##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:omXplore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings omXplore_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omXplore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omXplore’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘omXplore’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'plots_tracking_server("tracker", ': unused argument (reset = reactive({
  Note: possible error in 'omXplore_intensity_server("iplot", ': unused argument (reset = reactive({
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Build_X_CC: no visible global function definition for ‘metadata’
Build_X_CC: no visible global function definition for ‘metadata<-’
Check_MSnSet_Consistency : <anonymous>: no visible global function
  definition for ‘experimentData’
MAE_Compatibility_with_Prostar_1x : <anonymous>: no visible binding for
  global variable ‘.colData’
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for ‘experimentData’
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for ‘metadata’
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for ‘metadata<-’
omXplore_intensity : server: possible error in
  plots_tracking_server("tracker", obj = reactive({: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in obj: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in }), i = reactive({:
  unused argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in i: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in }), reset = reactive({:
  unused argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in input$reset: unused
  argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in }), is.enabled =
  reactive({: unused argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in TRUE: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in })): unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in
  omXplore_intensity_server("iplot", obj = reactive({: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in }), track.indices =
  reactive({: unused argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in indices(): unused
  argument (reset = reactive({ input$reset }))
Undefined global functions or variables:
  .colData experimentData metadata metadata<-
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density-plot.Rd: RColorBrewer
  intensity-plots.Rd: RColorBrewer
  palette.Rd: RColorBrewer
  plot-variance.Rd: RColorBrewer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'intensity-plots.Rd'
  ‘remoteReset’ ‘is.enabled’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck/00check.log’
for details.