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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SmartPhos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SmartPhos_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SmartPhos.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SmartPhos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SmartPhos’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 36 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 ‘SmartPhos’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data        1.3Mb
    shiny-app   5.4Mb
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘DT’ ‘XML’ ‘cowplot’ ‘factoextra’ ‘ggbeeswarm’ ‘grid’ ‘plotly’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘tools’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
runFisher: no visible binding for global variable ‘signature’
runGSEAforPhospho: no visible binding for global variable ‘signature’
Undefined global functions or variables:
  signature
Consider adding
  importFrom("methods", "signature")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SmartPhos.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SmartPhos
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SmartPhos’ ...
** this is package ‘SmartPhos’ version ‘1.0.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SmartPhos)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SmartPhos)
> 
> test_check("SmartPhos")
harmonizing input:
  removing 5 sampleMap rows not in names(experiments)
harmonizing input:
  removing 5 sampleMap rows not in names(experiments)
Running gene set analysis:
Checking arguments...done!
Final gene/gene-set association: 20 genes and 22 gene sets
  Details:
  Calculating gene set statistics from 20 out of 65 gene-level statistics
  Removed 4366 genes from GSC due to lack of matching gene statistics
  Removed 28 gene sets containing no genes after gene removal
  Removed additionally 0 gene sets not matching the size limits
  Loaded additional information for 22 gene sets
Calculating gene set statistics...done!
Calculating gene set significance...done!
Adjusting for multiple testing...done!
Running gene set analysis:
Checking arguments...done!
Final gene/gene-set association: 20 genes and 22 gene sets
  Details:
  Calculating gene set statistics from 20 out of 65 gene-level statistics
  Removed 4366 genes from GSC due to lack of matching gene statistics
  Removed 28 gene sets containing no genes after gene removal
  Removed additionally 0 gene sets not matching the size limits
  Loaded additional information for 22 gene sets
Calculating gene set statistics...done!
Calculating gene set significance...done!
Adjusting for multiple testing...done!
Imputing along margin 2 (samples/columns).
Imputing along margin 2 (samples/columns).
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 309 ]
> 
> proc.time()
   user  system elapsed 
 20.864   1.677  22.666