
  function definition for ‘element_text’
Tab8_Adjusted_Survival_Curves_Server : <anonymous>: no visible global
  function definition for ‘ggplot’
Tab8_Adjusted_Survival_Curves_Server : <anonymous>: no visible global
  function definition for ‘theme_void’
Tab9_RPST_Ctree_Server : <anonymous>: no visible binding for global
  variable ‘.’
Tab9_RPST_Ctree_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab9_RPST_Ctree_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab9_RPST_Ctree_Server : <anonymous>: no visible global function
  definition for ‘mutate’
Tab9_RPST_Ctree_Server : <anonymous>: no visible global function
  definition for ‘select’
Tab9_RPST_Ctree_Server : <anonymous>: no visible binding for global
  variable ‘Time’
Tab9_RPST_Ctree_Server : <anonymous>: no visible binding for global
  variable ‘Node’
Tab9_RPST_Ctree_Server : <anonymous>: no visible binding for global
  variable ‘Cen’
Tab9_RPST_Ctree_Server : <anonymous>: no visible global function
  definition for ‘theme_bw’
Tab9_RPST_Ctree_Server : <anonymous>: no visible global function
  definition for ‘theme’
Tab9_RPST_Ctree_Server : <anonymous>: no visible global function
  definition for ‘element_text’
Tab9_RPST_Rpart_Server : <anonymous>: no visible binding for global
  variable ‘.’
Tab9_RPST_Rpart_Server : <anonymous>: no visible global function
  definition for ‘ggplot’
Tab9_RPST_Rpart_Server : <anonymous>: no visible global function
  definition for ‘theme_void’
Tab9_RPST_Rpart_Server : <anonymous>: no visible global function
  definition for ‘mutate’
Tab9_RPST_Rpart_Server : <anonymous>: no visible global function
  definition for ‘select’
Tab9_RPST_Rpart_Server : <anonymous>: no visible binding for global
  variable ‘Time’
Tab9_RPST_Rpart_Server : <anonymous>: no visible binding for global
  variable ‘Node’
Tab9_RPST_Rpart_Server : <anonymous>: no visible binding for global
  variable ‘Cen’
Tab9_RPST_Rpart_Server : <anonymous>: no visible global function
  definition for ‘theme_bw’
Tab9_RPST_Rpart_Server : <anonymous>: no visible global function
  definition for ‘theme’
Tab9_RPST_Rpart_Server : <anonymous>: 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/GNOSIS.Rcheck/00check.log’
for details.



Installation output

GNOSIS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GNOSIS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘GNOSIS’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: In normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
2: In normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
3: In normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
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’
** testing if installed package can be loaded from final location
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/Users/biocbuild/Library/Caches/org.R-project.R/R/R.cache": No such file or directory
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’
** testing if installed package keeps a record of temporary installation path
* DONE (GNOSIS)

Tests output


Example timings

GNOSIS.Rcheck/GNOSIS-Ex.timings

nameusersystemelapsed
GNOSIS0.0000.0010.001