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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:leapR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings leapR_0.99.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/leapR.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘leapR/DESCRIPTION’ ... OK
* this is package ‘leapR’ version ‘0.99.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘leapR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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:
  ‘gplots’ ‘methods’ ‘tibble’
  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
calcTTest: no visible global function definition for ‘is’
calcTTest : <anonymous>: no visible global function definition for
  ‘t.test’
cluster_enrichment: no visible global function definition for ‘is’
combine_omics: no visible global function definition for ‘as’
correlation_comparison_enrichment: no visible global function
  definition for ‘is’
correlation_comparison_enrichment: no visible global function
  definition for ‘cor’
correlation_enrichment: no visible global function definition for ‘is’
correlation_enrichment: no visible global function definition for ‘cor’
difference_enrichment_in_relationships: no visible global function
  definition for ‘is’
difference_enrichment_in_relationships : <anonymous>: no visible global
  function definition for ‘t.test’
difference_enrichment_in_relationships : <anonymous>: no visible global
  function definition for ‘is’
enrichment_by_fishers: no visible global function definition for
  ‘fisher.test’
enrichment_in_abundance: no visible global function definition for ‘is’
enrichment_in_abundance : <anonymous>: no visible global function
  definition for ‘t.test’
enrichment_in_abundance : <anonymous>: no visible global function
  definition for ‘is’
enrichment_in_groups: no visible global function definition for ‘is’
enrichment_in_groups : <anonymous>: no visible global function
  definition for ‘ks.test’
enrichment_in_relationships: no visible global function definition for
  ‘is’
enrichment_in_relationships : <anonymous>: no visible global function
  definition for ‘t.test’
enrichment_in_relationships : <anonymous>: no visible global function
  definition for ‘is’
leapR: no visible global function definition for ‘is’
Undefined global functions or variables:
  as cor fisher.test is ks.test t.test
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "cor", "fisher.test", "ks.test", "t.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 3 has 1)
checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 5 has 1)
checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 7 has 1)
checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 9 has 1)
checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 11 has 1)
checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 13 has 1)
checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 15 has 1)
checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 17 has 1)
* 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
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
leapR              2.441  0.348   6.859
cluster_enrichment 1.124  0.030   5.052
combine_omics      0.864  0.129  29.078
calcTTest          0.504  0.039   5.087
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/leapR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL leapR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘leapR’ ...
** this is package ‘leapR’ version ‘0.99.5’
** 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 (leapR)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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(leapR)
> data(ncipid)
> data(shortlist)
> data(longlist)
> 
> ##download file once for all tests
> pdata <- download.file("https://api.figshare.com/v2/file/download/56536217", method = "libcurl", destfile = "protData.rda")
trying URL 'https://api.figshare.com/v2/file/download/56536217'
Content type 'application/octet-stream' length 23253677 bytes (22.2 MB)
==================================================
downloaded 22.2 MB

> load("protData.rda")
> p <- file.remove("protData.rda")
> 
> test_check("leapR")
[ FAIL 0 | WARN 207 | SKIP 2 | PASS 4 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): ,

[ FAIL 0 | WARN 207 | SKIP 2 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 31.423   6.724  60.251