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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:queeems.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings queeems_0.99.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/queeems.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-27 07:38:31 UTC
* checking for file ‘queeems/DESCRIPTION’ ... OK
* this is package ‘queeems’ version ‘0.99.7’
* 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 ‘queeems’ 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 loading without being on the library search path ... 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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL queeems
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘queeems’ ...
** this is package ‘queeems’ version ‘0.99.7’
** 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 (queeems)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> # ><>< ================================================================ ><>< #
> # >< Quantify the Extent of Evolutionary Evidence in Molecular Sequences. >< #
> # ><><                       ~~~~~~~~~~~~~~~~~~~~                       ><>< #
> # ><><                    Master Function Test File.                    ><>< #
> # ><>< ================================================================ ><>< #
> 
> library(testthat)
> library(queeems)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: Seqinfo

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

> 
> test_check("queeems")

# :::::::
Protein base type:		  DNA
Number of sequences:		  8
Dimension of numeric output:	(base_size=4)-by-(site_size=1512)
# :::::::


 Below is/are citation(s) relevant to the queeems package:

Sadiq, H. (in progress). queeems: Quantify the Extent of Evolutionary Evidence in Molecular Sequences. R package.

Sadiq, H. (in progress). Bayesian Approach to Assessing Molecular Saturation. Preprint.

The corresponding BibTeX entry(ies) is/are as follows:

@Manual{,
	title = {queeems: Quantify the Extent of Evolutionary Evidence in Molecular Sequences},
	author = {Hassan Sadiq},
	year = {in progress},
	note = {R Package},
	url = {https://github.com/thsadiq/queeems},
}

@Manual{,
	title = {Bayesian Approach to Assessing Molecular Saturation},
	author = {Hassan Sadiq},
	year = {in progress},
	note = {Preprint},
} 


 Just testing! 


# :::::::
Counts generator:		  Non-Synonymous codons
Non-informative codon sites:	  403 (of 504)
Max. nuc. mismatch tolerance:	  3
# :::::::


::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Summarised Output for Entropy Analyses:
::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Entropy Estimation Method:	  Shannon
Synonymous Counts:		  TRUE
Non-informative Sites:		  61 / 99
Protein Entropy (H):		  0.3056
========================================================



:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Saturation Analyses Output Summary: Bayesian
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Invariant Sites:			 4/12
Saturated Sites:			 5/12
Overall Bayes Factor:			 62.94
Overall Decision:			 Saturated
===========================================================



Updated sequence file saved as:
	/tmp/RtmpIMXRUh/testfilter.fasta


::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Summarised Output for Entropy Analyses:
::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Entropy (H) Estimation Method:	  Renyi (α ≈ 0.20)
Non-informative Sites:		  3 / 10
Mean of H:			  0.3089
Standard Error of H:		  0.0275
Approx. Lower 95% C.I. of H:	  0.1858
Approx. Upper 95% C.I. of H:	  0.4320
========================================================

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 195 ]
> 
> # ><>< ================================================================ ><>< #
> # ><><                          CODE ENDS HERE                          ><>< #
> # ><>< ================================================================ ><>< #
> 
> proc.time()
   user  system elapsed 
 30.287   0.788  31.075