Lydia King
| Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 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) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:21 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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 877/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GNOSIS 1.0.0 (landing page) Lydia King
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
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. |
| 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: 2024-03-27 15:03:42 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 15:10:44 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 421.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GNOSIS.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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.
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)
GNOSIS.Rcheck/GNOSIS-Ex.timings
| name | user | system | elapsed | |
| GNOSIS | 0 | 0 | 0 | |