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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/COTAN.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘COTAN’ can be installed ... OK
* 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 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 ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
automatic.COTAN.object.creation 29.773  0.924  30.936
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6
< NULL
---
> All Done!
  Running ‘testthat.R’
 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/COTAN.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘COTAN’ ...
** using staged installation
** R
** data
** 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 (COTAN)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.185   0.067   0.242 

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
>
> proc.time()
   user  system elapsed
  0.372   0.039   0.408

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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.

> Sys.setenv(R_TESTS="")
> library(testthat)
> library(COTAN)
> test_check("COTAN")
[1] "Initializing S4 object"
[1] "Initializing S4 object"
[1] "Start estimation mu with linear method"
[1] 2000  815
[1] "Start PCA"
[1] "starting hclust"
[1] "cotan analysis"
[1] "mu estimator creation"
[1] "save effective constitutive genes"
[1] "start a minimization"
[1] "Next gene: Trim2 number 1810"
[1] "Final trance!"
[1] "a min: -0.08001708984375 | a max 24.5703125 | negative a %: 2.4"
[1] "coex dataframe creation"
[1] "creation of observed yes/yes contingency table"
[1] "mu estimator creation"
[1] "expected contingency tables creation"
[1] "The distance between estimated n of zeros and observed number of zero is 0.0241643297635317 over 2000"
[1] "Done"
[1] "coex estimation"
[1] "Cleaning RAM"
  [1] "0610009D07Rik" "0610010F05Rik" "1110001J03Rik" "1110004F10Rik"
  [5] "1110008F13Rik" "1110038B12Rik" "1500011B03Rik" "1500012F01Rik"
  [9] "1700020I14Rik" "1700021F05Rik" "1700025G04Rik" "1810022K09Rik"
 [13] "1810037I17Rik" "2010107E04Rik" "2010107G23Rik" "2210016L21Rik"
 [17] "2310036O22Rik" "2410002F23Rik" "2410006H16Rik" "2410015M20Rik"
 [21] "2410066E13Rik" "2610017I09Rik" "2610203C20Rik" "2700029M09Rik"
 [25] "2700060E02Rik" "2700094K13Rik" "2810004N23Rik" "2810008D09Rik"
 [29] "2810428I15Rik" "2900011O08Rik" "4833420G17Rik" "4833439L19Rik"
 [33] "4921524J17Rik" "4930506M07Rik" "4931428F04Rik" "6330403K07Rik"
 [37] "9130024F11Rik" "9330159F19Rik" "A030009H04Rik" "Aamp"         
 [41] "Abcf1"         "Abr"           "Abracl"        "Acat1"        
 [45] "Acat2"         "Acbd5"         "Acbd6"         "Acin1"        
 [49] "Aco2"          "Acot7"         "Actb"          "Actl6b"       
 [53] "Actr10"        "Actr1a"        "Actr2"         "Actr3"        
 [57] "Adam10"        "Add1"          "Add2"          "Adh5"         
 [61] "Adprh"         "Adss"          "Aes"           "Aff4"         
 [65] "Aggf1"         "Agrn"          "Ahi1"          "Ahsa1"        
 [69] "Ahsa2"         "Aimp1"         "Akap8"         "Akap8l"       
 [73] "Akap9"         "Akirin2"       "Akr1a1"        "Akt3"         
 [77] "Aldoa"         "Aldoc"         "Alg2"          "Amer2"        
 [81] "Anapc11"       "Anapc13"       "Anapc16"       "Anapc5"       
 [85] "Ank2"          "Ank3"          "Ankra2"        "Ankrd10"      
 [89] "Ankrd11"       "Ankrd12"       "Ankrd32"       "Anp32a"       
 [93] "Anp32b"        "Anp32e"        "Ap1m1"         "Ap1s1"        
 [97] "Ap2m1"         "Ap2s1"         "Ap3b2"         "Apba2"        
[1] "Get p-values on a set of genes on columns on a set of genes on rows"
[1] "Using function S"
[1] "function to generate S "
[1] "function to generate GDI dataframe"
[1] "Using S"
[1] "function to generate S "
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
 39.595   3.742  40.627