##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scoup.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scoup_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scoup.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scoup/DESCRIPTION’ ... OK
* this is package ‘scoup’ version ‘1.0.0’
* 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 ‘scoup’ 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
seqWriter 7.22   0.05   7.298
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘branchWise.R’
  Running ‘ouSensitivity.R’
  Running ‘sensitiveVnVs.R’
  Running ‘siteWise.R’
  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: OK

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scoup
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘scoup’ ...
** using staged installation
** R
** 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 (scoup)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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.

> # ><>< ================================================================= ><>< #
> # ><><                       Branch-wise Analyses.                       ><>< #
> # ><>< ================================================================= ><>< #
> 
> # Make package accessible in R session
> library(scoup)
Loading required package: Matrix
> 
> # Number of internal nodes on the desired balanced tree
> iNode <- 3
> 
> # Variance of non-synonymous selection coefficients
> nsnV <- 0.01
> 
> # Number of data replications for each parameter combination
> ## Edited count was used for the results presented in article
> nsim <- 1 # 50
> 
> # Ratio of the variance of the non-synonymous to synonymous coeff.
> ## Excluded values contributed to results presented in article
> vNvSvec <- c(0) # c(0, 1e-06, 1e-03, 0.1, 1, 10, 100)
> 
> # Sequence alignment size information
> seqsBwise <- seqDetails(c(nsite=1000, blength=0.10))
> 
> # Iterate over all listed coefficient variance ratios
> for(h in 1:length(vNvSvec)){
+   
+     # Iterate over the specified number of replicates
+     for(i in 1:nsim){
+       
+         # Create the parameter set applicable at each internal tree node
+         scInput <- rbind(vNvS=c(rep(0,iNode-1),vNvSvec[h]),
+                          nsynVar=rep(nsnV,iNode))
+         
+         # Create the applicable ("discrete") object for simulation function
+         adaptBranch <- discreteInput(list(p02xnodes=scInput))
+         
+         # Execute simulation
+         genSeq <- alignsim(adaptBranch, seqsBwise, NA)
+     }
+ }
> 
> # ><>< ================================================================= ><>< #
> # ><><                          CODE ENDS HERE.                          ><>< #
> # ><>< ================================================================= ><>< #
> 
> proc.time()
   user  system elapsed 
 17.329   0.333  17.735 

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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.

> # ><>< ================================================================= ><>< #
> # ><><                      OU Sensitivity Analyses                      ><>< #
> # ><>< ================================================================= ><>< #
> 
> # Make package accessible in R session
> library(scoup)
Loading required package: Matrix
> 
> # Number of extant taxa
> leaves <- 64
> 
> # Number of data replications for each parameter combination
> ## Edited count was used for the results presented in article
> sims <- 1 # 50
> 
> # OU reversion parameter (Theta) value
> ## Excluded values contributed to results in published article
> eThta <- c(0.01) # c(0.01, 0.1, 1)
> 
> # OU asymptotic variance value
> ## Excluded values contributed to results in published article 
> eVary <- c(0.0001) # c(0.0001, 0.01, 1)
> 
> # OU landscape shift parameters
> hbrunoStat <- hbInput(c(vNvS=1, nsynVar=0.01))
> 
> # Sequence alignment size information
> seqStat <- seqDetails(c(nsite=250, ntaxa=leaves))
> 
> # Iterate over all listed OU variance values
> for(g in 1:length(eVary)){
+   
+     # Iterate over all listed OU reversion parameter values
+     for(h in 1:length(eThta)){
+ 
+         # Create appropriate simulation function ("ou") object
+         adaptStat <- ouInput(c(eVar=eVary[g],Theta=eThta[h]))
+ 
+         # Iterate over the specified number of replicates
+         for(i in 1:sims){
+ 
+             # Execute simulation
+             simData <- alignsim(adaptStat, seqStat, hbrunoStat, NA)
+         }
+     }
+ }
> 
> # ><>< ================================================================= ><>< #
> # ><><                          CODE ENDS HERE.                          ><>< #
> # ><>< ================================================================= ><>< #
> 
> proc.time()
   user  system elapsed 
 11.467   0.291  11.798 

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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.

