Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/GNOSIS
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
lconway macOS 12.6.5 Monterey/x86_64   OK     WARNINGS     WARNINGS     OK  
nebbiolo2 Linux (Ubuntu 22.04.2 LTS)/x86_64   OK     WARNINGS     skipped     OK  

lconway Summary

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Package: GNOSIS
Version: 0.99.2
RVersion: 4.3
BiocVersion: 3.18
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GNOSIS
BuildTime: 0 minutes 52.99 seconds
CheckCommand: BiocCheckGitClone('GNOSIS') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3132/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.install-out.txt GNOSIS_0.99.2.tar.gz && BiocCheck('GNOSIS_0.99.2.tar.gz', `new-package`=TRUE)
CheckTime: 4 minutes 21.24 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh GNOSIS_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 39.72 seconds
PackageFileSize: 3454.63 KiB
BuildID:: GNOSIS_20231016085940
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: GNOSIS. Starting Build package. Starting Check package. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0.

lconway BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘GNOSIS/DESCRIPTION’ ... OK
* preparing ‘GNOSIS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘GNOSIS_0.99.2.tar.gz’

lconway CHECK output

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===============================

 BiocCheckGitClone('GNOSIS')

===============================

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: GNOSIS
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GNOSIS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GNOSIS’ version ‘0.99.2’
* 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/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking startup messages can be suppressed ... [11s/11s] 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 ... [40s/41s] WARNING
Found a .Internal call in the following function:
  ‘vapply’
with calls to .Internal functions
  ‘vapply’

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.

In addition to the above warning(s), found the following notes:

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 ... [0s/0s] OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] 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 ... [4s/4s] OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.Rcheck/00check.log’
for details.






===============================

 BiocCheck('GNOSIS_0.99.2.tar.gz')

===============================

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: GNOSIS
─ PackageVersion: 0.99.2
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp86WzUo/file16d54133b8b9a/GNOSIS
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp86WzUo/file16d546df2f1d5
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      Sequencing, Classification, DNASeq, FunctionalGenomics,
      DriverMutation, SomaticMutation, VariantAnnotation,
      FeatureExtraction
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of GNOSIS...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 83 functions greater than 50 lines.
* Checking man page documentation...
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’
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 1076 lines (7%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 23 lines
      (0%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES

See the GNOSIS.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

lconway BUILD BIN output

[top]

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir GNOSIS_0.99.2.tar.gz'
>>>>>>> 

* installing *source* package ‘GNOSIS’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
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: 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: 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)

nebbiolo2 Summary

[top]

Package: GNOSIS
Version: 0.99.2
RVersion: 4.3
BiocVersion: 3.18
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GNOSIS
BuildTime: 1 minutes 8.89 seconds
CheckCommand: BiocCheckGitClone('GNOSIS') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3132/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.install-out.txt GNOSIS_0.99.2.tar.gz && BiocCheck('GNOSIS_0.99.2.tar.gz', `new-package`=TRUE)
CheckTime: 5 minutes 38.78 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 3454.58 KiB
BuildID:: GNOSIS_20231016085940
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: GNOSIS. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0.

nebbiolo2 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘GNOSIS/DESCRIPTION’ ... OK
* preparing ‘GNOSIS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘GNOSIS_0.99.2.tar.gz’

nebbiolo2 CHECK output

[top]

===============================

 BiocCheckGitClone('GNOSIS')

===============================

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: GNOSIS
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GNOSIS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GNOSIS’ version ‘0.99.2’
* 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 ‘/home/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [14s/14s] OK
* checking startup messages can be suppressed ... [14s/14s] 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 ... [54s/54s] WARNING
Found a .Internal call in the following function:
  ‘vapply’
with calls to .Internal functions
  ‘vapply’

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.

In addition to the above warning(s), found the following notes:

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 ... [0s/0s] OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [16s/16s] 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 ... [2s/2s] OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.Rcheck/00check.log’
for details.






===============================

 BiocCheck('GNOSIS_0.99.2.tar.gz')

===============================

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: GNOSIS
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpYkWCCI/file44b1d3bd22cf1/GNOSIS
─ installDir: /tmp/RtmpYkWCCI/file44b1d6426a5b1
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3132/5a4c04388d29c02543b37b70be07f7a87244886e/GNOSIS.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      Sequencing, Classification, DNASeq, FunctionalGenomics,
      DriverMutation, SomaticMutation, VariantAnnotation,
      FeatureExtraction
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of GNOSIS...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 83 functions greater than 50 lines.
* Checking man page documentation...
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’
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 1076 lines (7%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 23 lines
      (0%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES

See the GNOSIS.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

nebbiolo2 BUILD BIN output

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