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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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/COTAN.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.0.0’
* 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 line endings in shell scripts ... 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 51.093   2.56  53.667
* 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-3.15-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
** 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 (COTAN)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 
  0.346   0.080   0.402 

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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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
      rowname CTATTGATCAAA GCCGAGTAAGTC CACGCCGTCCCA TAAATACGTTAT GCGGAGCCTCCT
1119     Nnat    73.168400    43.104810    46.784146    18.684677     51.86938
1834   Tuba1a    30.128165    57.823526    36.613679     8.304301     54.92052
1787   Tmsb10    20.444112    14.718716    11.187513    16.608602     10.67899
51       Actb    11.836065    15.770052     9.153420     4.152151     13.73013
917    Malat1     5.380029    10.513368     3.051140    31.141129      6.10228
1841    Tubb5    11.836065    10.513368    13.221606     0.000000      9.15342
1838    Tubb3     5.380029    11.564705     2.034093     0.000000     13.73013
1788   Tmsb4x     2.152012     7.359358    26.443213     6.228226      3.05114
1837   Tubb2b     5.380029    10.513368     7.119327     2.076075     10.67899
1460    Rpl32     2.152012    13.667379     8.136373    12.456452      6.10228
801  Hsp90ab1     5.380029     6.308021     6.102280    16.608602      6.10228
1694    Stmn2     9.684053     3.154010     4.068187     2.076075      0.00000
1513     Rtn1     7.532041     1.051337    15.255700     0.000000      4.57671
939  Marcksl1     4.304024     6.308021     6.102280     0.000000     12.20456
757     H3f3b     7.532041     8.410695     6.102280     4.152151      7.62785
     CCTTCCACACTG
1119     7.070896
1834    45.960822
1787    37.122203
51       3.535448
917      1.767724
1841    12.374068
1838    21.212687
1788     7.070896
1837    15.909515
1460     1.767724
801      3.535448
1694    24.748135
1513    10.606344
939      8.838620
757      1.767724
[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 0.02416432976353 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 
 66.838   6.822  67.032