> # ><>< ================================================================= ><>< #
> # ><><                    vN/vS Sensitivity Analyses.                    ><>< #
> # ><>< ================================================================= ><>< #
> 
> # Make package accessible in R session
> library(scoup)
Loading required package: Matrix
> 
> # Number of extant taxa
> xtant <- 64
> 
> # Number of data replications for each parameter combination
> ## Edited count was used for the results presented in article
> simSize <- 1 # 50
> 
> # Variance of the non-synonymous selection coefficients
> ## Excluded values contributed to results presented in article
> nsynVary <- c(0) # c(0, 0.001, 0.1)
> 
> # Ratio of the variance of the non-synonymous to synonymous coeff.
> ## Excluded values contributed to results presented in article
> vNvSvec <- c(0) # c(0, 0.001,  1, 10)
> 
> # Sequence alignment size information
> seqStat <- seqDetails(c(nsite=250, ntaxa=xtant))
> 
> # Iterate over all listed coefficient variance ratios
> for(a in 1:length(vNvSvec)){
+ 
+     # Iterate over all listed non-synonymous coefficients variance
+     for(b in 1:length(nsynVary)){
+       
+         # Create appropriate simulation function ("omega") object
+         adaptData <- wInput(list(vNvS=vNvSvec[a],nsynVar=nsynVary[b]))
+         
+         # Iterate over the specified number of replicates
+         for(i in 1:simSize){
+           
+             # Execute simulation
+             simulateSeq <- alignsim(adaptData, seqStat, NA)
+         }
+     }
+ }
> 
> # ><>< ================================================================= ><>< #
> # ><><                          CODE ENDS HERE.                          ><>< #
> # ><>< ================================================================= ><>< #
> 
> proc.time()
   user  system elapsed 
 17.165   0.342  17.549 

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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.

> # ><>< ================================================================= ><>< #
> # ><><                        Site-wise Analyses.                        ><>< #
> # ><>< ================================================================= ><>< #
> 
> # Make package accessible in R session
> library(scoup)
Loading required package: Matrix
> 
> # Number of codon sites
> sitesize<- 100
> 
> # Variance of non-synonymous selection coefficients
> nsynVary <- 0.01
> 
> # Number of extant taxa
> taxasize <- 1024
> 
> # Sequence alignment size information
> seqsEntry <- seqDetails(c(nsite=sitesize, ntaxa=taxasize))
> 
> # Create the applicable ("ou") object for simulation function
> ## eVar= OU asymptotic variance, Theta=OU reversion parameter
> adaptEntry <- ouInput(c(eVar=0.1,Theta=1))
> 
> # Ratio of the variance of the non-synonymous to synonymous coeff.
> ## Excluded values contributed to results presented in article
> sratio <- c(0) # c(0, 1e-06, 1e-03, 0.1, 1, 10, 1000)
> 
> # Iterate over all listed coefficient variance ratios
> for(a0 in 1:length(sratio)){
+   
+     # OU landscape shift parameters
+     mValues <- hbInput(c(vNvS=sratio[a0], nsynVar=nsynVary))
+     
+     # Execute simulation
+     simSeq <- alignsim(adaptEntry, seqsEntry, mValues, NA)
+ }
> 
> 
> # ><>< ================================================================= ><>< #
> # ><><                          CODE ENDS HERE.                          ><>< #
> # ><>< ================================================================= ><>< #
> 
> proc.time()
   user  system elapsed 
 12.082   0.341  12.482 

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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.

> # ><>< ================================================================ ><>< #
> # ><><     scoup: Simulate Codon Sequences with Darwinian Selection     ><>< #
> # ><><          Incorporated  as an Ornstein-Uhlenbeck Process          ><>< #
> # ><><                       ~~~~~~~~~~~~~~~~~~~~                       ><>< #
> # ><><                    Master Function Test File.                    ><>< #
> # ><>< ================================================================ ><>< #
> 
> library(testthat)
> library(scoup)
Loading required package: Matrix
> 
> test_check("scoup")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 30 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 30 ]
> 
> # ><>< ================================================================ ><>< #
> # ><><                          CODE ENDS HERE                          ><>< #
> # ><>< ================================================================ ><>< #
> 
> proc.time()
   user  system elapsed 
  4.884   0.272   5.182